AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010006


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010006.t1 MTR_5g068000 82.573 241 32 2 2 232 1 241 2.03e-141 395
MS.gene010006.t1 MTR_5g016960 50.769 65 28 3 168 232 538 598 4.16e-12 65.5
MS.gene010006.t1 MTR_3g025940 39.189 74 43 2 160 232 375 447 1.68e-11 63.5
MS.gene010006.t1 MTR_5g016920 50.980 51 24 1 182 232 98 147 6.50e-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
MS.gene010006.t1 AT3G15070 45.161 62 33 1 168 229 412 472 1.41e-11 63.9
MS.gene010006.t1 AT3G15070 45.161 62 33 1 168 229 412 472 1.41e-11 63.9
MS.gene010006.t1 AT5G42940 37.681 69 41 2 160 227 612 679 1.83e-11 63.5
MS.gene010006.t1 AT5G42940 37.681 69 41 2 160 227 612 679 1.83e-11 63.5
MS.gene010006.t1 AT4G34040 40.741 54 31 1 176 229 611 663 3.21e-11 62.8
MS.gene010006.t1 AT2G15530 45.098 51 27 1 179 229 629 678 5.88e-11 62.0
MS.gene010006.t1 AT5G67120 48.000 50 25 1 177 226 220 268 8.00e-11 60.8

Find 49 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCGTGAGAATCTTGAATT+TGG 0.134776 5.3:-54328843 MS.gene010006:CDS
AAAGCTCCAATCAACCTTTA+AGG 0.240288 5.3:-54329331 MS.gene010006:CDS
AAATTTACCTGCGACCTTAA+AGG 0.244607 5.3:+54329317 None:intergenic
GAACAACAAGTAACAATTAA+TGG 0.277286 5.3:-54329679 MS.gene010006:CDS
TCCATTGTTTCTCTCACTTT+AGG 0.294080 5.3:+54329622 None:intergenic
GATGTAATGTCAGGAAAATT+TGG 0.316379 5.3:-54328624 MS.gene010006:intron
TTTGACGTTCCCAAGCAATT+TGG 0.318565 5.3:+54329351 None:intergenic
AAGATTCTCACGACGAATAT+TGG 0.334926 5.3:+54328851 None:intergenic
CATCTTCCACAACCGATTAA+TGG 0.339547 5.3:-54329100 MS.gene010006:CDS
GAGAGAAACAATGGAGTATA+TGG 0.346210 5.3:-54329614 MS.gene010006:intron
CTGCGACCTTAAAGGTTGAT+TGG 0.360105 5.3:+54329325 None:intergenic
CTTCAAGCAATTTCAAAAGT+AGG 0.364624 5.3:-54329849 MS.gene010006:CDS
GTCGTGAGAATCTTGAATTT+GGG 0.369527 5.3:-54328842 MS.gene010006:CDS
AAGACTGGCTCCTAGCTATA+AGG 0.376635 5.3:-54328541 MS.gene010006:CDS
GTGACGAAGACGTTCTCTTT+CGG 0.384876 5.3:+54329750 None:intergenic
GGTTGGTTTGGACCATTAAT+CGG 0.394654 5.3:+54329088 None:intergenic
GTTTCTCTCACTTTAGGATC+AGG 0.407404 5.3:+54329628 None:intergenic
TGGGGTAACACAGGTTGGTT+TGG 0.407758 5.3:+54329076 None:intergenic
TATTATAGGTCCAAATTGCT+TGG 0.412627 5.3:-54329361 MS.gene010006:intron
TTCAAGCAATTTCAAAAGTA+GGG 0.416269 5.3:-54329848 MS.gene010006:CDS
TGTTCAACAATCTGACCAAC+TGG 0.418248 5.3:+54329697 None:intergenic
GGATCATCTTCAAATAGCTC+TGG 0.423511 5.3:+54329808 None:intergenic
AATAGCTCTGGGTACATAGC+TGG 0.462378 5.3:+54329820 None:intergenic
CATTAATCGGTTGTGGAAGA+TGG 0.472050 5.3:+54329101 None:intergenic
CTTCTACTTTGCGTATCCAT+CGG 0.475904 5.3:+54328883 None:intergenic
