AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1353270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1353270 MtrunA17_Chr1g0212681 96.721 61 2 0 1 61 142 202 8.22e-39 127
Msa1353270 MtrunA17_Chr7g0222751 43.333 60 34 0 2 61 149 208 6.37e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1353270 AT2G39470.2 62.295 61 23 0 1 61 138 198 1.50e-21 83.2
Msa1353270 AT2G39470.1 62.295 61 23 0 1 61 146 206 1.88e-21 83.2

Find 40 sgRNAs with CRISPR-Local

Find 132 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAATGTTGTCTCTCTATC+TGG 0.111535 tig0013114:+89897 None:intergenic
ATATTGTTGGTCTTTGGTTT+GGG 0.234233 tig0013114:+90336 None:intergenic
TATATTGTTGGTCTTTGGTT+TGG 0.266254 tig0013114:+90335 None:intergenic
TCGCGTAATTTCGAAGAAAT+TGG 0.279462 tig0013114:+89852 None:intergenic
TAATCAGGTTATTACTGATT+TGG 0.282582 tig0013114:-90378 Msa1353270:intron
GAAGAAAGATATCAGAGATT+TGG 0.298345 tig0013114:-90489 Msa1353270:five_prime_UTR
TGTCATATATTGTTGGTCTT+TGG 0.307687 tig0013114:+90330 None:intergenic
TTCTTGTTGTATTATCTAAC+AGG 0.316196 tig0013114:+89981 None:intergenic
ATTAGCTTACATAAGGAGTT+AGG 0.337131 tig0013114:+89680 None:intergenic
TAGTTGTTGTATTATCTAAC+AGG 0.354589 tig0013114:+90005 None:intergenic
AAGAAAGATATCAGAGATTT+GGG 0.360869 tig0013114:-90488 Msa1353270:five_prime_UTR
TGAATTCAGCGGACGATAGA+TGG 0.362525 tig0013114:-90197 Msa1353270:intron
TCTTGCATGTCATATATTGT+TGG 0.373534 tig0013114:+90323 None:intergenic
CTGATATCTTTCTTCTCAGT+TGG 0.377354 tig0013114:+90497 None:intergenic
ATTTACAGTTACAAAATGTA+AGG 0.400765 tig0013114:-90532 Msa1353270:intron
ACGACACTTGCGATAGGAAA+TGG 0.406015 tig0013114:-90113 Msa1353270:CDS
TCAATGTTGTCTCTCTATCT+GGG 0.426637 tig0013114:+89898 None:intergenic
CTTACATTTATCCCTCAGAT+TGG 0.440474 tig0013114:-90978 Msa1353270:five_prime_UTR
TTCTTTGAGAGAATATTTGT+TGG 0.444553 tig0013114:+90055 None:intergenic
GAATGTTATTAGCTTACATA+AGG 0.450271 tig0013114:+89673 None:intergenic
CATTTATCCCTCAGATTGGA+AGG 0.470985 tig0013114:-90974 Msa1353270:five_prime_UTR
ATCATAATCACCTCTTCCAT+TGG 0.486106 tig0013114:+90464 None:intergenic
TCAGTATAATATAATAATGC+TGG 0.521133 tig0013114:-89752 Msa1353270:three_prime_UTR
TCCTATCGCAAGTGTCGTAA+AGG 0.521687 tig0013114:+90118 None:intergenic
AAGATACTACACATTAATTG+TGG 0.525487 tig0013114:-89638 None:intergenic
TAATAACATTCACTTTGTAC+AGG 0.528493 tig0013114:-89661 Msa1353270:three_prime_UTR
TATACAATGGCATGAACTCA+TGG 0.528571 tig0013114:-89704 Msa1353270:three_prime_UTR
TATCAGAGATTTGGGTCCAA+TGG 0.538055 tig0013114:-90480 Msa1353270:exon
