AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003140

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003140.t1 MTR_2g027100 98.193 166 3 0 1 166 1 166 1.25e-116 327
MS.gene003140.t1 MTR_8g088320 47.239 163 73 2 1 157 161 316 3.06e-41 140
MS.gene003140.t1 MTR_3g067585 43.949 157 86 1 1 157 1 155 2.48e-39 131
MS.gene003140.t1 MTR_2g011590 43.137 153 85 1 5 157 4 154 4.94e-39 130
MS.gene003140.t1 MTR_2g030230 45.860 157 84 1 1 157 168 323 9.80e-38 132
MS.gene003140.t1 MTR_8g107340 42.675 157 88 1 1 157 17 171 1.02e-36 125
MS.gene003140.t1 MTR_6g069470 40.764 157 91 2 1 157 13 167 1.35e-36 124
MS.gene003140.t1 MTR_3g017500 46.497 157 83 1 1 157 209 364 4.20e-35 125
MS.gene003140.t1 MTR_3g017500 46.497 157 83 1 1 157 239 394 1.18e-34 125
MS.gene003140.t1 MTR_8g038400 43.949 157 87 1 1 157 206 361 1.54e-32 119
MS.gene003140.t1 MTR_1g031650 42.953 149 82 2 5 152 6 152 2.37e-30 108
MS.gene003140.t1 MTR_4g084280 39.474 152 90 1 1 152 1 150 2.59e-30 108
MS.gene003140.t1 MTR_1g031650 41.379 116 66 1 37 152 2 115 1.22e-20 82.8
MS.gene003140.t1 MTR_1g008950 34.375 96 61 2 6 99 4 99 5.89e-12 60.1
MS.gene003140.t1 MTR_8g032320 36.458 96 59 2 6 99 4 99 6.47e-12 60.5
MS.gene003140.t1 MTR_6g084400 38.053 113 61 5 7 113 484 593 2.74e-11 61.2
MS.gene003140.t1 MTR_1g045930 35.556 90 56 2 6 93 127 216 5.32e-11 60.5
MS.gene003140.t1 MTR_8g032300 36.264 91 56 2 6 94 4 94 5.44e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003140.t1 AT5G47710 69.880 166 50 0 1 166 1 166 1.07e-83 244
MS.gene003140.t1 AT5G47710 69.880 166 50 0 1 166 1 166 1.07e-83 244
MS.gene003140.t1 AT5G47710 69.880 166 50 0 1 166 1 166 1.07e-83 244
MS.gene003140.t1 AT5G47710 69.880 166 50 0 1 166 1 166 1.07e-83 244
MS.gene003140.t1 AT1G70790 46.154 156 82 2 5 159 6 160 7.06e-40 133
MS.gene003140.t1 AT1G70790 46.154 156 82 2 5 159 6 160 7.06e-40 133
MS.gene003140.t1 AT1G70790 46.154 156 82 2 5 159 6 160 7.06e-40 133
MS.gene003140.t1 AT1G73580 44.586 157 85 1 1 157 4 158 8.40e-39 130
MS.gene003140.t1 AT2G01540 44.156 154 84 2 5 157 6 158 9.96e-38 127
MS.gene003140.t1 AT4G05330 45.223 157 85 1 1 157 140 295 1.31e-37 130
MS.gene003140.t1 AT4G05330 45.223 157 85 1 1 157 175 330 4.97e-37 130
MS.gene003140.t1 AT4G05330 45.223 157 85 1 1 157 175 330 4.97e-37 130
MS.gene003140.t1 AT3G17980 42.038 157 89 2 1 157 13 167 5.31e-37 125
MS.gene003140.t1 AT5G37740 41.139 158 92 1 1 157 1 158 6.92e-37 125
MS.gene003140.t1 AT4G21160 43.949 157 87 1 1 157 176 331 7.13e-37 130
MS.gene003140.t1 AT4G21160 43.949 157 87 1 1 157 176 331 7.13e-37 130
