AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene039020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039020.t1 MTR_7g113680 56.180 267 93 9 5 262 53 304 9.36e-80 243
MS.gene039020.t1 MTR_1g082660 60.000 235 74 11 5 228 2 227 2.51e-74 227
MS.gene039020.t1 MTR_3g099180 67.361 144 37 3 86 228 36 170 8.65e-62 194
MS.gene039020.t1 MTR_3g099180 67.361 144 37 3 86 228 36 170 9.98e-62 194
MS.gene039020.t1 MTR_2g023340 55.034 149 52 3 87 226 67 209 4.63e-52 170
MS.gene039020.t1 MTR_2g081600 60.241 83 32 1 104 185 21 103 2.09e-30 110
MS.gene039020.t1 MTR_2g081630 60.241 83 32 1 104 185 21 103 2.19e-30 110
MS.gene039020.t1 MTR_3g012030 41.026 78 46 0 106 183 9 86 3.77e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039020.t1 AT1G56170 86.154 130 14 2 84 212 55 181 2.89e-78 235
MS.gene039020.t1 AT1G56170 86.154 130 14 2 84 212 55 181 2.89e-78 235
MS.gene039020.t1 AT1G08970 71.528 144 38 3 87 228 62 204 7.29e-69 213
MS.gene039020.t1 AT1G08970 71.528 144 38 3 87 228 62 204 7.29e-69 213
MS.gene039020.t1 AT1G08970 71.528 144 38 3 87 228 62 204 7.29e-69 213
MS.gene039020.t1 AT1G08970 71.528 144 38 3 87 228 62 204 7.29e-69 213
MS.gene039020.t1 AT5G63470 57.635 203 67 5 43 236 20 212 1.63e-68 212
MS.gene039020.t1 AT5G63470 57.635 203 67 5 43 236 20 212 1.63e-68 212
MS.gene039020.t1 AT1G54830 69.930 143 39 2 87 228 52 191 4.73e-68 210
MS.gene039020.t1 AT1G54830 69.930 143 39 2 87 228 52 191 4.73e-68 210
MS.gene039020.t1 AT1G54830 69.930 143 39 2 87 228 52 191 4.73e-68 210
MS.gene039020.t1 AT3G48590 67.089 158 47 2 73 228 33 187 2.74e-67 209
MS.gene039020.t1 AT5G50480 47.879 165 70 4 83 245 35 185 2.22e-47 157
MS.gene039020.t1 AT5G27910 41.111 180 86 6 81 258 15 176 2.46e-39 135
MS.gene039020.t1 AT5G50490 39.429 175 93 4 74 246 8 171 9.95e-36 126
MS.gene039020.t1 AT5G50470 48.148 108 47 2 83 184 44 148 2.96e-30 113
MS.gene039020.t1 AT5G38140 45.000 100 51 2 84 182 48 144 2.39e-26 102

Find 74 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCAATCCCATGTTGGCTTC+TGG 0.242345 2.2:+24489141 MS.gene039020:CDS
TAGAGTTGACTTTGCGATCT+TGG 0.263614 2.2:+24489463 MS.gene039020:CDS
TTTGCTCAATTTCTTGCATT+TGG 0.264134 2.2:-24489311 None:intergenic
TCTTCTTTCAATTCATCTCT+TGG 0.282962 2.2:-24489585 None:intergenic
TACGCGCAAGTGGGAGAGTA+TGG 0.334677 2.2:-24489350 None:intergenic
ATCAGCAGCTTCAAATGTTC+TGG 0.343397 2.2:+24489283 MS.gene039020:CDS
