AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene81713

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene81713.t1 MTR_1g060700 95.192 312 12 3 1 311 178 487 0.0 600
MS.gene81713.t1 MTR_2g067000 82.043 323 21 12 1 311 1 298 1.14e-161 452
MS.gene81713.t1 MTR_8g093500 58.491 53 22 0 181 233 125 177 3.01e-13 68.9
MS.gene81713.t1 MTR_3g101810 58.491 53 22 0 181 233 182 234 1.87e-12 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene81713.t1 AT1G30670 43.529 170 94 1 135 304 95 262 5.52e-33 122
MS.gene81713.t1 AT2G34820 40.845 213 117 3 97 304 81 289 1.79e-28 111
MS.gene81713.t1 AT3G21330 60.377 53 21 0 181 233 280 332 2.23e-13 70.5
MS.gene81713.t1 AT5G01305 50.000 58 29 0 181 238 48 105 1.39e-12 65.5
MS.gene81713.t1 AT4G00120 52.830 53 25 0 181 233 123 175 6.40e-12 63.9

Find 49 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTGGAATGCTTCAACTTA+TGG 0.195386 1.3:-44021181 MS.gene81713:CDS
GACACAAGAACTTGGGAAAT+TGG 0.222603 1.3:-44021280 MS.gene81713:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 1.3:+44021246 None:intergenic
TTGGTGAAATCTTCCTCATT+TGG 0.290806 1.3:+44021564 None:intergenic
ATCAAAACCTACCATTCTTA+AGG 0.300143 1.3:-44019954 MS.gene81713:CDS
TCAAATAGTTAGAGGGAAAA+TGG 0.318116 1.3:+44021739 None:intergenic
AAATAAAACTATTCTTGCTT+TGG 0.325467 1.3:+44019893 None:intergenic
TGGTGAAATCTTCCTCATTT+GGG 0.332786 1.3:+44021565 None:intergenic
TCTCCTCGTAGCATAGCTTT+TGG 0.368098 1.3:+44021520 None:intergenic
TCAAAGGAAGCAAAAGGGTT+AGG 0.369513 1.3:+44021429 None:intergenic
AGTAGTGATTTCTAAGTTGT+TGG 0.372241 1.3:+44021803 None:intergenic
GTAGTTTGAATAGGTTGATA+AGG 0.378786 1.3:+44021825 None:intergenic
TACAGTTTCTCTTGAACAAA+TGG 0.383908 1.3:+44020043 None:intergenic
AAGGGTCTGAAACAGCTTGC+TGG 0.388228 1.3:-44019935 MS.gene81713:CDS
AGTTGATCTTGACAAAGGTT+AGG 0.389660 1.3:+44021648 None:intergenic
AATGTGGTGACAAACTCTTT+TGG 0.390869 1.3:+44019998 None:intergenic
AAGTTGTTGGTAGTTTGAAT+AGG 0.402079 1.3:+44021816 None:intergenic
TTGATTATTTCAGGAAGAAA+AGG 0.406675 1.3:-44020107 MS.gene81713:intron
GAACTTGGGAAATTGGTTCC+TGG 0.427238 1.3:-44021273 MS.gene81713:CDS
TAGTTTGAATAGGTTGATAA+GGG 0.429054 1.3:+44021826 None:intergenic
AGTTTCATTCAAATAGTTAG+AGG 0.435549 1.3:+44021731 None:intergenic
TCAAAACCTACCATTCTTAA+GGG 0.456430 1.3:-44019953 MS.gene81713:CDS
CAAAGGAAGCAAAAGGGTTA+GGG 0.461232 1.3:+44021430 None:intergenic
TTGTGTAGATCTTCACTTGG+AGG 0.465635 1.3:+44020079 None:intergenic