MS.gene003140.t1 AT4G21160 43.949 157 87 1 1 157 176 331 7.13e-37 130
MS.gene003140.t1 AT4G21160 43.949 157 87 1 1 157 176 331 7.13e-37 130
MS.gene003140.t1 AT1G66360 39.490 157 95 0 1 157 1 157 2.13e-36 124
MS.gene003140.t1 AT1G70810 41.401 157 90 2 1 157 1 155 6.85e-36 122
MS.gene003140.t1 AT3G07940 45.860 157 84 1 1 157 224 379 5.84e-35 125
MS.gene003140.t1 AT1G48590 40.127 157 92 2 1 157 6 160 2.41e-34 119
MS.gene003140.t1 AT1G48590 40.127 157 92 2 1 157 6 160 2.41e-34 119
MS.gene003140.t1 AT1G48590 40.127 157 92 2 1 157 37 191 5.04e-34 119
MS.gene003140.t1 AT1G23140 38.854 157 94 2 1 157 1 155 5.42e-34 117
MS.gene003140.t1 AT5G37740 38.690 168 92 2 1 157 1 168 1.89e-33 117
MS.gene003140.t1 AT1G70800 36.943 157 97 1 1 157 10 164 1.58e-31 112
MS.gene003140.t1 AT1G70790 42.975 121 67 2 40 159 4 123 7.58e-27 99.0
MS.gene003140.t1 AT1G48590 32.484 157 72 3 1 157 37 159 9.60e-20 81.3

Find 37 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTATGTTGTTCTCAAATT+AGG 0.114099 2.1:-63394634 MS.gene003140:CDS
TTTGAAAGCTGATGACAAAA+TGG 0.206431 2.1:-63393771 MS.gene003140:CDS
ATTATAATGAGTGAACAATT+AGG 0.300153 2.1:-63394721 None:intergenic
ACCCTTGGGAGTTCTCAATT+TGG 0.326299 2.1:-63394269 MS.gene003140:intron
TGTTCTCAAATTAGGAAATC+AGG 0.369709 2.1:-63394626 MS.gene003140:intron
CTTCCGGTGAGCAAACATTA+AGG 0.379148 2.1:-63393682 MS.gene003140:CDS
CCTAATTTGAGAACAACATA+AGG 0.397853 2.1:+63394634 None:intergenic
GCGCGGTTGTGCAGAATGTT+TGG 0.408048 2.1:-63393598 MS.gene003140:CDS
ATAGCTGTTTGAATCCGGTT+TGG 0.419279 2.1:-63394321 MS.gene003140:CDS
AAGGGAAAAGGTTGGTGATC+CGG 0.421394 2.1:-63394675 MS.gene003140:CDS
TTGAAAGCTGATGACAAAAT+GGG 0.427442 2.1:-63393770 MS.gene003140:CDS
AGCAGTATCAATTGTGTTAA+CGG 0.427721 2.1:-63393620 MS.gene003140:CDS
CATTAATAGCTGTTTGAATC+CGG 0.434724 2.1:-63394326 MS.gene003140:CDS
TTATAATGAGTGAACAATTA+GGG 0.440831 2.1:-63394720 None:intergenic
TTTCTCTTTGACAGAACCCT+TGG 0.442241 2.1:-63394284 MS.gene003140:CDS
TTCAGCTCTTCATTCCAAAC+CGG 0.443481 2.1:+63394307 None:intergenic
TTGTGCAGAATGTTTGGTTA+AGG 0.448350 2.1:-63393592 MS.gene003140:CDS
AATCTAGCTGCAGAGACTAA+TGG 0.452322 2.1:+63393725 None:intergenic
TTCTCTTTGACAGAACCCTT+GGG 0.470160 2.1:-63394283 MS.gene003140:CDS
AGGGAAAAGGTTGGTGATCC+GGG 0.470972 2.1:-63394674 MS.gene003140:CDS
CTGCAGAGACTAATGGTTGA+AGG 0.477932 2.1:+63393732 None:intergenic
CAAACAGCTATTAATGACCT+TGG 0.491295 2.1:+63394333 None:intergenic
GAGTGTCAATTCTATCTCTC+CGG 0.491542 2.1:+63393553 None:intergenic
TCATAGTTGTGCAAGGGAAA+AGG 0.522477 2.1:-63394687 MS.gene003140:CDS
GATCACTGGTCTTGAAATCC+CGG 0.525136 2.1:+63394656 None:intergenic