GAGGCTGCTGGTTAGAATAT+AGG 0.350073 2.2:-24489740 None:intergenic
GTTGGTGTTGCTGCTGTTGA+TGG 0.352589 2.2:-24489260 None:intergenic
TATAGGGCTGCATGATCAAC+TGG 0.360730 2.2:-24489723 None:intergenic
GGTGGAAATGCTGTGCTTGC+TGG 0.362971 2.2:-24489239 None:intergenic
TTAACTTGTCATGGATAATT+CGG 0.369534 2.2:+24489032 None:intergenic
AAGTGGCTGGAGGCTGTGTT+GGG 0.387279 2.2:-24489188 None:intergenic
GTCCCACCACAACATCCTTT+AGG 0.406073 2.2:+24489675 MS.gene039020:CDS
AGGCTGCTGGTTAGAATATA+GGG 0.421798 2.2:-24489739 None:intergenic
TCAGCTGGAGCACCGATTAT+CGG 0.426072 2.2:-24489636 None:intergenic
CAACATCCTTTAGGTCCTAC+AGG 0.429195 2.2:+24489684 MS.gene039020:CDS
AAGCCTACTATTCCGATAAT+CGG 0.435007 2.2:+24489624 MS.gene039020:CDS
AAAGTGGCTGGAGGCTGTGT+TGG 0.435441 2.2:-24489189 None:intergenic
CCAGAAGCCAACATGGGATT+GGG 0.438408 2.2:-24489141 None:intergenic
GCCAGAAGCCAACATGGGAT+TGG 0.445176 2.2:-24489142 None:intergenic
AGTGAGAAGAATAGACCATT+TGG 0.446634 2.2:-24489107 None:intergenic
TGTGGTGGGACATAATAATA+TGG 0.447642 2.2:-24489663 None:intergenic
ATTTATTAAGAGTCTGTTTG+CGG 0.454383 2.2:-24489828 None:intergenic
GTGCTTGCTGGTATGCGAAT+TGG 0.457941 2.2:-24489227 None:intergenic
CCACAGGAGGTCGAGGCTGC+TGG 0.460527 2.2:-24489752 None:intergenic
GCTGGAGGCTGTGTTGGGGT+AGG 0.482836 2.2:-24489183 None:intergenic
TCAGCAGCTTCAAATGTTCT+GGG 0.497192 2.2:+24489284 MS.gene039020:CDS
CTCCTGTGGCTTTCATGCCA+TGG 0.498225 2.2:+24489766 MS.gene039020:CDS
CGCACCAGGTACTAGCCAAA+TGG 0.499512 2.2:+24489092 MS.gene039020:CDS
GCACCGATTATCGGAATAGT+AGG 0.501513 2.2:-24489627 None:intergenic
ATCATCCCTGTAGGACCTAA+AGG 0.501857 2.2:-24489690 None:intergenic
GAGCTTCTGCTGAAATCATC+CGG 0.503953 2.2:-24489404 None:intergenic
TAATAATATGGCATATCAGC+TGG 0.509819 2.2:-24489651 None:intergenic
TCCTCTTGTTCTCTTCTGTG+TGG 0.511755 2.2:-24489488 None:intergenic
AGGTCCTACAGGGATGATCA+TGG 0.513342 2.2:+24489695 MS.gene039020:CDS
ACATGGGATTGGGAACAGTC+TGG 0.517231 2.2:-24489131 None:intergenic
ATGAAAGCCACAGGAGGTCG+AGG 0.520693 2.2:-24489759 None:intergenic
AGAGATGAATTGAAAGAAGA+GGG 0.526767 2.2:+24489588 MS.gene039020:CDS
GAGTCTGTTTGCGGCTGTTG+TGG 0.537428 2.2:-24489819 None:intergenic
TGAAAGCCGATGAAGATGTC+CGG 0.548255 2.2:+24489385 MS.gene039020:CDS
GTGGGCGGAATTAGCAAAAG+TGG 0.552229 2.2:-24489205 None:intergenic
GAATTGAAAGAAGAGGGGCT+TGG 0.553111 2.2:+24489594 MS.gene039020:CDS