ACAATTGTGCTGCATTTGTC+TGG 0.487482 5.3:-54328799 MS.gene010006:intron
ATTATAGGTCCAAATTGCTT+GGG 0.489909 5.3:-54329360 MS.gene010006:intron
TATGCCCTCTTTGCAATACA+AGG 0.492492 5.3:-54328514 MS.gene010006:CDS
TGTCAGGAAAATTTGGCTGC+TGG 0.496813 5.3:-54328617 MS.gene010006:intron
TTTGGACCATTAATCGGTTG+TGG 0.503702 5.3:+54329094 None:intergenic
TCACGTAGATATTGAAAGAC+TGG 0.509822 5.3:+54329787 None:intergenic
CAATCAACCTTTAAGGTCGC+AGG 0.515350 5.3:-54329324 MS.gene010006:intron
ACATGAGTTGCATCAAAGAC+TGG 0.516295 5.3:-54328556 MS.gene010006:CDS
TGGAGAAGAAATTGAAAGAC+TGG 0.520154 5.3:-54328597 MS.gene010006:CDS
AAGAACATTATGATGTCTCT+AGG 0.527328 5.3:-54329892 None:intergenic
GAAATTACTAAGATTCCAGT+TGG 0.554578 5.3:-54329712 MS.gene010006:CDS
GATCATCTTCAAATAGCTCT+GGG 0.557026 5.3:+54329809 None:intergenic
ATGCCCTTGTATTGCAAAGA+GGG 0.563590 5.3:+54328510 None:intergenic
GGCATACATTCCTTATAGCT+AGG 0.586348 5.3:+54328531 None:intergenic
TCCTAAAGTGAGAGAAACAA+TGG 0.600914 5.3:-54329623 MS.gene010006:CDS
TCGTGAGAATCTTGAATTTG+GGG 0.614713 5.3:-54328841 MS.gene010006:CDS
ATGTCTCTAGGTCGAACTGA+AGG 0.617564 5.3:-54329880 MS.gene010006:CDS
TGCAGAAACTTAACAACCGA+TGG 0.625238 5.3:-54328899 MS.gene010006:CDS
GCTCTGGGTACATAGCTGGA+AGG 0.649258 5.3:+54329824 None:intergenic
TATGCCCTTGTATTGCAAAG+AGG 0.660563 5.3:+54328509 None:intergenic
AGAATAACTATATACAGCCA+CGG 0.685225 5.3:-54328926 MS.gene010006:CDS
ATGCCCTCTTTGCAATACAA+GGG 0.686099 5.3:-54328513 MS.gene010006:CDS
TTAAGTTTCTGCAGCCACCG+TGG 0.730006 5.3:+54328909 None:intergenic
ATAACTATATACAGCCACGG+TGG 0.806563 5.3:-54328923 MS.gene010006:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATGTTACATTTACTAATT+AGG - chr5.3:54328928-54328947 MS.gene010006:intron 15.0%
!! TATATTGCAACTATTTAATT+AGG + chr5.3:54328893-54328912 None:intergenic 15.0%
!! TATGTTACATTTACTAATTA+GGG - chr5.3:54328929-54328948 MS.gene010006:intron 15.0%
!! TTATTCTTCAATTAAAATCA+AGG + chr5.3:54329440-54329459 None:intergenic 15.0%
!! AACATTTACAATATCATTTG+AGG - chr5.3:54329617-54329636 MS.gene010006:CDS 20.0%
!! ATAGTTGCAATATAAGAAAA+AGG - chr5.3:54328899-54328918 MS.gene010006:CDS 20.0%
!! TCAACTTCTAATCAAATATT+TGG - chr5.3:54329195-54329214 MS.gene010006:intron 20.0%
!! TCTAATCAAATATTTGGTAT+TGG - chr5.3:54329201-54329220 MS.gene010006:intron 20.0%
!!! AATCTTCTAAAGTAAATTCA+TGG - chr5.3:54328812-54328831 MS.gene010006:CDS 20.0%
! AACAAATTTGATGTAATGTC+AGG - chr5.3:54329746-54329765 MS.gene010006:CDS 25.0%
! ATAATTTGATTGCTGAAGAT+GGG + chr5.3:54329325-54329344 None:intergenic 25.0%
! GAACAACAAGTAACAATTAA+TGG - chr5.3:54328700-54328719 MS.gene010006:intron 25.0%
! GTGTGTATTTATTTGAATCT+TGG - chr5.3:54328847-54328866 MS.gene010006:CDS 25.0%