AGAGTATCGCGGCGAGAGAA+AGG 0.466876 1.3:-44021323 MS.gene81713:CDS
ACTGAGAAGACACAAGAACT+TGG 0.467410 1.3:-44021288 MS.gene81713:CDS
TCTGCCTCAAAGGAAGCAAA+AGG 0.471457 1.3:+44021423 None:intergenic
GTTGATCTTGACAAAGGTTA+GGG 0.471678 1.3:+44021649 None:intergenic
TGTAGATCTTCACTTGGAGG+AGG 0.494574 1.3:+44020082 None:intergenic
GTGTTCATCTTTGGTCCACC+AGG 0.499817 1.3:+44021255 None:intergenic
CTGTTTCAGACCCTTAAGAA+TGG 0.516519 1.3:+44019943 None:intergenic
AGCAAAGGGTTCTGCCTCAA+AGG 0.518713 1.3:+44021413 None:intergenic
AGGGTCTGAAACAGCTTGCT+GGG 0.522554 1.3:-44019934 MS.gene81713:CDS
GTTTCATTCAAATAGTTAGA+GGG 0.549802 1.3:+44021732 None:intergenic
AAGTTTCTTCAAGCTCAAGT+TGG 0.567049 1.3:-44021198 MS.gene81713:CDS
ACTTATGGAAACATTTAGCA+AGG 0.569731 1.3:-44021166 MS.gene81713:intron
AGTTTGTGTAGATCTTCACT+TGG 0.582386 1.3:+44020076 None:intergenic
TTCAGACCCTTAAGAATGGT+AGG 0.583734 1.3:+44019947 None:intergenic
GAGTTCAAAAGCTCTTGTTG+TGG 0.586358 1.3:+44021486 None:intergenic
CTGAGAAGACACAAGAACTT+GGG 0.588293 1.3:-44021287 MS.gene81713:CDS
GTGAGAAGAAAGTTGCTGAA+AGG 0.592639 1.3:-44021359 MS.gene81713:CDS
CAAGTAGTTGATCTTGACAA+AGG 0.597726 1.3:+44021643 None:intergenic
CTGCCTCAAAGGAAGCAAAA+GGG 0.606158 1.3:+44021424 None:intergenic
CTTGGGAAATTGGTTCCTGG+TGG 0.623404 1.3:-44021270 MS.gene81713:CDS
AATAGTTAGAGGGAAAATGG+TGG 0.625963 1.3:+44021742 None:intergenic
ATTATTATGATTGCTCAATG+TGG 0.674695 1.3:+44019982 None:intergenic
ATGCTACGAGGAGAAAAGAG+AGG 0.681365 1.3:-44021511 MS.gene81713:CDS
TATCTCGTCGCAGAGTATCG+CGG 0.686396 1.3:-44021334 MS.gene81713:CDS
ACGCCAAAAGCTATGCTACG+AGG 0.715032 1.3:-44021523 MS.gene81713:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTAAATTTAAAAAAATAT+TGG + chr1.3:44021349-44021368 None:intergenic 0.0%
!!! TAATTAATTTTGCTTAAATA+TGG - chr1.3:44021558-44021577 MS.gene81713:CDS 10.0%
!! AATATATATGTGGATTTATT+TGG + chr1.3:44021587-44021606 None:intergenic 15.0%
!! ATTATTGACAAATATATATG+TGG + chr1.3:44021597-44021616 None:intergenic 15.0%
!! TATTGTTGTAAATATCTAAA+TGG - chr1.3:44020950-44020969 MS.gene81713:intron 15.0%
!!! ATTATTTATTTTGTGTTCTT+AGG - chr1.3:44020688-44020707 MS.gene81713:intron 15.0%
!!! TCTAATTACTTTTTTTTTTG+TGG - chr1.3:44021514-44021533 MS.gene81713:CDS 15.0%
!! GGAATTGTTATAAAAAATGA+CGG - chr1.3:44021101-44021120 MS.gene81713:intron 20.0%
!!! TTTTGAGTTTATAATACCTA+GGG - chr1.3:44020799-44020818 MS.gene81713:intron 20.0%