AGATTTGGGTCCAATGGAAG+AGG 0.563882 tig0013114:-90474 Msa1353270:intron
AGATACTACACATTAATTGT+GGG 0.575783 tig0013114:-89637 None:intergenic
TATTGTTGGTCTTTGGTTTG+GGG 0.579380 tig0013114:+90337 None:intergenic
TGGAAAACATTATTATACAA+TGG 0.592201 tig0013114:-90177 Msa1353270:CDS
TTTACAGTTACAAAATGTAA+GGG 0.596231 tig0013114:-90531 Msa1353270:intron
ACATACAGAAGTTCAACTGC+AGG 0.600541 tig0013114:-89797 Msa1353270:three_prime_UTR
AAAATGATTATAAGTGACAC+AGG 0.614397 tig0013114:-89946 Msa1353270:three_prime_UTR
AATTATAATAAAATATACAA+TGG 0.614405 tig0013114:-89717 Msa1353270:three_prime_UTR
AACAATATATGACATGCAAG+AGG 0.615986 tig0013114:-90321 Msa1353270:intron
TATCACACTGAGATTTGAGA+TGG 0.618997 tig0013114:+90079 None:intergenic
TATCGCAAGTGTCGTAAAGG+AGG 0.624367 tig0013114:+90121 None:intergenic
TCCTTTACGACACTTGCGAT+AGG 0.629042 tig0013114:-90119 Msa1353270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATAGTTAATATGAAAACAA+GGG + tig0013114:89726-89745 None:intergenic 20.0%
!! TGATAGTTAATATGAAAACA+AGG + tig0013114:89727-89746 None:intergenic 20.0%
!!! TTTTAAAAAGACTGATAATG+AGG + tig0013114:89769-89788 None:intergenic 20.0%
!! TTTGCGTAACTATATTAATA+AGG - tig0013114:89860-89879 Msa1353270:three_prime_UTR 20.0%
!! TTGCGTAACTATATTAATAA+GGG - tig0013114:89861-89880 Msa1353270:three_prime_UTR 20.0%
!! ATTTACAGTTACAAAATGTA+AGG - tig0013114:90089-90108 Msa1353270:exon 20.0%
!! TTTACAGTTACAAAATGTAA+GGG - tig0013114:90090-90109 Msa1353270:exon 20.0%
!!! TTCTTTTGGAAAAAACAAAT+TGG + tig0013114:90351-90370 None:intergenic 20.0%
!!! TTTTTCCAAAAGAATATCTT+AGG - tig0013114:90357-90376 Msa1353270:CDS 20.0%
!! TGGAAAACATTATTATACAA+TGG - tig0013114:90444-90463 Msa1353270:intron 20.0%
!! TCAGTATAATATAATAATGC+TGG - tig0013114:90869-90888 Msa1353270:intron 20.0%
!! GATAGTTAATATGAAAACAA+GGG + tig0013114:89726-89745 None:intergenic 20.0%
!! TGATAGTTAATATGAAAACA+AGG + tig0013114:89727-89746 None:intergenic 20.0%
!!! TTTTAAAAAGACTGATAATG+AGG + tig0013114:89769-89788 None:intergenic 20.0%
!! TTTGCGTAACTATATTAATA+AGG - tig0013114:89860-89879 Msa1353270:three_prime_UTR 20.0%
!! TTGCGTAACTATATTAATAA+GGG - tig0013114:89861-89880 Msa1353270:three_prime_UTR 20.0%
!! ATTTACAGTTACAAAATGTA+AGG - tig0013114:90089-90108 Msa1353270:exon 20.0%
!! TTTACAGTTACAAAATGTAA+GGG - tig0013114:90090-90109 Msa1353270:exon 20.0%
!!! TTCTTTTGGAAAAAACAAAT+TGG + tig0013114:90351-90370 None:intergenic 20.0%
!!! TTTTTCCAAAAGAATATCTT+AGG - tig0013114:90357-90376 Msa1353270:CDS 20.0%