! TTCAAGCAATTTCAAAAGTA+GGG - chr5.3:54328531-54328550 MS.gene010006:CDS 25.0%
!! AAAGTTTCACTCTTGTTTAT+TGG - chr5.3:54328961-54328980 MS.gene010006:intron 25.0%
!! AAGTTTCACTCTTGTTTATT+GGG - chr5.3:54328962-54328981 MS.gene010006:intron 25.0%
!! TATCATTTGAGGTTAACTTA+AGG - chr5.3:54329628-54329647 MS.gene010006:CDS 25.0%
!!! AAATTCATGGAATTTGTTGT+TGG - chr5.3:54328825-54328844 MS.gene010006:CDS 25.0%
AAATTATCATGCTCAAAACG+AGG - chr5.3:54329338-54329357 MS.gene010006:CDS 30.0%
AGAATAACTATATACAGCCA+CGG - chr5.3:54329453-54329472 MS.gene010006:intron 30.0%
ATCTACGTGAGACTAAAAAA+AGG - chr5.3:54328605-54328624 MS.gene010006:CDS 30.0%
ATTATAGGTCCAAATTGCTT+GGG - chr5.3:54329019-54329038 MS.gene010006:intron 30.0%
CTTCAAGCAATTTCAAAAGT+AGG - chr5.3:54328530-54328549 MS.gene010006:CDS 30.0%
GAAATTACTAAGATTCCAGT+TGG - chr5.3:54328667-54328686 MS.gene010006:intron 30.0%
GATAATTTGATTGCTGAAGA+TGG + chr5.3:54329326-54329345 None:intergenic 30.0%
GATGTAATGTCAGGAAAATT+TGG - chr5.3:54329755-54329774 MS.gene010006:CDS 30.0%
TAATTTGATTGCTGAAGATG+GGG + chr5.3:54329324-54329343 None:intergenic 30.0%
TATTATAGGTCCAAATTGCT+TGG - chr5.3:54329018-54329037 MS.gene010006:intron 30.0%
TCTACGTGAGACTAAAAAAA+GGG - chr5.3:54328606-54328625 MS.gene010006:CDS 30.0%
!!! CACTAGTTTTCGTGTATTAT+AGG - chr5.3:54329004-54329023 MS.gene010006:intron 30.0%
AAAGCTCCAATCAACCTTTA+AGG - chr5.3:54329048-54329067 MS.gene010006:intron 35.0%
AAATTTACCTGCGACCTTAA+AGG + chr5.3:54329065-54329084 None:intergenic 35.0%
AAGATTCTCACGACGAATAT+TGG + chr5.3:54329531-54329550 None:intergenic 35.0%
GACTAGAGAAAACTACGATT+TGG + chr5.3:54329174-54329193 None:intergenic 35.0%
GAGAGAAACAATGGAGTATA+TGG - chr5.3:54328765-54328784 MS.gene010006:intron 35.0%
GATCATCTTCAAATAGCTCT+GGG + chr5.3:54328573-54328592 None:intergenic 35.0%
GTCGTGAGAATCTTGAATTT+GGG - chr5.3:54329537-54329556 MS.gene010006:intron 35.0%
TCACGTAGATATTGAAAGAC+TGG + chr5.3:54328595-54328614 None:intergenic 35.0%
TCCTAAAGTGAGAGAAACAA+TGG - chr5.3:54328756-54328775 MS.gene010006:intron 35.0%
TCGTGAGAATCTTGAATTTG+GGG - chr5.3:54329538-54329557 MS.gene010006:intron 35.0%
TGGAGAAGAAATTGAAAGAC+TGG - chr5.3:54329782-54329801 MS.gene010006:CDS 35.0%
! CAGCACAATTGTGTATTTTC+GGG + chr5.3:54329572-54329591 None:intergenic 35.0%
! GCAGCACAATTGTGTATTTT+CGG + chr5.3:54329573-54329592 None:intergenic 35.0%
! TCCATTGTTTCTCTCACTTT+AGG + chr5.3:54328760-54328779 None:intergenic 35.0%
ACAATTGTGCTGCATTTGTC+TGG - chr5.3:54329580-54329599 MS.gene010006:intron 40.0%
ACATGAGTTGCATCAAAGAC+TGG - chr5.3:54329823-54329842 MS.gene010006:CDS 40.0%
ATAACTATATACAGCCACGG+TGG - chr5.3:54329456-54329475 MS.gene010006:intron 40.0%