CTTCCTTAATGTTTGCTCAC+CGG 0.528914 2.1:+63393679 None:intergenic
GAGAACAACATAAGGATCAC+TGG 0.556443 2.1:+63394642 None:intergenic
AGGCTTCGCGAAGTAGAATC+CGG 0.566418 2.1:-63393572 MS.gene003140:CDS
TGAACAATTAGGGCAGCTAA+AGG 0.572900 2.1:-63394710 MS.gene003140:CDS
CGGTGAGCAAACATTAAGGA+AGG 0.588349 2.1:-63393678 MS.gene003140:CDS
CTAAAGGTCATAGTTGTGCA+AGG 0.591043 2.1:-63394694 MS.gene003140:CDS
CACCAAATTGAGAACTCCCA+AGG 0.603264 2.1:+63394267 None:intergenic
TAAAGGTCATAGTTGTGCAA+GGG 0.629000 2.1:-63394693 MS.gene003140:CDS
AGTTGTGCAAGGGAAAAGGT+TGG 0.639430 2.1:-63394683 MS.gene003140:CDS
ACCAAATTGAGAACTCCCAA+GGG 0.650902 2.1:+63394268 None:intergenic
GTAACAGACTGCAAAGACCA+AGG 0.673690 2.1:-63394350 MS.gene003140:intron
TATCAATTGTGTTAACGGCG+CGG 0.708048 2.1:-63393615 MS.gene003140:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTATTTCATTTTCATCTT+AGG - chr2.1:63393643-63393662 MS.gene003140:CDS 15.0%
!! GAATGAATCATTTAATATTG+AGG + chr2.1:63393857-63393876 None:intergenic 20.0%
!!! CTTATTTGAGTTTATCTAAT+AGG - chr2.1:63394173-63394192 MS.gene003140:intron 20.0%
!!! TAAGTTATTTCTATAGCAAA+GGG + chr2.1:63394318-63394337 None:intergenic 20.0%
!!! TTAAGTTATTTCTATAGCAA+AGG + chr2.1:63394319-63394338 None:intergenic 20.0%
!!! TTTTTTGTTTATATCTGAGA+GGG - chr2.1:63394386-63394405 MS.gene003140:intron 20.0%
! ATATAGTGCATTAAACTCTA+TGG + chr2.1:63394103-63394122 None:intergenic 25.0%
! GTTTGTTTATCTTCACATTA+AGG - chr2.1:63393665-63393684 MS.gene003140:CDS 25.0%
! TAATGCACTATATATTAGCT+TGG - chr2.1:63394110-63394129 MS.gene003140:intron 25.0%
! TGCAACTCAGTTATAAATAT+AGG + chr2.1:63394412-63394431 None:intergenic 25.0%
! TTATATAGGACTGTTTAGAA+TGG - chr2.1:63394150-63394169 MS.gene003140:intron 25.0%
!! GTACTCTACATGTTTTATAT+AGG - chr2.1:63394136-63394155 MS.gene003140:intron 25.0%
!!! AGTTGATGTATATTTTACTG+TGG - chr2.1:63394049-63394068 MS.gene003140:intron 25.0%
!!! ATTTACAATGCCTTGTTTAT+TGG - chr2.1:63394002-63394021 MS.gene003140:intron 25.0%
!!! GTTTTTTGTTTATATCTGAG+AGG - chr2.1:63394385-63394404 MS.gene003140:intron 25.0%
AAAGACAATTGTTTCCATAC+AGG + chr2.1:63394289-63394308 None:intergenic 30.0%
AGCAGTATCAATTGTGTTAA+CGG - chr2.1:63394615-63394634 MS.gene003140:intron 30.0%
ATTGCTAAAAAAACACCTGT+TGG - chr2.1:63393716-63393735 MS.gene003140:CDS 30.0%
CATTAATAGCTGTTTGAATC+CGG - chr2.1:63393909-63393928 MS.gene003140:intron 30.0%
CCTAATTTGAGAACAACATA+AGG + chr2.1:63393604-63393623 None:intergenic 30.0%
CCTTATGTTGTTCTCAAATT+AGG - chr2.1:63393601-63393620 MS.gene003140:CDS 30.0%
CTTCACATTAAGGACATATT+TGG - chr2.1:63393675-63393694 MS.gene003140:CDS 30.0%