!! TGGAAAACATTATTATACAA+TGG - tig0013114:90444-90463 Msa1353270:intron 20.0%
!! TCAGTATAATATAATAATGC+TGG - tig0013114:90869-90888 Msa1353270:intron 20.0%
! AAGAAAGATATCAGAGATTT+GGG - tig0013114:90133-90152 Msa1353270:CDS 25.0%
! TAGATTCTGTCTTAATGTTA+TGG - tig0013114:90181-90200 Msa1353270:CDS 25.0%
!! TAATCAGGTTATTACTGATT+TGG - tig0013114:90243-90262 Msa1353270:intron 25.0%
!! CAAAACCTAAGATATTCTTT+TGG + tig0013114:90365-90384 None:intergenic 25.0%
!!! AAGAATATCTTAGGTTTTGA+TGG - tig0013114:90366-90385 Msa1353270:CDS 25.0%
!! TTCTTTGAGAGAATATTTGT+TGG + tig0013114:90569-90588 None:intergenic 25.0%
! TAGTTGTTGTATTATCTAAC+AGG + tig0013114:90619-90638 None:intergenic 25.0%
!! TTCTTGTTGTATTATCTAAC+AGG + tig0013114:90643-90662 None:intergenic 25.0%
! AAAATGATTATAAGTGACAC+AGG - tig0013114:90675-90694 Msa1353270:intron 25.0%
!! GAATGTTATTAGCTTACATA+AGG + tig0013114:90951-90970 None:intergenic 25.0%
! TAATAACATTCACTTTGTAC+AGG - tig0013114:90960-90979 Msa1353270:five_prime_UTR 25.0%
! AAGAAAGATATCAGAGATTT+GGG - tig0013114:90133-90152 Msa1353270:CDS 25.0%
! TAGATTCTGTCTTAATGTTA+TGG - tig0013114:90181-90200 Msa1353270:CDS 25.0%
!! TAATCAGGTTATTACTGATT+TGG - tig0013114:90243-90262 Msa1353270:intron 25.0%
!! CAAAACCTAAGATATTCTTT+TGG + tig0013114:90365-90384 None:intergenic 25.0%
!!! AAGAATATCTTAGGTTTTGA+TGG - tig0013114:90366-90385 Msa1353270:CDS 25.0%
!! TTCTTTGAGAGAATATTTGT+TGG + tig0013114:90569-90588 None:intergenic 25.0%
! TAGTTGTTGTATTATCTAAC+AGG + tig0013114:90619-90638 None:intergenic 25.0%
!! TTCTTGTTGTATTATCTAAC+AGG + tig0013114:90643-90662 None:intergenic 25.0%
! AAAATGATTATAAGTGACAC+AGG - tig0013114:90675-90694 Msa1353270:intron 25.0%
!! GAATGTTATTAGCTTACATA+AGG + tig0013114:90951-90970 None:intergenic 25.0%
! TAATAACATTCACTTTGTAC+AGG - tig0013114:90960-90979 Msa1353270:five_prime_UTR 25.0%
! AATTTTACCTTCCAATCTGA+GGG + tig0013114:89676-89695 None:intergenic 30.0%
! TAAAAAGACTGATAATGAGG+TGG + tig0013114:89766-89785 None:intergenic 30.0%
GACAAACTTGTAGAAAATTG+TGG + tig0013114:90000-90019 None:intergenic 30.0%
GAAGAAAGATATCAGAGATT+TGG - tig0013114:90132-90151 Msa1353270:CDS 30.0%
!! ATATTGTTGGTCTTTGGTTT+GGG + tig0013114:90288-90307 None:intergenic 30.0%
!! TATATTGTTGGTCTTTGGTT+TGG + tig0013114:90289-90308 None:intergenic 30.0%
!! TGTCATATATTGTTGGTCTT+TGG + tig0013114:90294-90313 None:intergenic 30.0%
TCTTGCATGTCATATATTGT+TGG + tig0013114:90301-90320 None:intergenic 30.0%
AACAATATATGACATGCAAG+AGG - tig0013114:90300-90319 Msa1353270:intron 30.0%
