AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene046820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046820.t1 MTR_1g028470 86.147 231 14 2 8 225 68 293 3.77e-135 381
MS.gene046820.t1 MTR_3g090850 60.618 259 62 8 4 224 72 328 3.79e-90 268
MS.gene046820.t1 MTR_2g022280 49.741 193 89 1 32 224 1 185 5.35e-58 182
MS.gene046820.t1 MTR_0194s0050 37.900 219 129 2 6 222 163 376 4.59e-42 147
MS.gene046820.t1 MTR_3g099620 37.441 211 128 2 11 220 98 305 1.43e-37 133
MS.gene046820.t1 MTR_7g113830 37.209 215 125 3 9 222 96 301 1.52e-37 133
MS.gene046820.t1 MTR_1g082480 37.000 200 111 3 31 223 135 326 8.09e-33 121
MS.gene046820.t1 MTR_1g082480 37.158 183 101 2 31 207 135 309 2.81e-29 112
MS.gene046820.t1 MTR_8g066770 35.450 189 103 4 31 213 113 288 1.42e-28 109
MS.gene046820.t1 MTR_8g024210 35.714 196 109 2 30 224 179 358 2.13e-28 110
MS.gene046820.t1 MTR_5g064950 30.769 234 118 5 8 222 79 287 4.28e-26 102
MS.gene046820.t1 MTR_5g064950 31.797 217 105 4 8 206 79 270 1.36e-25 101
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046820.t1 AT5G53210 50.562 267 63 4 27 224 97 363 4.01e-71 221
MS.gene046820.t1 AT5G53210 46.371 248 64 4 27 205 97 344 3.39e-56 182
MS.gene046820.t1 AT3G06120 43.204 206 90 4 32 224 1 192 7.48e-50 161
MS.gene046820.t1 AT3G24140 40.179 224 119 5 9 224 177 393 7.17e-43 149
MS.gene046820.t1 AT3G24140 40.179 224 119 5 9 224 177 393 1.07e-42 149
MS.gene046820.t1 AT1G72210 35.047 214 113 5 17 222 113 308 5.76e-32 119
MS.gene046820.t1 AT1G72210 35.714 196 101 4 17 205 113 290 8.84e-31 115
MS.gene046820.t1 AT1G22490 37.255 204 113 5 21 223 107 296 5.27e-28 108
MS.gene046820.t1 AT4G01460 36.735 196 115 3 30 224 113 300 2.73e-26 103
MS.gene046820.t1 AT4G01460 36.735 196 115 3 30 224 113 300 2.73e-26 103
MS.gene046820.t1 AT1G22490 38.378 185 100 4 21 205 107 277 7.21e-26 102
MS.gene046820.t1 AT2G46810 35.204 196 107 4 31 224 120 297 2.37e-24 98.2
MS.gene046820.t1 AT2G46810 35.204 196 107 4 31 224 180 357 7.02e-24 98.2
MS.gene046820.t1 AT2G46810 35.204 196 107 4 31 224 192 369 7.27e-24 98.2
MS.gene046820.t1 AT5G65320 34.848 198 112 4 31 222 101 287 7.35e-23 94.4
MS.gene046820.t1 AT3G61950 33.163 196 110 5 31 224 126 302 5.63e-20 86.7
MS.gene046820.t1 AT2G46810 34.091 176 97 3 31 205 120 277 1.14e-19 86.3
MS.gene046820.t1 AT3G61950 33.163 196 110 5 31 224 177 353 1.24e-19 86.3
MS.gene046820.t1 AT5G65320 35.196 179 101 3 31 205 101 268 1.71e-19 84.7
MS.gene046820.t1 AT5G46690 32.710 214 116 6 21 213 78 284 2.68e-18 82.4
MS.gene046820.t1 AT5G46690 59.701 67 25 2 21 86 78 143 6.27e-18 80.9