ATGCCCTCTTTGCAATACAA+GGG - chr5.3:54329866-54329885 MS.gene010006:CDS 40.0%
ATGCCCTTGTATTGCAAAGA+GGG + chr5.3:54329872-54329891 None:intergenic 40.0%
CATCTTCCACAACCGATTAA+TGG - chr5.3:54329279-54329298 MS.gene010006:intron 40.0%
CATTAATCGGTTGTGGAAGA+TGG + chr5.3:54329281-54329300 None:intergenic 40.0%
CGTCGTGAGAATCTTGAATT+TGG - chr5.3:54329536-54329555 MS.gene010006:intron 40.0%
CTTCTACTTTGCGTATCCAT+CGG + chr5.3:54329499-54329518 None:intergenic 40.0%
GCTGCATTTGTCTGGTAATT+AGG - chr5.3:54329588-54329607 MS.gene010006:intron 40.0%
GGATCATCTTCAAATAGCTC+TGG + chr5.3:54328574-54328593 None:intergenic 40.0%
GGCATACATTCCTTATAGCT+AGG + chr5.3:54329851-54329870 None:intergenic 40.0%
TATGCCCTCTTTGCAATACA+AGG - chr5.3:54329865-54329884 MS.gene010006:CDS 40.0%
TATGCCCTTGTATTGCAAAG+AGG + chr5.3:54329873-54329892 None:intergenic 40.0%
TCTGATCCTGAAAAACTCGT+TGG + chr5.3:54329227-54329246 None:intergenic 40.0%
TGCAGAAACTTAACAACCGA+TGG - chr5.3:54329480-54329499 MS.gene010006:intron 40.0%
TGTTCAACAATCTGACCAAC+TGG + chr5.3:54328685-54328704 None:intergenic 40.0%
TTTGACGTTCCCAAGCAATT+TGG + chr5.3:54329031-54329050 None:intergenic 40.0%
TTTGGACCATTAATCGGTTG+TGG + chr5.3:54329288-54329307 None:intergenic 40.0%
! TATTGGCCAACGAGTTTTTC+AGG - chr5.3:54329218-54329237 MS.gene010006:intron 40.0%
!! CAATTGTGTATTTTCGGGAC+TGG + chr5.3:54329567-54329586 None:intergenic 40.0%
!! GGTTGGTTTGGACCATTAAT+CGG + chr5.3:54329294-54329313 None:intergenic 40.0%
!! GTTTCTCTCACTTTAGGATC+AGG + chr5.3:54328754-54328773 None:intergenic 40.0%
!!! ACGAGTTTTTCAGGATCAGA+CGG - chr5.3:54329227-54329246 MS.gene010006:intron 40.0%
ATGTCTCTAGGTCGAACTGA+AGG - chr5.3:54328499-54328518 MS.gene010006:CDS 45.0%
GTGACGAAGACGTTCTCTTT+CGG + chr5.3:54328632-54328651 None:intergenic 45.0%
TGTCAGGAAAATTTGGCTGC+TGG - chr5.3:54329762-54329781 MS.gene010006:CDS 45.0%
! AAGACTGGCTCCTAGCTATA+AGG - chr5.3:54329838-54329857 MS.gene010006:CDS 45.0%
! CTGCGACCTTAAAGGTTGAT+TGG + chr5.3:54329057-54329076 None:intergenic 45.0%
!! AATAGCTCTGGGTACATAGC+TGG + chr5.3:54328562-54328581 None:intergenic 45.0%
!! CAATCAACCTTTAAGGTCGC+AGG - chr5.3:54329055-54329074 MS.gene010006:intron 45.0%
GAAGATGGGGTAACACAGGT+TGG + chr5.3:54329311-54329330 None:intergenic 50.0%
TGCTGAAGATGGGGTAACAC+AGG + chr5.3:54329315-54329334 None:intergenic 50.0%
TTAAGTTTCTGCAGCCACCG+TGG + chr5.3:54329473-54329492 None:intergenic 50.0%
!! TGGGGTAACACAGGTTGGTT+TGG + chr5.3:54329306-54329325 None:intergenic 50.0%
! GCTCTGGGTACATAGCTGGA+AGG + chr5.3:54328558-54328577 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 54328496 54329905 54328496 ID=MS.gene010006
