AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1009280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1009280 MtrunA17_Chr7g0219691 84.946 93 11 1 1 90 763 855 6.35e-47 159
Msa1009280 MtrunA17_Chr7g0219721 84.946 93 11 1 1 90 763 855 7.21e-47 159
Msa1009280 MtrunA17_Chr7g0219781 73.404 94 21 1 1 90 766 859 4.29e-38 134
Msa1009280 MtrunA17_Chr7g0219671 71.111 90 22 1 1 86 763 852 8.89e-36 127
Msa1009280 MtrunA17_Chr7g0219761 73.239 71 19 0 1 71 18 88 1.78e-31 106
Msa1009280 MtrunA17_Chr7g0219681 77.778 63 14 0 1 63 754 816 5.92e-28 105
Msa1009280 MtrunA17_Chr7g0219571 53.333 90 39 2 1 88 765 853 9.22e-24 93.6
Msa1009280 MtrunA17_Chr7g0219651 53.333 90 39 2 1 88 1750 1838 3.32e-23 92.0
Msa1009280 MtrunA17_Chr7g0219651 55.556 81 34 2 1 81 754 832 1.84e-21 87.4
Msa1009280 MtrunA17_Chr4g0025961 43.119 109 45 2 1 93 758 865 7.71e-21 85.5
Msa1009280 MtrunA17_Chr7g0219581 63.077 65 23 1 1 65 189 252 1.90e-20 83.2
Msa1009280 MtrunA17_Chr7g0219601 48.352 91 43 2 1 87 749 839 3.31e-20 83.6
Msa1009280 MtrunA17_Chr7g0219611 45.652 92 49 1 1 91 745 836 5.44e-20 83.2
Msa1009280 MtrunA17_Chr7g0219621 62.500 64 23 1 1 64 156 218 6.13e-20 80.1
Msa1009280 MtrunA17_Chr6g0455321 51.852 54 26 0 1 54 765 818 1.21e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1009280 AT3G51550.1 38.144 97 51 3 1 88 765 861 8.55e-11 57.4

Find 15 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAAGTCTTCGTCTTCACT+CGG 0.438059 7_1:-10515729 Msa1009280:CDS
GTTTGTTGGCACTAAGGAAA+AGG 0.454452 7_1:-10516411 Msa1009280:CDS
TAGTAAGTTTGTTGGCACTA+AGG 0.466290 7_1:-10516417 Msa1009280:CDS
GAGGAGGATAGTAAGTTTGT+TGG 0.466467 7_1:-10516425 Msa1009280:CDS
TTGGGCTGTTTGCATGATGA+TGG 0.485327 7_1:-10516515 Msa1009280:CDS
ATTAGAGTTTGCATTGCAGT+TGG 0.491251 7_1:-10516456 Msa1009280:CDS
CCCGAGTGAAGACGAAGACT+TGG 0.502650 7_1:+10515728 None:intergenic
TGTCGATGAGTGATGTTGTT+GGG 0.555331 7_1:-10516481 Msa1009280:CDS
AAAAGGAAAAGAGTGAGCAA+AGG 0.564346 7_1:-10516394 Msa1009280:CDS
CCAAGTCTTCGTCTTCACTC+GGG 0.568127 7_1:-10515728 Msa1009280:CDS
AATTAAAGAACAATATCAAG+TGG 0.587386 7_1:+10515702 None:intergenic
ATGTCGATGAGTGATGTTGT+TGG 0.617473 7_1:-10516482 Msa1009280:CDS
GCAGTTGGAGATGAGTGAGG+AGG 0.681127 7_1:-10516441 Msa1009280:CDS
ATTGCAGTTGGAGATGAGTG+AGG 0.730101 7_1:-10516444 Msa1009280:CDS
TGCATGATGATGGAAATCAA+CGG 0.754214 7_1:-10516505 Msa1009280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAAATGTTATTTTCAAA+TGG - chr7_1:10515745-10515764 Msa1009280:intron 10.0%