MS.gene046820.t1 AT3G61950 33.951 162 88 3 31 192 126 268 2.47e-17 79.3
MS.gene046820.t1 AT3G61950 33.951 162 88 3 31 192 177 319 4.96e-17 79.0
MS.gene046820.t1 AT1G32640 27.568 185 108 5 26 207 445 606 4.13e-11 62.4

Find 30 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTATACTTGTTCACTATTA+AGG 0.194492 1.4:-83237658 MS.gene046820:intron
TATGGAGTTCTTGGACTAAT+TGG 0.233920 1.4:+83237948 None:intergenic
AACCGTTTCGTCACGAATTC+CGG 0.237314 1.4:-83237766 MS.gene046820:CDS
CTCATTGATGTTATCATTGA+TGG 0.240583 1.4:+83237860 None:intergenic
AGCCATTGATATGGAGTTCT+TGG 0.282669 1.4:+83237939 None:intergenic
TTTCTTAATAAAATGTTTGC+TGG 0.293141 1.4:+83237084 None:intergenic
CTAATTGGTAAGATTATTCT+AGG 0.295024 1.4:+83237963 None:intergenic
CATTGTTGTAGCCATTGATA+TGG 0.334687 1.4:+83237930 None:intergenic
ACCGTTTCGTCACGAATTCC+GGG 0.393233 1.4:-83237765 MS.gene046820:CDS
TGTGACTTCTTCAATTAAAG+AGG 0.419305 1.4:-83238530 MS.gene046820:CDS
ATGGAAGAAGCTGAAGAAGT+TGG 0.426375 1.4:+83237879 None:intergenic
GGACTTAGTGGTAAAGGTCT+TGG 0.429539 1.4:+83237984 None:intergenic
TTCGTCACGAATTCCGGGGC+AGG 0.440139 1.4:-83237760 MS.gene046820:CDS
AAGATTATTCTAGGACTTAG+TGG 0.440624 1.4:+83237972 None:intergenic
ATTCTAGGACTTAGTGGTAA+AGG 0.492814 1.4:+83237978 None:intergenic
CCCCGGAATTCGTGACGAAA+CGG 0.495669 1.4:+83237764 None:intergenic
TGTCGCGAATTCAACATCTT+CGG 0.496233 1.4:-83237835 MS.gene046820:CDS
CAAGTTCTTCAGCACTGAGT+TGG 0.510419 1.4:+83237117 None:intergenic
GTCCAAGAACTCCATATCAA+TGG 0.523072 1.4:-83237941 MS.gene046820:CDS
ATCTTCGGTTGCTGATGTTG+AGG 0.535328 1.4:-83237820 MS.gene046820:CDS
TTGGAGATGGCTCAGATGAA+AGG 0.570619 1.4:+83237898 None:intergenic
ACATCGTATGTCGCATATCA+CGG 0.587471 1.4:-83238488 MS.gene046820:CDS
GATCAAGCATCAATAGTTGA+AGG 0.590664 1.4:-83238094 MS.gene046820:CDS
AATAGTGAACAAGTATAGCA+TGG 0.592880 1.4:+83237662 None:intergenic
GAAGCTGAAGAAGTTGGAGA+TGG 0.605113 1.4:+83237885 None:intergenic
ATTATTCTAAGAGCCTGCCC+CGG 0.625886 1.4:+83237747 None:intergenic
CCGTTTCGTCACGAATTCCG+GGG 0.670932 1.4:-83237764 MS.gene046820:CDS
AAAGAGGAACAAAACAACGA+TGG 0.679841 1.4:-83238514 MS.gene046820:CDS
CAATGGCTACAACAATGTGG+TGG 0.701552 1.4:-83237924 MS.gene046820:CDS
TATCAATGGCTACAACAATG+TGG 0.711948 1.4:-83237927 MS.gene046820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATATAATTAATTATTAA+TGG + chr1.4:83238491-83238510 None:intergenic 0.0%
!! ATGAATTAAATAAACAATAT+TGG + chr1.4:83238402-83238421 None:intergenic 10.0%
!!! TTATTTATGTTTTTCAATTT+TGG - chr1.4:83238464-83238483 MS.gene046820:CDS 10.0%
!! TACTGTACAAAATATAAAAT+TGG - chr1.4:83238151-83238170 MS.gene046820:intron 15.0%