GATTGTTTGTCAATATGCAT+TGG + tig0013114:90392-90411 None:intergenic 30.0%
TTTCTGAATTCTGAATTCAG+CGG - tig0013114:90413-90432 Msa1353270:intron 30.0%
! ATTAGCTTACATAAGGAGTT+AGG + tig0013114:90944-90963 None:intergenic 30.0%
! AATTTTACCTTCCAATCTGA+GGG + tig0013114:89676-89695 None:intergenic 30.0%
! TAAAAAGACTGATAATGAGG+TGG + tig0013114:89766-89785 None:intergenic 30.0%
GACAAACTTGTAGAAAATTG+TGG + tig0013114:90000-90019 None:intergenic 30.0%
GAAGAAAGATATCAGAGATT+TGG - tig0013114:90132-90151 Msa1353270:CDS 30.0%
!! ATATTGTTGGTCTTTGGTTT+GGG + tig0013114:90288-90307 None:intergenic 30.0%
!! TATATTGTTGGTCTTTGGTT+TGG + tig0013114:90289-90308 None:intergenic 30.0%
!! TGTCATATATTGTTGGTCTT+TGG + tig0013114:90294-90313 None:intergenic 30.0%
TCTTGCATGTCATATATTGT+TGG + tig0013114:90301-90320 None:intergenic 30.0%
AACAATATATGACATGCAAG+AGG - tig0013114:90300-90319 Msa1353270:intron 30.0%
GATTGTTTGTCAATATGCAT+TGG + tig0013114:90392-90411 None:intergenic 30.0%
TTTCTGAATTCTGAATTCAG+CGG - tig0013114:90413-90432 Msa1353270:intron 30.0%
! ATTAGCTTACATAAGGAGTT+AGG + tig0013114:90944-90963 None:intergenic 30.0%
CTTACATTTATCCCTCAGAT+TGG - tig0013114:89662-89681 Msa1353270:three_prime_UTR 35.0%
! GAATTTTACCTTCCAATCTG+AGG + tig0013114:89677-89696 None:intergenic 35.0%
!! CATCATACTGATTCACAAGA+TGG - tig0013114:89696-89715 Msa1353270:three_prime_UTR 35.0%
ACACGAATTAGTACACACAA+TGG - tig0013114:89912-89931 Msa1353270:three_prime_UTR 35.0%
CAAAACTTACGATAAGACAG+AGG - tig0013114:89959-89978 Msa1353270:three_prime_UTR 35.0%
CTGATATCTTTCTTCTCAGT+TGG + tig0013114:90127-90146 None:intergenic 35.0%
ATCATAATCACCTCTTCCAT+TGG + tig0013114:90160-90179 None:intergenic 35.0%
AACCAGTTTGTGTCTTAATC+AGG - tig0013114:90228-90247 Msa1353270:intron 35.0%
AACCTGATTAAGACACAAAC+TGG + tig0013114:90233-90252 None:intergenic 35.0%
!! TATTGTTGGTCTTTGGTTTG+GGG + tig0013114:90287-90306 None:intergenic 35.0%
TATCACACTGAGATTTGAGA+TGG + tig0013114:90545-90564 None:intergenic 35.0%
TCAATGTTGTCTCTCTATCT+GGG + tig0013114:90726-90745 None:intergenic 35.0%
TCGCGTAATTTCGAAGAAAT+TGG + tig0013114:90772-90791 None:intergenic 35.0%
TATACAATGGCATGAACTCA+TGG - tig0013114:90917-90936 Msa1353270:intron 35.0%
CTTACATTTATCCCTCAGAT+TGG - tig0013114:89662-89681 Msa1353270:three_prime_UTR 35.0%
! GAATTTTACCTTCCAATCTG+AGG + tig0013114:89677-89696 None:intergenic 35.0%
!! CATCATACTGATTCACAAGA+TGG - tig0013114:89696-89715 Msa1353270:three_prime_UTR 35.0%
ACACGAATTAGTACACACAA+TGG - tig0013114:89912-89931 Msa1353270:three_prime_UTR 35.0%