!!! TTTAAAATGTTATTTTCAAA+TGG - chr7_1:10515745-10515764 Msa1009280:intron 10.0%
!! ATTGATGAAATATACTTAAG+CGG + chr7_1:10516224-10516243 None:intergenic 20.0%
!! TAATACCTTTAATCTTTGTT+CGG + chr7_1:10516247-10516266 None:intergenic 20.0%
!!! CAAAATGTCTTCTTTTAAAT+AGG + chr7_1:10516474-10516493 None:intergenic 20.0%
!!! CTATTTAAAAGAAGACATTT+TGG - chr7_1:10516472-10516491 Msa1009280:CDS 20.0%
!! ATTGATGAAATATACTTAAG+CGG + chr7_1:10516224-10516243 None:intergenic 20.0%
!! TAATACCTTTAATCTTTGTT+CGG + chr7_1:10516247-10516266 None:intergenic 20.0%
!!! CAAAATGTCTTCTTTTAAAT+AGG + chr7_1:10516474-10516493 None:intergenic 20.0%
!!! CTATTTAAAAGAAGACATTT+TGG - chr7_1:10516472-10516491 Msa1009280:CDS 20.0%
!! TCATAGAATCTTTTATGAAC+GGG + chr7_1:10515715-10515734 None:intergenic 25.0%
!! GTCATAGAATCTTTTATGAA+CGG + chr7_1:10515716-10515735 None:intergenic 25.0%
!!! ATGTTATTTTCAAATGGTGT+TGG - chr7_1:10515751-10515770 Msa1009280:intron 25.0%
!!! TGTTATTTTCAAATGGTGTT+GGG - chr7_1:10515752-10515771 Msa1009280:intron 25.0%
! AAATTACTTGTTCCATTGTT+TGG + chr7_1:10516108-10516127 None:intergenic 25.0%
! AAGTGGAATGAATAGAAATA+GGG + chr7_1:10516187-10516206 None:intergenic 25.0%
! AAAGTGGAATGAATAGAAAT+AGG + chr7_1:10516188-10516207 None:intergenic 25.0%
! TATACTTAAGCGGAATATAA+CGG + chr7_1:10516214-10516233 None:intergenic 25.0%
!! GCTTATAATTCAGCAATTTT+AGG - chr7_1:10516308-10516327 Msa1009280:intron 25.0%
! TAAGATACTTATAACTGTCA+CGG + chr7_1:10516507-10516526 None:intergenic 25.0%
!! TCATAGAATCTTTTATGAAC+GGG + chr7_1:10515715-10515734 None:intergenic 25.0%
!! GTCATAGAATCTTTTATGAA+CGG + chr7_1:10515716-10515735 None:intergenic 25.0%
!!! ATGTTATTTTCAAATGGTGT+TGG - chr7_1:10515751-10515770 Msa1009280:intron 25.0%
!!! TGTTATTTTCAAATGGTGTT+GGG - chr7_1:10515752-10515771 Msa1009280:intron 25.0%
! AAATTACTTGTTCCATTGTT+TGG + chr7_1:10516108-10516127 None:intergenic 25.0%
! AAGTGGAATGAATAGAAATA+GGG + chr7_1:10516187-10516206 None:intergenic 25.0%
! AAAGTGGAATGAATAGAAAT+AGG + chr7_1:10516188-10516207 None:intergenic 25.0%
! TATACTTAAGCGGAATATAA+CGG + chr7_1:10516214-10516233 None:intergenic 25.0%
!! GCTTATAATTCAGCAATTTT+AGG - chr7_1:10516308-10516327 Msa1009280:intron 25.0%
! TAAGATACTTATAACTGTCA+CGG + chr7_1:10516507-10516526 None:intergenic 25.0%
! TTGTCACATTTTACTGATGA+AGG - chr7_1:10515920-10515939 Msa1009280:intron 30.0%