!!! TTTTGCTAATTGATTATTTC+AGG - chr1.3:44021649-44021668 MS.gene81713:CDS 20.0%
!!! TTTTTGAGTTTATAATACCT+AGG - chr1.3:44020798-44020817 MS.gene81713:intron 20.0%
!!! TTTTTTATAACAATTCCTCA+TGG + chr1.3:44021098-44021117 None:intergenic 20.0%
! AAACTCATCCACAAAAAAAT+TGG + chr1.3:44020307-44020326 None:intergenic 25.0%
! AAAGACAAAATTGAGACAAT+AGG + chr1.3:44021043-44021062 None:intergenic 25.0%
! AGAAAAACATCAAATTCACT+TGG + chr1.3:44020728-44020747 None:intergenic 25.0%
! AGTTTCATTCAAATAGTTAG+AGG + chr1.3:44020037-44020056 None:intergenic 25.0%
! ATTATTATGATTGCTCAATG+TGG + chr1.3:44021786-44021805 None:intergenic 25.0%
! GTTTCATTCAAATAGTTAGA+GGG + chr1.3:44020036-44020055 None:intergenic 25.0%
! GTTTCATTTGAGTAAAAACA+AGG + chr1.3:44020093-44020112 None:intergenic 25.0%
! TAATGCTATTGTTGTAGATT+TGG - chr1.3:44020977-44020996 MS.gene81713:intron 25.0%
! TGTTAGGATTAAGAAAATGT+TGG - chr1.3:44021131-44021150 MS.gene81713:intron 25.0%
! TTGATTATTTCAGGAAGAAA+AGG - chr1.3:44021658-44021677 MS.gene81713:CDS 25.0%
! TTGTTTGTTCATTGCATATT+TGG - chr1.3:44020823-44020842 MS.gene81713:intron 25.0%
!!! AATTTTTTTTGAAGCAGCAA+AGG + chr1.3:44020370-44020389 None:intergenic 25.0%
!!! ACTTTTTCTTCTCAAAATGA+TGG - chr1.3:44020153-44020172 MS.gene81713:intron 25.0%
!!! ATCATTTTGAGAAGAAAAAG+TGG + chr1.3:44020154-44020173 None:intergenic 25.0%
!!! ATTTTTTTTGAAGCAGCAAA+GGG + chr1.3:44020369-44020388 None:intergenic 25.0%
!!! TAGTTTGAATAGGTTGATAA+GGG + chr1.3:44019942-44019961 None:intergenic 25.0%
ACTCAAATGATTACAAGCAA+AGG + chr1.3:44020865-44020884 None:intergenic 30.0%
ACTTATGGAAACATTTAGCA+AGG - chr1.3:44020599-44020618 MS.gene81713:intron 30.0%
AGTAGTGATTTCTAAGTTGT+TGG + chr1.3:44019965-44019984 None:intergenic 30.0%
ATCAAAACCTACCATTCTTA+AGG - chr1.3:44021811-44021830 MS.gene81713:CDS 30.0%
CTATGTAACTGTTTAACACA+AGG - chr1.3:44021317-44021336 MS.gene81713:CDS 30.0%
TACAGTTTCTCTTGAACAAA+TGG + chr1.3:44021725-44021744 None:intergenic 30.0%
TCAAAACCTACCATTCTTAA+GGG - chr1.3:44021812-44021831 MS.gene81713:CDS 30.0%
TCAAATAGTTAGAGGGAAAA+TGG + chr1.3:44020029-44020048 None:intergenic 30.0%
TTATTAGAGCTCATAGTTGA+AGG - chr1.3:44020663-44020682 MS.gene81713:intron 30.0%
! GAATGAAATTTTCCCAAATG+AGG - chr1.3:44020188-44020207 MS.gene81713:intron 30.0%
! TTTTGGACATGTAAGGTAAT+TGG + chr1.3:44020223-44020242 None:intergenic 30.0%
!! AAATGACGGATTGAATTGTT+AGG - chr1.3:44021115-44021134 MS.gene81713:intron 30.0%
