AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0810020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0810020 MtrunA17_Chr5g0425991 91.781 219 12 1 1 219 1 213 6.00e-142 395
Msa0810020 MtrunA17_Chr3g0115791 58.333 168 47 9 64 218 2 159 9.71e-48 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0810020 AT1G78170.1 37.391 230 107 10 1 211 1 212 2.08e-27 104
Msa0810020 AT1G22250.1 42.609 115 59 2 111 218 85 199 2.90e-17 77.0
Msa0810020 AT4G08910.1 39.286 112 52 2 108 203 86 197 2.95e-17 77.4

Find 37 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGATCAAGAATTCTTTA+AGG 0.147055 5_3:+37938512 Msa0810020:CDS
GATTACATAGACTTATTTAT+TGG 0.200096 5_3:-37939314 None:intergenic
CACCTTTGCCTTCAGATAAA+TGG 0.203598 5_3:+37938595 Msa0810020:CDS
TTAAGAACATACATAAATTT+AGG 0.233603 5_3:-37939516 None:intergenic
CTTCACAAAAGAAGAGAAAA+TGG 0.266395 5_3:+37938475 Msa0810020:CDS
AAACCACTCTTGTTTGAATA+TGG 0.302002 5_3:+37938392 Msa0810020:exon
ATCAATTAGCAAGAATAAAA+AGG 0.319819 5_3:+37939045 Msa0810020:CDS
TATTATATATTTCAAACAAA+AGG 0.340498 5_3:+37939361 Msa0810020:three_prime_UTR
CAAGAACAACCACTTCTAAT+TGG 0.345178 5_3:+37939290 Msa0810020:three_prime_UTR
AAGGATCTTACACATGATCT+TGG 0.370919 5_3:+37938531 Msa0810020:CDS
GGATGCATGAATTTGCAATT+AGG 0.374086 5_3:-37939205 None:intergenic
CAAATTATACAACTCCTTAG+AGG 0.387146 5_3:-37939405 None:intergenic
GTATGTTTCTTAAAGTTGTA+AGG 0.399346 5_3:+37939546 Msa0810020:three_prime_UTR
TTAATCTACCTCTACCTCTA+AGG 0.434008 5_3:+37939391 Msa0810020:three_prime_UTR
AGGATCTTACACATGATCTT+GGG 0.444226 5_3:+37938532 Msa0810020:CDS
GCAACAATACCTCACAGTTC+AGG 0.455526 5_3:+37938617 Msa0810020:CDS
ATTATATATTTCAAACAAAA+GGG 0.459409 5_3:+37939362 Msa0810020:three_prime_UTR
AATTTGGAAGGGTTCTGATC+TGG 0.466878 5_3:-37939232 None:intergenic
GAAGGGTTCTGATCTGGTGG+TGG 0.491999 5_3:-37939226 None:intergenic
AAGAATTCTTGATCAGAAAG+TGG 0.498028 5_3:-37938507 None:intergenic
GTGAAGTTCAATATCAAAGA+TGG 0.498275 5_3:-37938565 None:intergenic
AAGGAGTTGTATAATTTGAC+TGG 0.504963 5_3:+37939410 Msa0810020:three_prime_UTR
TAAGTACTACTAATTCATCA+TGG 0.522676 5_3:+37939080 Msa0810020:CDS
TTCACAAAAGAAGAGAAAAT+GGG 0.522716 5_3:+37938476 Msa0810020:CDS
ATACAACTCCTTAGAGGTAG+AGG 0.527574 5_3:-37939399 None:intergenic
TATTGTTGCCATTTATCTGA+AGG 0.533510 5_3:-37938603 None:intergenic