CAAAACTTACGATAAGACAG+AGG - tig0013114:89959-89978 Msa1353270:three_prime_UTR 35.0%
CTGATATCTTTCTTCTCAGT+TGG + tig0013114:90127-90146 None:intergenic 35.0%
ATCATAATCACCTCTTCCAT+TGG + tig0013114:90160-90179 None:intergenic 35.0%
AACCAGTTTGTGTCTTAATC+AGG - tig0013114:90228-90247 Msa1353270:intron 35.0%
AACCTGATTAAGACACAAAC+TGG + tig0013114:90233-90252 None:intergenic 35.0%
!! TATTGTTGGTCTTTGGTTTG+GGG + tig0013114:90287-90306 None:intergenic 35.0%
TATCACACTGAGATTTGAGA+TGG + tig0013114:90545-90564 None:intergenic 35.0%
TCAATGTTGTCTCTCTATCT+GGG + tig0013114:90726-90745 None:intergenic 35.0%
TCGCGTAATTTCGAAGAAAT+TGG + tig0013114:90772-90791 None:intergenic 35.0%
TATACAATGGCATGAACTCA+TGG - tig0013114:90917-90936 Msa1353270:intron 35.0%
CATTTATCCCTCAGATTGGA+AGG - tig0013114:89666-89685 Msa1353270:three_prime_UTR 40.0%
TATCAGAGATTTGGGTCCAA+TGG - tig0013114:90141-90160 Msa1353270:CDS 40.0%
CTCAATGTTGTCTCTCTATC+TGG + tig0013114:90727-90746 None:intergenic 40.0%
ACATACAGAAGTTCAACTGC+AGG - tig0013114:90824-90843 Msa1353270:intron 40.0%
! GGAGTTTTCAATGCAATCAC+AGG - tig0013114:90845-90864 Msa1353270:intron 40.0%
CATTTATCCCTCAGATTGGA+AGG - tig0013114:89666-89685 Msa1353270:three_prime_UTR 40.0%
TATCAGAGATTTGGGTCCAA+TGG - tig0013114:90141-90160 Msa1353270:CDS 40.0%
CTCAATGTTGTCTCTCTATC+TGG + tig0013114:90727-90746 None:intergenic 40.0%
ACATACAGAAGTTCAACTGC+AGG - tig0013114:90824-90843 Msa1353270:intron 40.0%
! GGAGTTTTCAATGCAATCAC+AGG - tig0013114:90845-90864 Msa1353270:intron 40.0%
! TTCCCCAGGAATTTGACTTC+AGG - tig0013114:90038-90057 Msa1353270:three_prime_UTR 45.0%
! TCCCCAGGAATTTGACTTCA+GGG - tig0013114:90039-90058 Msa1353270:three_prime_UTR 45.0%
TGCCCTGAAGTCAAATTCCT+GGG + tig0013114:90044-90063 None:intergenic 45.0%
AGATTTGGGTCCAATGGAAG+AGG - tig0013114:90147-90166 Msa1353270:CDS 45.0%
TGAATTCAGCGGACGATAGA+TGG - tig0013114:90424-90443 Msa1353270:intron 45.0%
! TATCGCAAGTGTCGTAAAGG+AGG + tig0013114:90503-90522 None:intergenic 45.0%
TCCTTTACGACACTTGCGAT+AGG - tig0013114:90502-90521 Msa1353270:five_prime_UTR 45.0%
! TCCTATCGCAAGTGTCGTAA+AGG + tig0013114:90506-90525 None:intergenic 45.0%
ACGACACTTGCGATAGGAAA+TGG - tig0013114:90508-90527 Msa1353270:five_prime_UTR 45.0%
! TTCCCCAGGAATTTGACTTC+AGG - tig0013114:90038-90057 Msa1353270:three_prime_UTR 45.0%
! TCCCCAGGAATTTGACTTCA+GGG - tig0013114:90039-90058 Msa1353270:three_prime_UTR 45.0%
TGCCCTGAAGTCAAATTCCT+GGG + tig0013114:90044-90063 None:intergenic 45.0%
AGATTTGGGTCCAATGGAAG+AGG - tig0013114:90147-90166 Msa1353270:CDS 45.0%