!!! AGTTTTAAATGAAACTAGTT+AGG - chr1.4:83237333-83237352 MS.gene046820:intron 20.0%
!!! GTTTTAAATGAAACTAGTTA+GGG - chr1.4:83237334-83237353 MS.gene046820:intron 20.0%
!!! TTTTAAATGAAACTAGTTAG+GGG - chr1.4:83237335-83237354 MS.gene046820:intron 20.0%
! AGAATCAATATTGAATACTG+TGG - chr1.4:83238185-83238204 MS.gene046820:intron 25.0%
! ATTACTCTTCTATATGGTTT+AGG - chr1.4:83237543-83237562 MS.gene046820:intron 25.0%
! ATTGAATACTGTGGTAATAA+TGG - chr1.4:83238194-83238213 MS.gene046820:intron 25.0%
! CAACTAATTACTCTTCTATA+TGG - chr1.4:83237537-83237556 MS.gene046820:intron 25.0%
! CATAACAATTAACATCATTC+TGG - chr1.4:83238340-83238359 MS.gene046820:intron 25.0%
! CTAATTGGTAAGATTATTCT+AGG + chr1.4:83237702-83237721 None:intergenic 25.0%
! TAAAATTTCCTTGTGTAGAT+TGG - chr1.4:83238513-83238532 MS.gene046820:CDS 25.0%
! TTACTCTTCTATATGGTTTA+GGG - chr1.4:83237544-83237563 MS.gene046820:intron 25.0%
! TTGGTGAAAAAATCAATGTA+TGG - chr1.4:83238375-83238394 MS.gene046820:intron 25.0%
!!! GATACAAATTTTGATCCTTT+TGG - chr1.4:83238102-83238121 MS.gene046820:intron 25.0%
!!! TGAAACTTTTCTTTGTTTCT+TGG + chr1.4:83237644-83237663 None:intergenic 25.0%
AATAGTGAACAAGTATAGCA+TGG + chr1.4:83238003-83238022 None:intergenic 30.0%
ATTCAATTCCAATCTACACA+AGG + chr1.4:83238524-83238543 None:intergenic 30.0%
ATTCTGGCATTGTATGTATT+TGG - chr1.4:83238356-83238375 MS.gene046820:intron 30.0%
ATTGTTATGATATACATCCC+TGG + chr1.4:83238329-83238348 None:intergenic 30.0%
CATAAACCAGACCAAATTAA+TGG - chr1.4:83237369-83237388 MS.gene046820:intron 30.0%
CTCATTGATGTTATCATTGA+TGG + chr1.4:83237805-83237824 None:intergenic 30.0%
GCTATACTTGTTCACTATTA+AGG - chr1.4:83238004-83238023 MS.gene046820:intron 30.0%
TGTGACTTCTTCAATTAAAG+AGG - chr1.4:83237132-83237151 MS.gene046820:CDS 30.0%
TTGTATCTCTTGTTAGCATA+AGG + chr1.4:83238089-83238108 None:intergenic 30.0%
! ACTCTTTTGACATAAAAGCA+AGG + chr1.4:83237259-83237278 None:intergenic 30.0%
! TTCTTTGTTTCTTGGATTCT+AGG + chr1.4:83237636-83237655 None:intergenic 30.0%
!! AAGATTATTCTAGGACTTAG+TGG + chr1.4:83237693-83237712 None:intergenic 30.0%
AAAGAGGAACAAAACAACGA+TGG - chr1.4:83237148-83237167 MS.gene046820:intron 35.0%
CAAAAAATGACAGCTACTAG+AGG + chr1.4:83238130-83238149 None:intergenic 35.0%
CATTGTTGTAGCCATTGATA+TGG + chr1.4:83237735-83237754 None:intergenic 35.0%
GATCAAGCATCAATAGTTGA+AGG - chr1.4:83237568-83237587 MS.gene046820:intron 35.0%
GTAATGTACTTCACTACTGT+AGG + chr1.4:83238238-83238257 None:intergenic 35.0%
TATCAATGGCTACAACAATG+TGG - chr1.4:83237735-83237754 MS.gene046820:CDS 35.0%
TATGGAGTTCTTGGACTAAT+TGG + chr1.4:83237717-83237736 None:intergenic 35.0%