CTTGCTGGTATGCGAATTGG+TGG 0.555433 2.2:-24489224 None:intergenic
GACCATGGCATGAAAGCCAC+AGG 0.561895 2.2:-24489768 None:intergenic
TCTGTTTGCGGCTGTTGTGG+TGG 0.570337 2.2:-24489816 None:intergenic
GGTGTTGCTGCTGTTGATGG+TGG 0.572770 2.2:-24489257 None:intergenic
AATCATCCGGACATCTTCAT+CGG 0.573019 2.2:-24489391 None:intergenic
GCGGAATTAGCAAAAGTGGC+TGG 0.573546 2.2:-24489201 None:intergenic
AGGTGTGCCAGAAGCCAACA+TGG 0.576129 2.2:-24489148 None:intergenic
AAGAGATGAATTGAAAGAAG+AGG 0.576346 2.2:+24489587 MS.gene039020:CDS
GGGGTAGGAACAGCTAGAGC+AGG 0.581108 2.2:-24489168 None:intergenic
TAGACCATTTGGCTAGTACC+TGG 0.582406 2.2:-24489096 None:intergenic
GACTGTTCCCAATCCCATGT+TGG 0.582414 2.2:+24489134 MS.gene039020:CDS
TCTGCGATCGGAGTCGCACC+AGG 0.583461 2.2:+24489078 MS.gene039020:CDS
GAAAGAAGAGGGGCTTGGAA+TGG 0.586004 2.2:+24489599 MS.gene039020:CDS
GACCTAAAGGATGTTGTGGT+GGG 0.590318 2.2:-24489677 None:intergenic
TCCACACAGAAGAGAACAAG+AGG 0.590738 2.2:+24489487 MS.gene039020:CDS
CCAGCAGCCTCGACCTCCTG+TGG 0.590845 2.2:+24489752 MS.gene039020:CDS
GGTCCTACAGGGATGATCAT+GGG 0.598225 2.2:+24489696 MS.gene039020:CDS
TTTCCCATGATCATCCCTGT+AGG 0.601110 2.2:-24489699 None:intergenic
ACATTTGAAGCTGCTGATGT+TGG 0.603398 2.2:-24489278 None:intergenic
CATCAGCAACAATCTGCGAT+CGG 0.623433 2.2:+24489066 MS.gene039020:CDS
GTAGGACCTAAAGGATGTTG+TGG 0.634993 2.2:-24489681 None:intergenic
AGTGGCTGGAGGCTGTGTTG+GGG 0.638626 2.2:-24489187 None:intergenic
GGACCTAAAGGATGTTGTGG+TGG 0.645250 2.2:-24489678 None:intergenic
TTGCTGGTATGCGAATTGGT+GGG 0.649667 2.2:-24489223 None:intergenic
CTGGTATGCGAATTGGTGGG+CGG 0.667066 2.2:-24489220 None:intergenic
ATAGGGCTGCATGATCAACT+GGG 0.669210 2.2:-24489722 None:intergenic
AACATCCTTTAGGTCCTACA+GGG 0.669689 2.2:+24489685 MS.gene039020:CDS
TGAATGTGTGCATTTGACCA+TGG 0.670369 2.2:-24489783 None:intergenic
GAATTAGCAAAAGTGGCTGG+AGG 0.677288 2.2:-24489198 None:intergenic
CATGGCATGAAAGCCACAGG+AGG 0.683115 2.2:-24489765 None:intergenic
GAGATGAATTGAAAGAAGAG+GGG 0.683256 2.2:+24489589 MS.gene039020:CDS
GGTGTGCCAGAAGCCAACAT+GGG 0.688166 2.2:-24489147 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATGATGTTTTTGATTTCT+TGG + chr2.2:24489551-24489570 MS.gene039020:CDS 20.0%
AAGAGATGAATTGAAAGAAG+AGG + chr2.2:24489587-24489606 MS.gene039020:CDS 30.0%
AGAGATGAATTGAAAGAAGA+GGG + chr2.2:24489588-24489607 MS.gene039020:CDS 30.0%
TAATAATATGGCATATCAGC+TGG - chr2.2:24489654-24489673 None:intergenic 30.0%