chr5.3 mRNA 54328496 54329905 54328496 ID=MS.gene010006.t1;Parent=MS.gene010006
chr5.3 exon 54329615 54329905 54329615 ID=MS.gene010006.t1.exon1;Parent=MS.gene010006.t1
chr5.3 CDS 54329615 54329905 54329615 ID=cds.MS.gene010006.t1;Parent=MS.gene010006.t1
chr5.3 exon 54329325 54329375 54329325 ID=MS.gene010006.t1.exon2;Parent=MS.gene010006.t1
chr5.3 CDS 54329325 54329375 54329325 ID=cds.MS.gene010006.t1;Parent=MS.gene010006.t1
chr5.3 exon 54329087 54329161 54329087 ID=MS.gene010006.t1.exon3;Parent=MS.gene010006.t1
chr5.3 CDS 54329087 54329161 54329087 ID=cds.MS.gene010006.t1;Parent=MS.gene010006.t1
chr5.3 exon 54328800 54328946 54328800 ID=MS.gene010006.t1.exon4;Parent=MS.gene010006.t1
chr5.3 CDS 54328800 54328946 54328800 ID=cds.MS.gene010006.t1;Parent=MS.gene010006.t1
chr5.3 exon 54328496 54328633 54328496 ID=MS.gene010006.t1.exon5;Parent=MS.gene010006.t1
chr5.3 CDS 54328496 54328633 54328496 ID=cds.MS.gene010006.t1;Parent=MS.gene010006.t1
Gene Sequence

>MS.gene010006

ATGATGTCTCTAGGTCGAACTGAAGGTGATAGTTCTTCAAGCAATTTCAAAAGTAGGGACCTTCCAGCTATGTACCCAGAGCTATTTGAAGATGATCCAGTCTTTCAATATCTACGTGAGACTAAAAAAAGGGCCGAAAGAGAACGTCTTCGTCACATGCGTAAGTCAGTTGAAATTACTAAGATTCCAGTTGGTCAGATTGTTGAACAACAAGTAACAATTAATGGAAATGTTGAGCTACGACGAATTTATGTTCCTGATCCTAAAGTGAGAGAAACAATGGAGTATATGGTATGTATGTTTATTATTTATTTATAATCTTCTAAAGTAAATTCATGGAATTTGTTGTTGGTGTGTATTTATTTGAATCTTGGATTATATTTAACAATTACAACCTAATTAAATAGTTGCAATATAAGAAAAAGGAATACGATATGTTACATTTACTAATTAGGGTTGATACTTAAAGTTTCACTCTTGTTTATTGGGATCATCATTTCATCTTCATCACTAGTTTTCGTGTATTATAGGTCCAAATTGCTTGGGAACGTCAAAGCTCCAATCAACCTTTAAGGTCGCAGGTAAATTTTCACATAACTATGTATGTATTTTTTTATATTAAATGCATATATATGATATGTGATTATGATATAACTGCATAATTAATTTCTTTATCCAAATCGTAGTTTTCTCTAGTCATCAACTTCTAATCAAATATTTGGTATTGGCCAACGAGTTTTTCAGGATCAGACGGCAATAGACTACTATAATGTTGTGTTACGCCATCTTCCACAACCGATTAATGGTCCAAACCAACCTGTGTTACCCCATCTTCAGCAATCAAATTATCATGCTCAAAACGAGGTATTACATTGTCTCTTTCTATTTTTACTTTTTATTATTCTTTGTGCTTAAATTAAAGAGTTATTGTTAGATAAATTCCTTGATTTTAATTGAAGAATAACTATATACAGCCACGGTGGCTGCAGAAACTTAACAACCGATGGATACGCAAAGTAGAAGCAACAATGACCAATATTCGTCGTGAGAATCTTGAATTTGGGGATGCCAGTCCCGAAAATACACAATTGTGCTGCATTTGTCTGGTAATTAGGTTTTTTAACATTTACAATATCATTTGAGGTTAACTTAAGGAATGCATGCATGTCACTTCAGTTCATTTTCAATTTATGTCGCGTTCTATATACTTTATTTCGTTAGATCGAAAGTCTATTATGCATGTGTTTTCTAACAAATTTGATGTAATGTCAGGAAAATTTGGCTGCTGGAGAAGAAATTGAAAGACTGGACTGTGCACATAGATTTCACATGAGTTGCATCAAAGACTGGCTCCTAGCTATAAGGAATGTATGCCCTCTTTGCAATACAAGGGCATATCATTTGATTTAA

Protein sequence

>MS.gene010006.t1

MMSLGRTEGDSSSSNFKSRDLPAMYPELFEDDPVFQYLRETKKRAERERLRHMRKSVEITKIPVGQIVEQQVTINGNVELRRIYVPDPKVRETMEYMVQIAWERQSSNQPLRSQDQTAIDYYNVVLRHLPQPINGPNQPNNYIQPRWLQKLNNRWIRKVEATMTNIRRENLEFGDASPENTQLCCICLENLAAGEEIERLDCAHRFHMSCIKDWLLAIRNVCPLCNTRAYHLI