!! AAGTTGTTGGTAGTTTGAAT+AGG + chr1.3:44019952-44019971 None:intergenic 30.0%
!! GTAGTTTGAATAGGTTGATA+AGG + chr1.3:44019943-44019962 None:intergenic 30.0%
!!! GAACTCAACCAATTTTTTTG+TGG - chr1.3:44020296-44020315 MS.gene81713:intron 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG - chr1.3:44020567-44020586 MS.gene81713:intron 35.0%
AATAGTTAGAGGGAAAATGG+TGG + chr1.3:44020026-44020045 None:intergenic 35.0%
AGGAAACGGTTAATAAGAAG+AGG - chr1.3:44021239-44021258 MS.gene81713:CDS 35.0%
AGTTGATCTTGACAAAGGTT+AGG + chr1.3:44020120-44020139 None:intergenic 35.0%
AGTTGGAATGCTTCAACTTA+TGG - chr1.3:44020584-44020603 MS.gene81713:intron 35.0%
AGTTTGTGTAGATCTTCACT+TGG + chr1.3:44021692-44021711 None:intergenic 35.0%
ATTCCTCATGGAGTAAAAGA+TGG + chr1.3:44021086-44021105 None:intergenic 35.0%
ATTGAGACAATAGGTAGTCA+TGG + chr1.3:44021034-44021053 None:intergenic 35.0%
CAAGTAGTTGATCTTGACAA+AGG + chr1.3:44020125-44020144 None:intergenic 35.0%
CAAGTGTATATCAAATGAGC+TGG - chr1.3:44021294-44021313 MS.gene81713:CDS 35.0%
CGGTTAATAAGAAGAGGAAA+TGG - chr1.3:44021245-44021264 MS.gene81713:CDS 35.0%
GGTCAATAAACAAGAGAGTT+AGG - chr1.3:44021266-44021285 MS.gene81713:CDS 35.0%
GTTGATCTTGACAAAGGTTA+GGG + chr1.3:44020119-44020138 None:intergenic 35.0%
TGGTGAAATCTTCCTCATTT+GGG + chr1.3:44020203-44020222 None:intergenic 35.0%
TTGGTGAAATCTTCCTCATT+TGG + chr1.3:44020204-44020223 None:intergenic 35.0%
! AATGTGGTGACAAACTCTTT+TGG + chr1.3:44021770-44021789 None:intergenic 35.0%
! ATACCATCTTTTACTCCATG+AGG - chr1.3:44021080-44021099 MS.gene81713:intron 35.0%
ACTGAGAAGACACAAGAACT+TGG - chr1.3:44020477-44020496 MS.gene81713:intron 40.0%
ATCTCTGCTGTGTTCATCTT+TGG + chr1.3:44020522-44020541 None:intergenic 40.0%
CAAAGGAAGCAAAAGGGTTA+GGG + chr1.3:44020338-44020357 None:intergenic 40.0%
CTGAGAAGACACAAGAACTT+GGG - chr1.3:44020478-44020497 MS.gene81713:intron 40.0%
CTGTTTCAGACCCTTAAGAA+TGG + chr1.3:44021825-44021844 None:intergenic 40.0%
GACACAAGAACTTGGGAAAT+TGG - chr1.3:44020485-44020504 MS.gene81713:intron 40.0%
GAGTTCAAAAGCTCTTGTTG+TGG + chr1.3:44020282-44020301 None:intergenic 40.0%
GCAATGAACAAACAAACCCT+AGG + chr1.3:44020818-44020837 None:intergenic 40.0%
GTGAGAAGAAAGTTGCTGAA+AGG - chr1.3:44020406-44020425 MS.gene81713:intron 40.0%
GTGTGTGTGTGTTAAGGAAA+CGG - chr1.3:44021225-44021244 MS.gene81713:CDS 40.0%
TCAAAGGAAGCAAAAGGGTT+AGG + chr1.3:44020339-44020358 None:intergenic 40.0%