! TGTCACATTTTACTGATGAA+GGG - chr7_1:10515921-10515940 Msa1009280:intron 30.0%
! TTCTTCAGTTCTGATTGAAT+TGG + chr7_1:10515996-10516015 None:intergenic 30.0%
CACTATATAGCAGAAAACAA+AGG + chr7_1:10516022-10516041 None:intergenic 30.0%
TCCATTGTTTGGAAAATGAA+CGG + chr7_1:10516097-10516116 None:intergenic 30.0%
AGTGTTTGAGTATTATACGA+TGG + chr7_1:10516139-10516158 None:intergenic 30.0%
ATCGTATAATACTCAAACAC+TGG - chr7_1:10516138-10516157 Msa1009280:intron 30.0%
TCAATCCGAACAAAGATTAA+AGG - chr7_1:10516239-10516258 Msa1009280:intron 30.0%
!! TTAATTTGTCACCACATTCA+GGG + chr7_1:10516429-10516448 None:intergenic 30.0%
TGGTGACAAATTAACGAAAA+CGG - chr7_1:10516435-10516454 Msa1009280:CDS 30.0%
!!! GTGAAGTCTTTGGAATATTT+TGG + chr7_1:10516538-10516557 None:intergenic 30.0%
! TTGTCACATTTTACTGATGA+AGG - chr7_1:10515920-10515939 Msa1009280:intron 30.0%
! TGTCACATTTTACTGATGAA+GGG - chr7_1:10515921-10515940 Msa1009280:intron 30.0%
! TTCTTCAGTTCTGATTGAAT+TGG + chr7_1:10515996-10516015 None:intergenic 30.0%
CACTATATAGCAGAAAACAA+AGG + chr7_1:10516022-10516041 None:intergenic 30.0%
TCCATTGTTTGGAAAATGAA+CGG + chr7_1:10516097-10516116 None:intergenic 30.0%
AGTGTTTGAGTATTATACGA+TGG + chr7_1:10516139-10516158 None:intergenic 30.0%
ATCGTATAATACTCAAACAC+TGG - chr7_1:10516138-10516157 Msa1009280:intron 30.0%
TCAATCCGAACAAAGATTAA+AGG - chr7_1:10516239-10516258 Msa1009280:intron 30.0%
!! TTAATTTGTCACCACATTCA+GGG + chr7_1:10516429-10516448 None:intergenic 30.0%
TGGTGACAAATTAACGAAAA+CGG - chr7_1:10516435-10516454 Msa1009280:CDS 30.0%
!!! GTGAAGTCTTTGGAATATTT+TGG + chr7_1:10516538-10516557 None:intergenic 30.0%
!! TGCATGATGATGGAAATCAA+CGG - chr7_1:10515780-10515799 Msa1009280:intron 35.0%
ATTAGAGTTTGCATTGCAGT+TGG - chr7_1:10515829-10515848 Msa1009280:intron 35.0%
!! TAGTAAGTTTGTTGGCACTA+AGG - chr7_1:10515868-10515887 Msa1009280:intron 35.0%
AAAAGGAAAAGAGTGAGCAA+AGG - chr7_1:10515891-10515910 Msa1009280:intron 35.0%
! TTCAGTTCTGATTGAATTGG+TGG + chr7_1:10515993-10516012 None:intergenic 35.0%
! TCCGTTCATTTTCCAAACAA+TGG - chr7_1:10516093-10516112 Msa1009280:intron 35.0%
TGGAATGAATAGAAATAGGG+CGG + chr7_1:10516184-10516203 None:intergenic 35.0%
! CGGAATATAACGGAATAAAG+TGG + chr7_1:10516204-10516223 None:intergenic 35.0%
!! GTTAATTTGTCACCACATTC+AGG + chr7_1:10516430-10516449 None:intergenic 35.0%
!! TGCATGATGATGGAAATCAA+CGG - chr7_1:10515780-10515799 Msa1009280:intron 35.0%
ATTAGAGTTTGCATTGCAGT+TGG - chr7_1:10515829-10515848 Msa1009280:intron 35.0%