! GATGTTGAGGTTAAGTTTTG+TGG - chr1.4:83237855-83237874 MS.gene046820:CDS 35.0%
!! ATTCTAGGACTTAGTGGTAA+AGG + chr1.4:83237687-83237706 None:intergenic 35.0%
ACATCGTATGTCGCATATCA+CGG - chr1.4:83237174-83237193 MS.gene046820:intron 40.0%
ACCAGACCAAATTAATGGTC+TGG - chr1.4:83237374-83237393 MS.gene046820:intron 40.0%
ACTGGACCAGACCATTAATT+TGG + chr1.4:83237383-83237402 None:intergenic 40.0%
AGCCATTGATATGGAGTTCT+TGG + chr1.4:83237726-83237745 None:intergenic 40.0%
ATGGAAGAAGCTGAAGAAGT+TGG + chr1.4:83237786-83237805 None:intergenic 40.0%
ATTGCATCAACCGTAGACTA+CGG + chr1.4:83237431-83237450 None:intergenic 40.0%
GTCCAAGAACTCCATATCAA+TGG - chr1.4:83237721-83237740 MS.gene046820:CDS 40.0%
TAACTACGAACCGTAGTCTA+CGG - chr1.4:83237418-83237437 MS.gene046820:intron 40.0%
TAGACTACGGTTCGTAGTTA+GGG + chr1.4:83237418-83237437 None:intergenic 40.0%
TGTCGCGAATTCAACATCTT+CGG - chr1.4:83237827-83237846 MS.gene046820:CDS 40.0%
! ACCAGACCATTAATTTGGTC+TGG + chr1.4:83237378-83237397 None:intergenic 40.0%
!! TTCACATTTCTGAGACACCA+GGG - chr1.4:83238309-83238328 MS.gene046820:intron 40.0%
!! TTTCACATTTCTGAGACACC+AGG - chr1.4:83238308-83238327 MS.gene046820:intron 40.0%
AACCGTTTCGTCACGAATTC+CGG - chr1.4:83237896-83237915 MS.gene046820:CDS 45.0%
AGACTACGGTTCGTAGTTAG+GGG + chr1.4:83237417-83237436 None:intergenic 45.0%
ATCTTCGGTTGCTGATGTTG+AGG - chr1.4:83237842-83237861 MS.gene046820:CDS 45.0%
CAATGGCTACAACAATGTGG+TGG - chr1.4:83237738-83237757 MS.gene046820:CDS 45.0%
GAAGCTGAAGAAGTTGGAGA+TGG + chr1.4:83237780-83237799 None:intergenic 45.0%
GGACTTAGTGGTAAAGGTCT+TGG + chr1.4:83237681-83237700 None:intergenic 45.0%
GTAGACTACGGTTCGTAGTT+AGG + chr1.4:83237419-83237438 None:intergenic 45.0%
TTGGAGATGGCTCAGATGAA+AGG + chr1.4:83237767-83237786 None:intergenic 45.0%
! ATTATTCTAAGAGCCTGCCC+CGG + chr1.4:83237918-83237937 None:intergenic 45.0%
! CAAGTTCTTCAGCACTGAGT+TGG + chr1.4:83238548-83238567 None:intergenic 45.0%
! TTAGGGGTGTGCAAAAGAAC+TGG + chr1.4:83237401-83237420 None:intergenic 45.0%
!!! TAATTTTAATCTTAATAAAA+AGG + chr1.4:83237475-83237494 None:intergenic 5.0%
ACCGTTTCGTCACGAATTCC+GGG - chr1.4:83237897-83237916 MS.gene046820:CDS 50.0%
CAGCTACTAGAGGCTCCAAA+AGG + chr1.4:83238120-83238139 None:intergenic 50.0%
CCCCGGAATTCGTGACGAAA+CGG + chr1.4:83237901-83237920 None:intergenic 55.0%
CCGTTTCGTCACGAATTCCG+GGG - chr1.4:83237898-83237917 MS.gene046820:CDS 55.0%
TTCGTCACGAATTCCGGGGC+AGG - chr1.4:83237902-83237921 MS.gene046820:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 83237088 83238596 83237088 ID=MS.gene046820