TCTTCTTTCAATTCATCTCT+TGG - chr2.2:24489588-24489607 None:intergenic 30.0%
TTTGCTCAATTTCTTGCATT+TGG - chr2.2:24489314-24489333 None:intergenic 30.0%
! TGCTACATCATTCTTTTGTA+GGG - chr2.2:24489517-24489536 None:intergenic 30.0%
AAGCCTACTATTCCGATAAT+CGG + chr2.2:24489624-24489643 MS.gene039020:CDS 35.0%
AGTGAGAAGAATAGACCATT+TGG - chr2.2:24489110-24489129 None:intergenic 35.0%
GAGATGAATTGAAAGAAGAG+GGG + chr2.2:24489589-24489608 MS.gene039020:CDS 35.0%
! ATTTTCTTTATACGCGCAAG+TGG - chr2.2:24489363-24489382 None:intergenic 35.0%
! CTGCTACATCATTCTTTTGT+AGG - chr2.2:24489518-24489537 None:intergenic 35.0%
! TGTGGTGGGACATAATAATA+TGG - chr2.2:24489666-24489685 None:intergenic 35.0%
! TTTTCTTTATACGCGCAAGT+GGG - chr2.2:24489362-24489381 None:intergenic 35.0%
AACATCCTTTAGGTCCTACA+GGG + chr2.2:24489685-24489704 MS.gene039020:CDS 40.0%
AATCATCCGGACATCTTCAT+CGG - chr2.2:24489394-24489413 None:intergenic 40.0%
ATCAGCAGCTTCAAATGTTC+TGG + chr2.2:24489283-24489302 MS.gene039020:CDS 40.0%
TCAGCAGCTTCAAATGTTCT+GGG + chr2.2:24489284-24489303 MS.gene039020:CDS 40.0%
TGAATGTGTGCATTTGACCA+TGG - chr2.2:24489786-24489805 None:intergenic 40.0%
! ACATTTGAAGCTGCTGATGT+TGG - chr2.2:24489281-24489300 None:intergenic 40.0%
! AGGCTGCTGGTTAGAATATA+GGG - chr2.2:24489742-24489761 None:intergenic 40.0%
! CATGCTTTTGCAAATACGAC+TGG - chr2.2:24489429-24489448 None:intergenic 40.0%
! TAGAGTTGACTTTGCGATCT+TGG + chr2.2:24489463-24489482 MS.gene039020:CDS 40.0%
ATAGGGCTGCATGATCAACT+GGG - chr2.2:24489725-24489744 None:intergenic 45.0%
ATCATCCCTGTAGGACCTAA+AGG - chr2.2:24489693-24489712 None:intergenic 45.0%
CAACATCCTTTAGGTCCTAC+AGG + chr2.2:24489684-24489703 MS.gene039020:CDS 45.0%
CATCAGCAACAATCTGCGAT+CGG + chr2.2:24489066-24489085 MS.gene039020:CDS 45.0%
GAATTAGCAAAAGTGGCTGG+AGG - chr2.2:24489201-24489220 None:intergenic 45.0%
GAATTGAAAGAAGAGGGGCT+TGG + chr2.2:24489594-24489613 MS.gene039020:CDS 45.0%
GACCTAAAGGATGTTGTGGT+GGG - chr2.2:24489680-24489699 None:intergenic 45.0%
GAGCTTCTGCTGAAATCATC+CGG - chr2.2:24489407-24489426 None:intergenic 45.0%
GTAGGACCTAAAGGATGTTG+TGG - chr2.2:24489684-24489703 None:intergenic 45.0%
TAGACCATTTGGCTAGTACC+TGG - chr2.2:24489099-24489118 None:intergenic 45.0%
TATAGGGCTGCATGATCAAC+TGG - chr2.2:24489726-24489745 None:intergenic 45.0%
TCCACACAGAAGAGAACAAG+AGG + chr2.2:24489487-24489506 MS.gene039020:CDS 45.0%