!! TAGTAAGTTTGTTGGCACTA+AGG - chr7_1:10515868-10515887 Msa1009280:intron 35.0%
AAAAGGAAAAGAGTGAGCAA+AGG - chr7_1:10515891-10515910 Msa1009280:intron 35.0%
! TTCAGTTCTGATTGAATTGG+TGG + chr7_1:10515993-10516012 None:intergenic 35.0%
! TCCGTTCATTTTCCAAACAA+TGG - chr7_1:10516093-10516112 Msa1009280:intron 35.0%
TGGAATGAATAGAAATAGGG+CGG + chr7_1:10516184-10516203 None:intergenic 35.0%
! CGGAATATAACGGAATAAAG+TGG + chr7_1:10516204-10516223 None:intergenic 35.0%
!! GTTAATTTGTCACCACATTC+AGG + chr7_1:10516430-10516449 None:intergenic 35.0%
ATGTCGATGAGTGATGTTGT+TGG - chr7_1:10515803-10515822 Msa1009280:intron 40.0%
TGTCGATGAGTGATGTTGTT+GGG - chr7_1:10515804-10515823 Msa1009280:intron 40.0%
GAGGAGGATAGTAAGTTTGT+TGG - chr7_1:10515860-10515879 Msa1009280:intron 40.0%
! GTTTGTTGGCACTAAGGAAA+AGG - chr7_1:10515874-10515893 Msa1009280:intron 40.0%
! ACAAGTAGTAGTGATGACGA+TGG - chr7_1:10515959-10515978 Msa1009280:intron 40.0%
TGAATAGAAATAGGGCGGAA+TGG + chr7_1:10516179-10516198 None:intergenic 40.0%
!! ACTTGGTGCAATAATCGGTA+GGG + chr7_1:10516272-10516291 None:intergenic 40.0%
! TACCGATTATTGCACCAAGT+GGG - chr7_1:10516272-10516291 Msa1009280:intron 40.0%
ATGTCGATGAGTGATGTTGT+TGG - chr7_1:10515803-10515822 Msa1009280:intron 40.0%
TGTCGATGAGTGATGTTGTT+GGG - chr7_1:10515804-10515823 Msa1009280:intron 40.0%
GAGGAGGATAGTAAGTTTGT+TGG - chr7_1:10515860-10515879 Msa1009280:intron 40.0%
! GTTTGTTGGCACTAAGGAAA+AGG - chr7_1:10515874-10515893 Msa1009280:intron 40.0%
! ACAAGTAGTAGTGATGACGA+TGG - chr7_1:10515959-10515978 Msa1009280:intron 40.0%
TGAATAGAAATAGGGCGGAA+TGG + chr7_1:10516179-10516198 None:intergenic 40.0%
!! ACTTGGTGCAATAATCGGTA+GGG + chr7_1:10516272-10516291 None:intergenic 40.0%
! TACCGATTATTGCACCAAGT+GGG - chr7_1:10516272-10516291 Msa1009280:intron 40.0%
TTGGGCTGTTTGCATGATGA+TGG - chr7_1:10515770-10515789 Msa1009280:intron 45.0%
ATTGCAGTTGGAGATGAGTG+AGG - chr7_1:10515841-10515860 Msa1009280:intron 45.0%
!! CACTTGGTGCAATAATCGGT+AGG + chr7_1:10516273-10516292 None:intergenic 45.0%
! CTACCGATTATTGCACCAAG+TGG - chr7_1:10516271-10516290 Msa1009280:intron 45.0%
!! GTCCCACTTGGTGCAATAAT+CGG + chr7_1:10516277-10516296 None:intergenic 45.0%
! CTTTTCATTCGTGTCCCACT+TGG + chr7_1:10516289-10516308 None:intergenic 45.0%
!! CGAAGACTTGGTGAAGTCTT+TGG + chr7_1:10516548-10516567 None:intergenic 45.0%
ACCAAGTCTTCGTCTTCACT+CGG - chr7_1:10516556-10516575 Msa1009280:CDS 45.0%