TTCAGACCCTTAAGAATGGT+AGG + chr1.3:44021821-44021840 None:intergenic 40.0%
TTGTGTAGATCTTCACTTGG+AGG + chr1.3:44021689-44021708 None:intergenic 40.0%
! TAACCCTTTTGCTTCCTTTG+AGG - chr1.3:44020338-44020357 MS.gene81713:intron 40.0%
! TAGCATAGCTTTTGGCGTTT+TGG + chr1.3:44020240-44020259 None:intergenic 40.0%
!! TTTGGCGTTTTGGACATGTA+AGG + chr1.3:44020230-44020249 None:intergenic 40.0%
ATGCTACGAGGAGAAAAGAG+AGG - chr1.3:44020254-44020273 MS.gene81713:intron 45.0%
CTGCCTCAAAGGAAGCAAAA+GGG + chr1.3:44020344-44020363 None:intergenic 45.0%
GTGTGTGTGTGTGTGTGTTA+AGG - chr1.3:44021219-44021238 MS.gene81713:CDS 45.0%
TCTGCCTCAAAGGAAGCAAA+AGG + chr1.3:44020345-44020364 None:intergenic 45.0%
TGTAGATCTTCACTTGGAGG+AGG + chr1.3:44021686-44021705 None:intergenic 45.0%
! GAACTTGGGAAATTGGTTCC+TGG - chr1.3:44020492-44020511 MS.gene81713:intron 45.0%
! TCTCCTCGTAGCATAGCTTT+TGG + chr1.3:44020248-44020267 None:intergenic 45.0%
ACGCCAAAAGCTATGCTACG+AGG - chr1.3:44020242-44020261 MS.gene81713:intron 50.0%
AGAGAGAGAGAGAGAGAGAG+AGG - chr1.3:44021156-44021175 MS.gene81713:intron 50.0%
AGCAAAGGGTTCTGCCTCAA+AGG + chr1.3:44020355-44020374 None:intergenic 50.0%
GAGAGAGAGAGAGAGAGAGA+GGG - chr1.3:44021157-44021176 MS.gene81713:intron 50.0%
GTGTTCATCTTTGGTCCACC+AGG + chr1.3:44020513-44020532 None:intergenic 50.0%
! AAGGGTCTGAAACAGCTTGC+TGG - chr1.3:44021830-44021849 MS.gene81713:CDS 50.0%
! AGGGTCTGAAACAGCTTGCT+GGG - chr1.3:44021831-44021850 MS.gene81713:CDS 50.0%
! CTTGGGAAATTGGTTCCTGG+TGG - chr1.3:44020495-44020514 MS.gene81713:intron 50.0%
!! TATCTCGTCGCAGAGTATCG+CGG - chr1.3:44020431-44020450 MS.gene81713:intron 50.0%
AGAGAGAGAGAGAGAGAGGG+AGG - chr1.3:44021164-44021183 MS.gene81713:intron 55.0%
GAGAGAGAGAGAGAGAGGGA+GGG - chr1.3:44021165-44021184 MS.gene81713:intron 55.0%
!! AGAGTATCGCGGCGAGAGAA+AGG - chr1.3:44020442-44020461 MS.gene81713:intron 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 44019901 44021886 44019901 ID=MS.gene81713
chr1.3 mRNA 44019901 44021886 44019901 ID=MS.gene81713.t1;Parent=MS.gene81713
chr1.3 exon 44021167 44021886 44021167 ID=MS.gene81713.t1.exon1;Parent=MS.gene81713.t1
chr1.3 CDS 44021167 44021886 44021167 ID=cds.MS.gene81713.t1;Parent=MS.gene81713.t1
chr1.3 exon 44019901 44020116 44019901 ID=MS.gene81713.t1.exon2;Parent=MS.gene81713.t1
chr1.3 CDS 44019901 44020116 44019901 ID=cds.MS.gene81713.t1;Parent=MS.gene81713.t1
Gene Sequence

>MS.gene81713