TCCTCTTGTTCTCTTCTGTG+TGG - chr2.2:24489491-24489510 None:intergenic 45.0%
TGAAAGCCGATGAAGATGTC+CGG + chr2.2:24489385-24489404 MS.gene039020:CDS 45.0%
TTGCTGGTATGCGAATTGGT+GGG - chr2.2:24489226-24489245 None:intergenic 45.0%
TTTCCCATGATCATCCCTGT+AGG - chr2.2:24489702-24489721 None:intergenic 45.0%
! GAGGCTGCTGGTTAGAATAT+AGG - chr2.2:24489743-24489762 None:intergenic 45.0%
!! GCACCGATTATCGGAATAGT+AGG - chr2.2:24489630-24489649 None:intergenic 45.0%
ACATGGGATTGGGAACAGTC+TGG - chr2.2:24489134-24489153 None:intergenic 50.0%
AGGTCCTACAGGGATGATCA+TGG + chr2.2:24489695-24489714 MS.gene039020:CDS 50.0%
CCAGAAGCCAACATGGGATT+GGG - chr2.2:24489144-24489163 None:intergenic 50.0%
CTTGCTGGTATGCGAATTGG+TGG - chr2.2:24489227-24489246 None:intergenic 50.0%
GAAAGAAGAGGGGCTTGGAA+TGG + chr2.2:24489599-24489618 MS.gene039020:CDS 50.0%
GACTGTTCCCAATCCCATGT+TGG + chr2.2:24489134-24489153 MS.gene039020:CDS 50.0%
GCGGAATTAGCAAAAGTGGC+TGG - chr2.2:24489204-24489223 None:intergenic 50.0%
GGACCTAAAGGATGTTGTGG+TGG - chr2.2:24489681-24489700 None:intergenic 50.0%
GGTCCTACAGGGATGATCAT+GGG + chr2.2:24489696-24489715 MS.gene039020:CDS 50.0%
GTCCCACCACAACATCCTTT+AGG + chr2.2:24489675-24489694 MS.gene039020:CDS 50.0%
GTGGGCGGAATTAGCAAAAG+TGG - chr2.2:24489208-24489227 None:intergenic 50.0%
! GTGCTTGCTGGTATGCGAAT+TGG - chr2.2:24489230-24489249 None:intergenic 50.0%
!! GTTGGTGTTGCTGCTGTTGA+TGG - chr2.2:24489263-24489282 None:intergenic 50.0%
!! TCAGCTGGAGCACCGATTAT+CGG - chr2.2:24489639-24489658 None:intergenic 50.0%
AAAGTGGCTGGAGGCTGTGT+TGG - chr2.2:24489192-24489211 None:intergenic 55.0%
AAGTGGCTGGAGGCTGTGTT+GGG - chr2.2:24489191-24489210 None:intergenic 55.0%
AGGTGTGCCAGAAGCCAACA+TGG - chr2.2:24489151-24489170 None:intergenic 55.0%
ATGAAAGCCACAGGAGGTCG+AGG - chr2.2:24489762-24489781 None:intergenic 55.0%
CATGGCATGAAAGCCACAGG+AGG - chr2.2:24489768-24489787 None:intergenic 55.0%
CGCACCAGGTACTAGCCAAA+TGG + chr2.2:24489092-24489111 MS.gene039020:CDS 55.0%
CTCCTGTGGCTTTCATGCCA+TGG + chr2.2:24489766-24489785 MS.gene039020:CDS 55.0%
CTGGTATGCGAATTGGTGGG+CGG - chr2.2:24489223-24489242 None:intergenic 55.0%
GACCATGGCATGAAAGCCAC+AGG - chr2.2:24489771-24489790 None:intergenic 55.0%
GAGTCTGTTTGCGGCTGTTG+TGG - chr2.2:24489822-24489841 None:intergenic 55.0%
GCCAGAAGCCAACATGGGAT+TGG - chr2.2:24489145-24489164 None:intergenic 55.0%