TTGGGCTGTTTGCATGATGA+TGG - chr7_1:10515770-10515789 Msa1009280:intron 45.0%
ATTGCAGTTGGAGATGAGTG+AGG - chr7_1:10515841-10515860 Msa1009280:intron 45.0%
!! CACTTGGTGCAATAATCGGT+AGG + chr7_1:10516273-10516292 None:intergenic 45.0%
! CTACCGATTATTGCACCAAG+TGG - chr7_1:10516271-10516290 Msa1009280:intron 45.0%
!! GTCCCACTTGGTGCAATAAT+CGG + chr7_1:10516277-10516296 None:intergenic 45.0%
! CTTTTCATTCGTGTCCCACT+TGG + chr7_1:10516289-10516308 None:intergenic 45.0%
!! CGAAGACTTGGTGAAGTCTT+TGG + chr7_1:10516548-10516567 None:intergenic 45.0%
ACCAAGTCTTCGTCTTCACT+CGG - chr7_1:10516556-10516575 Msa1009280:CDS 45.0%
TAGTTGTCCTGCCCTGAATG+TGG - chr7_1:10516415-10516434 Msa1009280:CDS 50.0%
TTTGTCACCACATTCAGGGC+AGG + chr7_1:10516425-10516444 None:intergenic 50.0%
CCAAGTCTTCGTCTTCACTC+GGG - chr7_1:10516557-10516576 Msa1009280:CDS 50.0%
TAGTTGTCCTGCCCTGAATG+TGG - chr7_1:10516415-10516434 Msa1009280:CDS 50.0%
TTTGTCACCACATTCAGGGC+AGG + chr7_1:10516425-10516444 None:intergenic 50.0%
CCAAGTCTTCGTCTTCACTC+GGG - chr7_1:10516557-10516576 Msa1009280:CDS 50.0%
GCAGTTGGAGATGAGTGAGG+AGG - chr7_1:10515844-10515863 Msa1009280:intron 55.0%
CCCGAGTGAAGACGAAGACT+TGG + chr7_1:10516560-10516579 None:intergenic 55.0%
GCAGTTGGAGATGAGTGAGG+AGG - chr7_1:10515844-10515863 Msa1009280:intron 55.0%
CCCGAGTGAAGACGAAGACT+TGG + chr7_1:10516560-10516579 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 10515704 10516603 10515704 ID=Msa1009280;Name=Msa1009280
chr7_1 mRNA 10515704 10516603 10515704 ID=Msa1009280-mRNA-1;Parent=Msa1009280;Name=Msa1009280-mRNA-1;_AED=0.50;_eAED=0.50;_QI=0|0|0|0.5|0|0|2|0|97
chr7_1 exon 10516363 10516603 10516363 ID=Msa1009280-mRNA-1:exon:2863;Parent=Msa1009280-mRNA-1
chr7_1 exon 10515704 10515756 10515704 ID=Msa1009280-mRNA-1:exon:2862;Parent=Msa1009280-mRNA-1
chr7_1 CDS 10516363 10516603 10516363 ID=Msa1009280-mRNA-1:cds;Parent=Msa1009280-mRNA-1
chr7_1 CDS 10515704 10515756 10515704 ID=Msa1009280-mRNA-1:cds;Parent=Msa1009280-mRNA-1
Gene Sequence

>Msa1009280

ATGGTGGACCCGTTCATAAAAGATTCTATGACAAGTGAGTGTTTAAAATGTTATTTTCAAATGGTGTTGGGCTGTTTGCATGATGATGGAAATCAACGGATGTCGATGAGTGATGTTGTTGGGACATTAGAGTTTGCATTGCAGTTGGAGATGAGTGAGGAGGATAGTAAGTTTGTTGGCACTAAGGAAAAGGAAAAGAGTGAGCAAAGGATAGAATTGTCACATTTTACTGATGAAGGGAACTTCACCAAGTCTTCGTCTTCACTCGGGCATCCACTTGATATTGTTCTTTAA

Protein sequence

>Msa1009280

MVDPFIKDSMTSECLKCYFQMVLGCLHDDGNQRMSMSDVVGTLEFALQLEMSEEDSKFVGTKEKEKSEQRIELSHFTDEGNFTKSSSSLGHPLDIVL*