TGTGAAGCATCAAAATCTGT+AGG 0.557840 5_3:-37938459 None:intergenic
CACATGTCAAATTAAGCTCA+AGG 0.558418 5_3:-37938964 None:intergenic
AATTTGCAATTAGGACAAGA+AGG 0.564845 5_3:-37939196 None:intergenic
TTTATTGGACCAATTAGAAG+TGG 0.571145 5_3:-37939299 None:intergenic
TTGGAAGGGTTCTGATCTGG+TGG 0.597114 5_3:-37939229 None:intergenic
TGCCATTTATCTGAAGGCAA+AGG 0.597180 5_3:-37938597 None:intergenic
TGGTTATCATCATCATCAGA+TGG 0.614533 5_3:+37939100 Msa0810020:CDS
AGACCATATTCAAACAAGAG+TGG 0.639805 5_3:-37938395 None:intergenic
ACATAAATTTATGATACACA+AGG 0.669913 5_3:-37939466 None:intergenic
TTGTATGAAGTGTCACATGT+TGG 0.683627 5_3:+37939153 Msa0810020:CDS
TATTATATACCTGAACTGTG+AGG 0.723748 5_3:-37938626 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATAAAATATATTAACCT+CGG - chr5_3:37938705-37938724 None:intergenic 10.0%
!! TATTATATATTTCAAACAAA+AGG + chr5_3:37939361-37939380 Msa0810020:three_prime_UTR 10.0%
!! ATTATATATTTCAAACAAAA+GGG + chr5_3:37939362-37939381 Msa0810020:three_prime_UTR 10.0%
!! AAAATAAAATATATTAACCT+CGG - chr5_3:37938705-37938724 None:intergenic 10.0%
!! TATTATATATTTCAAACAAA+AGG + chr5_3:37939361-37939380 Msa0810020:three_prime_UTR 10.0%
!! ATTATATATTTCAAACAAAA+GGG + chr5_3:37939362-37939381 Msa0810020:three_prime_UTR 10.0%
!!! GAGGTTAATATATTTTATTT+TGG + chr5_3:37938704-37938723 Msa0810020:intron 15.0%
!! TTATAATATTATTGCTACAT+CGG - chr5_3:37938751-37938770 None:intergenic 15.0%
!! TTAAGAACATACATAAATTT+AGG - chr5_3:37939519-37939538 None:intergenic 15.0%
!!! GAGGTTAATATATTTTATTT+TGG + chr5_3:37938704-37938723 Msa0810020:intron 15.0%
!! TTATAATATTATTGCTACAT+CGG - chr5_3:37938751-37938770 None:intergenic 15.0%
!! TTAAGAACATACATAAATTT+AGG - chr5_3:37939519-37939538 None:intergenic 15.0%
!! ATCAATTAGCAAGAATAAAA+AGG + chr5_3:37939045-37939064 Msa0810020:CDS 20.0%
!! GATTACATAGACTTATTTAT+TGG - chr5_3:37939317-37939336 None:intergenic 20.0%
!! ACATAAATTTATGATACACA+AGG - chr5_3:37939469-37939488 None:intergenic 20.0%
!! ATCAATTAGCAAGAATAAAA+AGG + chr5_3:37939045-37939064 Msa0810020:CDS 20.0%
!! GATTACATAGACTTATTTAT+TGG - chr5_3:37939317-37939336 None:intergenic 20.0%
!! ACATAAATTTATGATACACA+AGG - chr5_3:37939469-37939488 None:intergenic 20.0%
! TTCACAAAAGAAGAGAAAAT+GGG + chr5_3:37938476-37938495 Msa0810020:CDS 25.0%
! TTCTGATCAAGAATTCTTTA+AGG + chr5_3:37938512-37938531 Msa0810020:CDS 25.0%