GGTGGAAATGCTGTGCTTGC+TGG - chr2.2:24489242-24489261 None:intergenic 55.0%
GGTGTGCCAGAAGCCAACAT+GGG - chr2.2:24489150-24489169 None:intergenic 55.0%
TACGCGCAAGTGGGAGAGTA+TGG - chr2.2:24489353-24489372 None:intergenic 55.0%
TCTGTTTGCGGCTGTTGTGG+TGG - chr2.2:24489819-24489838 None:intergenic 55.0%
!! CCCAATCCCATGTTGGCTTC+TGG + chr2.2:24489141-24489160 MS.gene039020:CDS 55.0%
!! GGTGTTGCTGCTGTTGATGG+TGG - chr2.2:24489260-24489279 None:intergenic 55.0%
AGTGGCTGGAGGCTGTGTTG+GGG - chr2.2:24489190-24489209 None:intergenic 60.0%
GGGGTAGGAACAGCTAGAGC+AGG - chr2.2:24489171-24489190 None:intergenic 60.0%
GCTGGAGGCTGTGTTGGGGT+AGG - chr2.2:24489186-24489205 None:intergenic 65.0%
TCTGCGATCGGAGTCGCACC+AGG + chr2.2:24489078-24489097 MS.gene039020:CDS 65.0%
CCACAGGAGGTCGAGGCTGC+TGG - chr2.2:24489755-24489774 None:intergenic 70.0%
CCAGCAGCCTCGACCTCCTG+TGG + chr2.2:24489752-24489771 MS.gene039020:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 24489042 24489845 24489042 ID=MS.gene039020
chr2.2 mRNA 24489042 24489845 24489042 ID=MS.gene039020.t1;Parent=MS.gene039020
chr2.2 exon 24489042 24489845 24489042 ID=MS.gene039020.t1.exon1;Parent=MS.gene039020.t1
chr2.2 CDS 24489042 24489845 24489042 ID=cds.MS.gene039020.t1;Parent=MS.gene039020.t1
Gene Sequence

>MS.gene039020

ATGGATAATTCGGATCAGATTCAACATCAGCAACAATCTGCGATCGGAGTCGCACCAGGTACTAGCCAAATGGTCTATTCTTCTCACTACCAGACTGTTCCCAATCCCATGTTGGCTTCTGGCACACCTGCTCTAGCTGTTCCTACCCCAACACAGCCTCCAGCCACTTTTGCTAATTCCGCCCACCAATTCGCATACCAGCAAGCACAGCATTTCCACCATCAACAGCAGCAACACCAACATCAGCAGCTTCAAATGTTCTGGGCAAACCAAATGCAAGAAATTGAGCAAACATTCGACTTTAAAAACCATACTCTCCCACTTGCGCGTATAAAGAAAATAATGAAAGCCGATGAAGATGTCCGGATGATTTCAGCAGAAGCTCCAGTCGTATTTGCAAAAGCATGCGAAATGTTTATATTAGAGTTGACTTTGCGATCTTGGATCCACACAGAAGAGAACAAGAGGAGAACCCTACAAAAGAATGATGTAGCAGCAGCTATTGCAAGAAATGATGTTTTTGATTTCTTGGTTGATATCATTCCAAGAGATGAATTGAAAGAAGAGGGGCTTGGAATGGCAAAGCCTACTATTCCGATAATCGGTGCTCCAGCTGATATGCCATATTATTATGTCCCACCACAACATCCTTTAGGTCCTACAGGGATGATCATGGGAAACCCAGTTGATCATGCAGCCCTATATTCTAACCAGCAGCCTCGACCTCCTGTGGCTTTCATGCCATGGTCAAATGCACACATTCAGCAACAGCAGCCACCACAACAGCCGCAAACAGACTCTTAA

Protein sequence

>MS.gene039020.t1

MDNSDQIQHQQQSAIGVAPGTSQMVYSSHYQTVPNPMLASGTPALAVPTPTQPPATFANSAHQFAYQQAQHFHHQQQQHQHQQLQMFWANQMQEIEQTFDFKNHTLPLARIKKIMKADEDVRMISAEAPVVFAKACEMFILELTLRSWIHTEENKRRTLQKNDVAAAIARNDVFDFLVDIIPRDELKEEGLGMAKPTIPIIGAPADMPYYYVPPQHPLGPTGMIMGNPVDHAALYSNQQPRPPVAFMPWSNAHIQQQQPPQQPQTDS