chr1.4 mRNA 83237088 83238596 83237088 ID=MS.gene046820.t1;Parent=MS.gene046820
chr1.4 exon 83238408 83238596 83238408 ID=MS.gene046820.t1.exon1;Parent=MS.gene046820.t1
chr1.4 CDS 83238408 83238596 83238408 ID=cds.MS.gene046820.t1;Parent=MS.gene046820.t1
chr1.4 exon 83238053 83238119 83238053 ID=MS.gene046820.t1.exon2;Parent=MS.gene046820.t1
chr1.4 CDS 83238053 83238119 83238053 ID=cds.MS.gene046820.t1;Parent=MS.gene046820.t1
chr1.4 exon 83237659 83238014 83237659 ID=MS.gene046820.t1.exon3;Parent=MS.gene046820.t1
chr1.4 CDS 83237659 83238014 83237659 ID=cds.MS.gene046820.t1;Parent=MS.gene046820.t1
chr1.4 exon 83237088 83237153 83237088 ID=MS.gene046820.t1.exon4;Parent=MS.gene046820.t1
chr1.4 CDS 83237088 83237153 83237088 ID=cds.MS.gene046820.t1;Parent=MS.gene046820.t1
Gene Sequence

>MS.gene046820

ATGAGCATGCTGAGACATCACAGAAAATGCAAGAGACAGAAGATTGTGACTTCTTCAATTAAAGAGGAACAAAACAACGATGGACAACATCGTATGTCGCATATCACGGTCGAACGCAATCGAAGAAAGCAAATGAATGAGCAGCTATCTATCTTGAAGTCACTTATGCCTTGCTTTTATGTCAAAAGAGTGAGTACATATTAACTAACTTGTCACAAATTCAAATTCTAAATAATTTTTTTCAAAGTTTTAAATGAAACTAGTTAGGGGTGTGCATGATTCATAAACCAGACCAAATTAATGGTCTGGTCCAGTTCTTTTGCACACCCCTAACTACGAACCGTAGTCTACGGTTGATGCAATAACAATTGCAATTGTTTGAAACCTTTTTATTAAGATTAAAATTATGTTTATCTTTCTTTAAATTATTATTTTTTGCATAAAAAATGCAACTAATTACTCTTCTATATGGTTTAGGGAGATCAAGCATCAATAGTTGAAGGTGTAATTGATTACATCAACGAGTTACATCAACTACTACAATGCCTAGAATCCAAGAAACAAAGAAAAGTTTCAGTGAAGTAACAAGTCCAAGACCTTTACCACTAAGTCCTAGAATAATCTTACCAATTAGTCCAAGAACTCCATATCAATGGCTACAACAATGTGGTGGTTACCTTTCATCTGAGCCATCTCCAACTTCTTCAGCTTCTTCCATCAATGATAACATCAATGAGCTTGTCGCGAATTCAACATCTTCGGTTGCTGATGTTGAGGTTAAGTTTTGTGGTTCACATGTGCTTTTGAAAACCGTTTCGTCACGAATTCCGGGGCAGGCTCTTAGAATAATGTCTGTTCTTGAAGATCTAATGCTTGAGATTGTTCATGTTAGAGTTAATACTGCTGATGAAACCATGCTATACTTGTTCACTATTAAGGTAACTGAATCTTTTGTTTATGCTTAATTAATTACTATTATTTACAACTACATTGATGATCCTTATGCTAACAAGAGATACAAATTTTGATCCTTTTGGAGCCTCTAGTAGCTGTCATTTTTTGTTACTGTACAAAATATAAAATTGGTAACTTTGATGAGAATCAATATTGAATACTGTGGTAATAATGGTAAATTCTTTGCTAAAAGCCTACAGTAGTGAAGTACATTACTACTGTATAGTATAATTATTAATCTATGACATGCAGTACACAAAGCATCTTTTCACATTTCTGAGACACCAGGGATGTATATCATAACAATTAACATCATTCTGGCATTGTATGTATTTGGTGAAAAAATCAATGTATGGTCCAATATTGTTTATTTAATTCATAGCAGCTAATGATTGAGTATGCATGTATCATATGTGATAATGTTATTTATGTTTTTCAATTTTGGTCCATTAATAATTAATTATATTTTCTTAAAATTTCCTTGTGTAGATTGGAATTGAATGCCAACTCAGTGCTGAAGAACTTGCTCAACAAATCCAGCAAACATTTTATTAA
Protein sequence

>MS.gene046820.t1

MSMLRHHRKCKRQKIVTSSIKEEQNNDGQHRMSHITVERNRRKQMNEQLSILKSLMPCFYVKRGDQASIVEGVIDYINELHQLLQLTSPRPLPLSPRIILPISPRTPYQWLQQCGGYLSSEPSPTSSASSINDNINELVANSTSSVADVEVKFCGSHVLLKTVSSRIPGQALRIMSVLEDLMLEIVHVRVNTADETMLYLFTIKIGIECQLSAEELAQQIQQTFY