! CGAAAATGTGCTTATAAAAA+GGG - chr5_3:37938661-37938680 None:intergenic 25.0%
! TAAGTACTACTAATTCATCA+TGG + chr5_3:37939080-37939099 Msa0810020:CDS 25.0%
! TTCTCTTCAAAAATTTGGAA+GGG - chr5_3:37939246-37939265 None:intergenic 25.0%
! GTATGTTTCTTAAAGTTGTA+AGG + chr5_3:37939546-37939565 Msa0810020:three_prime_UTR 25.0%
! TTCACAAAAGAAGAGAAAAT+GGG + chr5_3:37938476-37938495 Msa0810020:CDS 25.0%
! TTCTGATCAAGAATTCTTTA+AGG + chr5_3:37938512-37938531 Msa0810020:CDS 25.0%
! CGAAAATGTGCTTATAAAAA+GGG - chr5_3:37938661-37938680 None:intergenic 25.0%
! TAAGTACTACTAATTCATCA+TGG + chr5_3:37939080-37939099 Msa0810020:CDS 25.0%
! TTCTCTTCAAAAATTTGGAA+GGG - chr5_3:37939246-37939265 None:intergenic 25.0%
! GTATGTTTCTTAAAGTTGTA+AGG + chr5_3:37939546-37939565 Msa0810020:three_prime_UTR 25.0%
! AAACCACTCTTGTTTGAATA+TGG + chr5_3:37938392-37938411 Msa0810020:exon 30.0%
!!! AGAATCTTTTTTTGGACTCA+TGG - chr5_3:37938439-37938458 None:intergenic 30.0%
!!! TCTGTAGGAGAATCTTTTTT+TGG - chr5_3:37938447-37938466 None:intergenic 30.0%
CTTCACAAAAGAAGAGAAAA+TGG + chr5_3:37938475-37938494 Msa0810020:CDS 30.0%
AAGAATTCTTGATCAGAAAG+TGG - chr5_3:37938510-37938529 None:intergenic 30.0%
GTGAAGTTCAATATCAAAGA+TGG - chr5_3:37938568-37938587 None:intergenic 30.0%
! TATTGTTGCCATTTATCTGA+AGG - chr5_3:37938606-37938625 None:intergenic 30.0%
TATTATATACCTGAACTGTG+AGG - chr5_3:37938629-37938648 None:intergenic 30.0%
AATGTGCTTATAAAAAGGGA+CGG - chr5_3:37938657-37938676 None:intergenic 30.0%
GCGAAAATGTGCTTATAAAA+AGG - chr5_3:37938662-37938681 None:intergenic 30.0%
! TCGGCTCTAATTAAAAACTA+CGG - chr5_3:37938686-37938705 None:intergenic 30.0%
! TTAAATTTTCTCATGCAGTC+AGG + chr5_3:37938839-37938858 Msa0810020:intron 30.0%
! TAAATTTTCTCATGCAGTCA+GGG + chr5_3:37938840-37938859 Msa0810020:intron 30.0%
!!! GAGATGATTTTTCAGGTAAA+GGG - chr5_3:37938925-37938944 None:intergenic 30.0%
!!! AGAGATGATTTTTCAGGTAA+AGG - chr5_3:37938926-37938945 None:intergenic 30.0%
TTACCTGAAAAATCATCTCT+AGG + chr5_3:37938926-37938945 Msa0810020:CDS 30.0%
AATTTGCAATTAGGACAAGA+AGG - chr5_3:37939199-37939218 None:intergenic 30.0%
GTTCTCTTCAAAAATTTGGA+AGG - chr5_3:37939247-37939266 None:intergenic 30.0%
CCTTGTTCTCTTCAAAAATT+TGG - chr5_3:37939251-37939270 None:intergenic 30.0%
!! CCAAATTTTTGAAGAGAACA+AGG + chr5_3:37939248-37939267 Msa0810020:CDS 30.0%