TGAATTCAGCGGACGATAGA+TGG - tig0013114:90424-90443 Msa1353270:intron 45.0%
! TATCGCAAGTGTCGTAAAGG+AGG + tig0013114:90503-90522 None:intergenic 45.0%
TCCTTTACGACACTTGCGAT+AGG - tig0013114:90502-90521 Msa1353270:five_prime_UTR 45.0%
! TCCTATCGCAAGTGTCGTAA+AGG + tig0013114:90506-90525 None:intergenic 45.0%
ACGACACTTGCGATAGGAAA+TGG - tig0013114:90508-90527 Msa1353270:five_prime_UTR 45.0%
!! AATTATAATAAAATATACAA+TGG - tig0013114:90904-90923 Msa1353270:intron 5.0%
!! AATTATAATAAAATATACAA+TGG - tig0013114:90904-90923 Msa1353270:intron 5.0%
! GTCTGAGTGATCTTTTCCCC+AGG - tig0013114:90024-90043 Msa1353270:three_prime_UTR 50.0%
GCCCTGAAGTCAAATTCCTG+GGG + tig0013114:90043-90062 None:intergenic 50.0%
GTGCCCTGAAGTCAAATTCC+TGG + tig0013114:90045-90064 None:intergenic 50.0%
! GTCTGAGTGATCTTTTCCCC+AGG - tig0013114:90024-90043 Msa1353270:three_prime_UTR 50.0%
GCCCTGAAGTCAAATTCCTG+GGG + tig0013114:90043-90062 None:intergenic 50.0%
GTGCCCTGAAGTCAAATTCC+TGG + tig0013114:90045-90064 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0013114 gene 89640 91003 89640 ID=Msa1353270;Name=Msa1353270
tig0013114 mRNA 89640 91003 89640 ID=Msa1353270-mRNA-1;Parent=Msa1353270;Name=Msa1353270-mRNA-1;_AED=0.22;_eAED=0.22;_QI=111|0.66|0.75|1|1|1|4|466|61
tig0013114 exon 89640 90210 89640 ID=Msa1353270-mRNA-1:exon:8572;Parent=Msa1353270-mRNA-1
tig0013114 exon 90322 90393 90322 ID=Msa1353270-mRNA-1:exon:8571;Parent=Msa1353270-mRNA-1
tig0013114 exon 90475 90546 90475 ID=Msa1353270-mRNA-1:exon:8570;Parent=Msa1353270-mRNA-1
tig0013114 exon 90956 91003 90956 ID=Msa1353270-mRNA-1:exon:8569;Parent=Msa1353270-mRNA-1
tig0013114 five_prime_UTR 90956 91003 90956 ID=Msa1353270-mRNA-1:five_prime_utr;Parent=Msa1353270-mRNA-1
tig0013114 five_prime_UTR 90484 90546 90484 ID=Msa1353270-mRNA-1:five_prime_utr;Parent=Msa1353270-mRNA-1
tig0013114 CDS 90475 90483 90475 ID=Msa1353270-mRNA-1:cds;Parent=Msa1353270-mRNA-1
tig0013114 CDS 90322 90393 90322 ID=Msa1353270-mRNA-1:cds;Parent=Msa1353270-mRNA-1
tig0013114 CDS 90106 90210 90106 ID=Msa1353270-mRNA-1:cds;Parent=Msa1353270-mRNA-1
tig0013114 three_prime_UTR 89640 90105 89640 ID=Msa1353270-mRNA-1:three_prime_utr;Parent=Msa1353270-mRNA-1
Gene Sequence

>Msa1353270

ATGGAAGAGGTTATTACTGATTTGGTGAAACATAGATATGCTGCCCCAAACCAAAGACCAACAATATATGACATGCAAGAGCGGACGATAGATGGAAAACATTATTATACAATGGAATATGTACTTACATCACGAAATTACGCTAGTGCCTCCTTTACGACACTTGCGATAGGAAATGGTAAGTAA

Protein sequence

>Msa1353270

MEEVITDLVKHRYAAPNQRPTIYDMQERTIDGKHYYTMEYVLTSRNYASASFTTLAIGNGK*