ATGGGAGCACTTAGCACATACTTCAACTATAATTGTTACCCTTATCAACCTATTCAAACTACCAACAACTTAGAAATCACTACTTTTCAACATCATGAACAAGAACAATTTGTGCAACAAAACCACCATTTTCCCTCTAACTATTTGAATGAAACTTCTCTTTTAGATGAAAGCTTCATTTTTCAAACTCCTTGTTTTTACTCAAATGAAACTTACCCTAACCTTTGTCAAGATCAACTACTTGTTGACTCCACTTTTTCTTCTCAAAATGATGGCTTTGTTTCAATGAATGAAATTTTCCCAAATGAGGAAGATTTCACCAATTACCTTACATGTCCAAAACGCCAAAAGCTATGCTACGAGGAGAAAAGAGAGGAACCACAACAAGAGCTTTTGAACTCAACCAATTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTTTTGCTTCCTTTGAGGCAGAACCCTTTGCTGCTTCAAAAAAAATTGTTGATGTTGTTCAATGTGAGAAGAAAGTTGCTGAAAGGACTATCTCGTCGCAGAGTATCGCGGCGAGAGAAAGGAGAAGAAAGATAACTGAGAAGACACAAGAACTTGGGAAATTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTAATGCTGCTGCTAATTATGTCAAGTTTCTTCAAGCTCAAGTTGGAATGCTTCAACTTATGGAAACATTTAGCAAGGTAACTGTTTTTATTTTTTTTATTTGTTGCAATGTTCTTATATTATTAGAGCTCATAGTTGAAGGTAATTATTTATTTTGTGTTCTTAGGTCTTATGTAACACTCCAAGTGAATTTGATGTTTTTCTTTTGAATGATGTTTTTTGCTTTTTATGTTATACTATGCTACTTGATTTAGTTTTTGAGTTTATAATACCTAGGGTTTGTTTGTTCATTGCATATTTGGTTACTTTGTTTGAAGACCTTTGCTTGTAATCATTTGAGTACATGTAGTTTGATCAAAAAATAGAGCATGTGTCTTCTATTGTAGTGTTATTATGTCATGTATTGTATTGTTGTAAATATCTAAATGGATATTAATGCTATTGTTGTAGATTTGGTTAGTTTTATCATTGATGTATGTAATGTAATCCATGACTACCTATTGTCTCAATTTTGTCTTTTTTATTTTGATTTTTTTATACCATCTTTTACTCCATGAGGAATTGTTATAAAAAATGACGGATTGAATTGTTAGGATTAAGAAAATGTTGGTTAGAGAGAGAGAGAGAGAGAGAGAGAGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGTGTGTGTGTGTGTGTGTGTGTGTGTTAAGGAAACGGTTAATAAGAAGAGGAAATGGTCAATAAACAAGAGAGTTAGGAACAACAAGTGTATATCAAATGAGCTGGCTATGTAACTGTTTAACACAAGGAATTTTCCAATATTTTTTTAAATTTAAATATTCACTATTTTTACTTTCTTTATATTTAGTGTAACATTTTTGTAAAAGCTAAATTTCTAGTGTAACTTTATATAATAAAATTAATTACTTAATGCTTATTTTATTTTATTTTTTTTTAATTACTTAATGCTTCGAATATTCATCTCTAATTACTTTTTTTTTTGTGGAAATTCTCTAATTACTTTTATTAATTAATTTTGCTTAAATATGGTGACCAAATAAATCCACATATATATTTGTCAATAATATAATAAAAAGAATTCACATATATAGCTTAGATTTTGCTAATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATCTACACAAACTACTTCTTTCTCCATTTGTTCAAGAGAAACTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCACATTGAGCAATCATAATAATGTTCAATCAAAACCTACCATTCTTAAGGGTCTGAAACAGCTTGCTGGGACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene81713.t1

MGALSTYFNYNCYPYQPIQTTNNLEITTFQHHEQEQFVQQNHHFPSNYLNETSLLDESFIFQTPCFYSNETYPNLCQDQLLVDSTFSSQNDGFVSMNEIFPNEEDFTNYLTCPKRQKLCYEEKREEPQQELLNSTNFFVDEFMTNPNPFASFEAEPFAASKKIVDVVQCEKKVAERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLNAAANYVKFLQAQVGMLQLMETFSKEEKEPPPSEDLHKLLLSPFVQEKLYSEEKCFVPKEFVTTLSNHNNVQSKPTILKGLKQLAGTEIEKKPKQE