TTTATTGGACCAATTAGAAG+TGG - chr5_3:37939302-37939321 None:intergenic 30.0%
CAAATTATACAACTCCTTAG+AGG - chr5_3:37939408-37939427 None:intergenic 30.0%
AAGGAGTTGTATAATTTGAC+TGG + chr5_3:37939410-37939429 Msa0810020:three_prime_UTR 30.0%
! TTTTCTCAACTCTTTCTTTC+TGG - chr5_3:37938375-37938394 None:intergenic 30.0%
! AAACCACTCTTGTTTGAATA+TGG + chr5_3:37938392-37938411 Msa0810020:exon 30.0%
!!! AGAATCTTTTTTTGGACTCA+TGG - chr5_3:37938439-37938458 None:intergenic 30.0%
!!! TCTGTAGGAGAATCTTTTTT+TGG - chr5_3:37938447-37938466 None:intergenic 30.0%
CTTCACAAAAGAAGAGAAAA+TGG + chr5_3:37938475-37938494 Msa0810020:CDS 30.0%
AAGAATTCTTGATCAGAAAG+TGG - chr5_3:37938510-37938529 None:intergenic 30.0%
GTGAAGTTCAATATCAAAGA+TGG - chr5_3:37938568-37938587 None:intergenic 30.0%
! TATTGTTGCCATTTATCTGA+AGG - chr5_3:37938606-37938625 None:intergenic 30.0%
TATTATATACCTGAACTGTG+AGG - chr5_3:37938629-37938648 None:intergenic 30.0%
AATGTGCTTATAAAAAGGGA+CGG - chr5_3:37938657-37938676 None:intergenic 30.0%
GCGAAAATGTGCTTATAAAA+AGG - chr5_3:37938662-37938681 None:intergenic 30.0%
! TCGGCTCTAATTAAAAACTA+CGG - chr5_3:37938686-37938705 None:intergenic 30.0%
! TTAAATTTTCTCATGCAGTC+AGG + chr5_3:37938839-37938858 Msa0810020:intron 30.0%
! TAAATTTTCTCATGCAGTCA+GGG + chr5_3:37938840-37938859 Msa0810020:intron 30.0%
!!! GAGATGATTTTTCAGGTAAA+GGG - chr5_3:37938925-37938944 None:intergenic 30.0%
!!! AGAGATGATTTTTCAGGTAA+AGG - chr5_3:37938926-37938945 None:intergenic 30.0%
TTACCTGAAAAATCATCTCT+AGG + chr5_3:37938926-37938945 Msa0810020:CDS 30.0%
AATTTGCAATTAGGACAAGA+AGG - chr5_3:37939199-37939218 None:intergenic 30.0%
GTTCTCTTCAAAAATTTGGA+AGG - chr5_3:37939247-37939266 None:intergenic 30.0%
CCTTGTTCTCTTCAAAAATT+TGG - chr5_3:37939251-37939270 None:intergenic 30.0%
!! CCAAATTTTTGAAGAGAACA+AGG + chr5_3:37939248-37939267 Msa0810020:CDS 30.0%
TTTATTGGACCAATTAGAAG+TGG - chr5_3:37939302-37939321 None:intergenic 30.0%
CAAATTATACAACTCCTTAG+AGG - chr5_3:37939408-37939427 None:intergenic 30.0%
AAGGAGTTGTATAATTTGAC+TGG + chr5_3:37939410-37939429 Msa0810020:three_prime_UTR 30.0%
AGACCATATTCAAACAAGAG+TGG - chr5_3:37938398-37938417 None:intergenic 35.0%
! TGTGAAGCATCAAAATCTGT+AGG - chr5_3:37938462-37938481 None:intergenic 35.0%
AAGGATCTTACACATGATCT+TGG + chr5_3:37938531-37938550 Msa0810020:CDS 35.0%
AGGATCTTACACATGATCTT+GGG + chr5_3:37938532-37938551 Msa0810020:CDS 35.0%
!! GTAGTTTTTAATTAGAGCCG+AGG + chr5_3:37938685-37938704 Msa0810020:intron 35.0%
! TGACCTAGAGATGATTTTTC+AGG - chr5_3:37938932-37938951 None:intergenic 35.0%
CACATGTCAAATTAAGCTCA+AGG - chr5_3:37938967-37938986 None:intergenic 35.0%
TGGTTATCATCATCATCAGA+TGG + chr5_3:37939100-37939119 Msa0810020:CDS 35.0%
! TTGTATGAAGTGTCACATGT+TGG + chr5_3:37939153-37939172 Msa0810020:CDS 35.0%
GGATGCATGAATTTGCAATT+AGG - chr5_3:37939208-37939227 None:intergenic 35.0%
CAAGAACAACCACTTCTAAT+TGG + chr5_3:37939290-37939309 Msa0810020:three_prime_UTR 35.0%
TTAATCTACCTCTACCTCTA+AGG + chr5_3:37939391-37939410 Msa0810020:three_prime_UTR 35.0%
AGACCATATTCAAACAAGAG+TGG - chr5_3:37938398-37938417 None:intergenic 35.0%
! TGTGAAGCATCAAAATCTGT+AGG - chr5_3:37938462-37938481 None:intergenic 35.0%
AAGGATCTTACACATGATCT+TGG + chr5_3:37938531-37938550 Msa0810020:CDS 35.0%
AGGATCTTACACATGATCTT+GGG + chr5_3:37938532-37938551 Msa0810020:CDS 35.0%
!! GTAGTTTTTAATTAGAGCCG+AGG + chr5_3:37938685-37938704 Msa0810020:intron 35.0%
! TGACCTAGAGATGATTTTTC+AGG - chr5_3:37938932-37938951 None:intergenic 35.0%
CACATGTCAAATTAAGCTCA+AGG - chr5_3:37938967-37938986 None:intergenic 35.0%
TGGTTATCATCATCATCAGA+TGG + chr5_3:37939100-37939119 Msa0810020:CDS 35.0%
! TTGTATGAAGTGTCACATGT+TGG + chr5_3:37939153-37939172 Msa0810020:CDS 35.0%
GGATGCATGAATTTGCAATT+AGG - chr5_3:37939208-37939227 None:intergenic 35.0%
CAAGAACAACCACTTCTAAT+TGG + chr5_3:37939290-37939309 Msa0810020:three_prime_UTR 35.0%
TTAATCTACCTCTACCTCTA+AGG + chr5_3:37939391-37939410 Msa0810020:three_prime_UTR 35.0%
CACCTTTGCCTTCAGATAAA+TGG + chr5_3:37938595-37938614 Msa0810020:CDS 40.0%
! TGCCATTTATCTGAAGGCAA+AGG - chr5_3:37938600-37938619 None:intergenic 40.0%
! AATTTGGAAGGGTTCTGATC+TGG - chr5_3:37939235-37939254 None:intergenic 40.0%
ATACAACTCCTTAGAGGTAG+AGG - chr5_3:37939402-37939421 None:intergenic 40.0%
CACCTTTGCCTTCAGATAAA+TGG + chr5_3:37938595-37938614 Msa0810020:CDS 40.0%
! TGCCATTTATCTGAAGGCAA+AGG - chr5_3:37938600-37938619 None:intergenic 40.0%
! AATTTGGAAGGGTTCTGATC+TGG - chr5_3:37939235-37939254 None:intergenic 40.0%
ATACAACTCCTTAGAGGTAG+AGG - chr5_3:37939402-37939421 None:intergenic 40.0%
!!! CTGAAGGCAAAGGTGTTTTG+AGG - chr5_3:37938590-37938609 None:intergenic 45.0%
GCAACAATACCTCACAGTTC+AGG + chr5_3:37938617-37938636 Msa0810020:CDS 45.0%
!!! CTGAAGGCAAAGGTGTTTTG+AGG - chr5_3:37938590-37938609 None:intergenic 45.0%
GCAACAATACCTCACAGTTC+AGG + chr5_3:37938617-37938636 Msa0810020:CDS 45.0%
! TTGGAAGGGTTCTGATCTGG+TGG - chr5_3:37939232-37939251 None:intergenic 50.0%
! TTGGAAGGGTTCTGATCTGG+TGG - chr5_3:37939232-37939251 None:intergenic 50.0%
! GAAGGGTTCTGATCTGGTGG+TGG - chr5_3:37939229-37939248 None:intergenic 55.0%
! GAAGGGTTCTGATCTGGTGG+TGG - chr5_3:37939229-37939248 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 37938375 37939601 37938375 ID=Msa0810020;Name=Msa0810020
chr5_3 mRNA 37938375 37939601 37938375 ID=Msa0810020-mRNA-1;Parent=Msa0810020;Name=Msa0810020-mRNA-1;_AED=0.02;_eAED=0.02;_QI=36|1|1|1|1|1|2|313|219
chr5_3 exon 37938375 37938638 37938375 ID=Msa0810020-mRNA-1:exon:11601;Parent=Msa0810020-mRNA-1
chr5_3 exon 37938857 37939601 37938857 ID=Msa0810020-mRNA-1:exon:11602;Parent=Msa0810020-mRNA-1
chr5_3 five_prime_UTR 37938375 37938410 37938375 ID=Msa0810020-mRNA-1:five_prime_utr;Parent=Msa0810020-mRNA-1
chr5_3 CDS 37938411 37938638 37938411 ID=Msa0810020-mRNA-1:cds;Parent=Msa0810020-mRNA-1
chr5_3 CDS 37938857 37939288 37938857 ID=Msa0810020-mRNA-1:cds;Parent=Msa0810020-mRNA-1
chr5_3 three_prime_UTR 37939289 37939601 37939289 ID=Msa0810020-mRNA-1:three_prime_utr;Parent=Msa0810020-mRNA-1
Gene Sequence

>Msa0810020

ATGGTCTCACTTCACAAAGCACTAGCCATGAGTCCAAAAAAAGATTCTCCTACAGATTTTGATGCTTCACAAAAGAAGAGAAAATGGGAAGAATCACCACTTTCTGATCAAGAATTCTTTAAGGATCTTACACATGATCTTGGGAAAAGAAAATCCATCTTTGATATTGAACTTCACCTCAAAACACCTTTGCCTTCAGATAAATGGCAACAATACCTCACAGTTCAGTCAGGGCAAATACAATTGTGTAACACAAAGATGAATATGAAAACACAAGAATCAAAAAGAGAGTACCCTTTACCTGAAAAATCATCTCTAGGTCATTTAAGCTTAGACCTTGAGCTTAATTTGACATGTGAATCATTGAAGAAAAAAGAAGAAAGTTATTTTGAAAAGAAGAATAATCTAGTGAATGAATCAATTAGCAAGAATAAAAAGGATTCAAGTTTTTTAAGTACTACTAATTCATCATGGTTATCATCATCATCAGATGGTGATGATTACAAAGAAATGATTGCAACAGTTTGTATGAAGTGTCACATGTTGGTAATGCTTTGCAAATCATCTCCTTCTTGTCCTAATTGCAAATTCATGCATCCACCACCAGATCAGAACCCTTCCAAATTTTTGAAGAGAACAAGGTTTAGTTTCTTGACATAA

Protein sequence

>Msa0810020

MVSLHKALAMSPKKDSPTDFDASQKKRKWEESPLSDQEFFKDLTHDLGKRKSIFDIELHLKTPLPSDKWQQYLTVQSGQIQLCNTKMNMKTQESKREYPLPEKSSLGHLSLDLELNLTCESLKKKEESYFEKKNNLVNESISKNKKDSSFLSTTNSSWLSSSSDGDDYKEMIATVCMKCHMLVMLCKSSPSCPNCKFMHPPPDQNPSKFLKRTRFSFLT*