GCATTAAAGACCAATAAACA+AGG + chr2.1:63394015-63394034 None:intergenic 30.0%
TGCATCTTCTAAGTTTAATG+TGG + chr2.1:63393794-63393813 None:intergenic 30.0%
TGTTCTCAAATTAGGAAATC+AGG - chr2.1:63393609-63393628 MS.gene003140:CDS 30.0%
TTGAAAGCTGATGACAAAAT+GGG - chr2.1:63394465-63394484 MS.gene003140:intron 30.0%
TTGAGTTTATCTAATAGGCT+TGG - chr2.1:63394178-63394197 MS.gene003140:intron 30.0%
TTTGAAAGCTGATGACAAAA+TGG - chr2.1:63394464-63394483 MS.gene003140:intron 30.0%
! CTGAGTTGCATTTTGAATAT+AGG - chr2.1:63394422-63394441 MS.gene003140:intron 30.0%
! TACAAGACAATTTTCAGAGT+CGG + chr2.1:63394589-63394608 None:intergenic 30.0%
!! GTTTATTGGTCTTTAATGCT+TGG - chr2.1:63394016-63394035 MS.gene003140:intron 30.0%
AATACACTTAACATGCCAAC+AGG + chr2.1:63393734-63393753 None:intergenic 35.0%
CAAACAGCTATTAATGACCT+TGG + chr2.1:63393905-63393924 None:intergenic 35.0%
GACATATTTGGATCAACAGT+GGG - chr2.1:63393687-63393706 MS.gene003140:CDS 35.0%
TAAAGGTCATAGTTGTGCAA+GGG - chr2.1:63393542-63393561 MS.gene003140:CDS 35.0%
TTGTGCAGAATGTTTGGTTA+AGG - chr2.1:63394643-63394662 MS.gene003140:CDS 35.0%
! ACAAGACAATTTTCAGAGTC+GGG + chr2.1:63394588-63394607 None:intergenic 35.0%
! GCACTATATATTAGCTTGGA+AGG - chr2.1:63394114-63394133 MS.gene003140:intron 35.0%
!! AACAAGGCATTGTAAATGTG+AGG + chr2.1:63393999-63394018 None:intergenic 35.0%
!! ATTGGTCTTTAATGCTTGGA+AGG - chr2.1:63394020-63394039 MS.gene003140:intron 35.0%
!! GACATTTTAAGAGTCTCTTC+CGG - chr2.1:63394537-63394556 MS.gene003140:intron 35.0%
!!! TTTTGAAGTAACAACAGGTG+TGG + chr2.1:63394715-63394734 None:intergenic 35.0%
AATCTAGCTGCAGAGACTAA+TGG + chr2.1:63394513-63394532 None:intergenic 40.0%
ACCAAATTGAGAACTCCCAA+GGG + chr2.1:63393970-63393989 None:intergenic 40.0%
ATAGCTGTTTGAATCCGGTT+TGG - chr2.1:63393914-63393933 MS.gene003140:intron 40.0%
CTAAAGGTCATAGTTGTGCA+AGG - chr2.1:63393541-63393560 MS.gene003140:CDS 40.0%
CTTCCTTAATGTTTGCTCAC+CGG + chr2.1:63394559-63394578 None:intergenic 40.0%
GAGAACAACATAAGGATCAC+TGG + chr2.1:63393596-63393615 None:intergenic 40.0%
GAGTGTCAATTCTATCTCTC+CGG + chr2.1:63394685-63394704 None:intergenic 40.0%
GGACATATTTGGATCAACAG+TGG - chr2.1:63393686-63393705 MS.gene003140:CDS 40.0%
TATCAATTGTGTTAACGGCG+CGG - chr2.1:63394620-63394639 MS.gene003140:intron 40.0%
TCATAGTTGTGCAAGGGAAA+AGG - chr2.1:63393548-63393567 MS.gene003140:CDS 40.0%
TGAACAATTAGGGCAGCTAA+AGG - chr2.1:63393525-63393544 MS.gene003140:CDS 40.0%
TTCAGCTCTTCATTCCAAAC+CGG + chr2.1:63393931-63393950 None:intergenic 40.0%
TTCTCTTTGACAGAACCCTT+GGG - chr2.1:63393952-63393971 MS.gene003140:intron 40.0%
TTTCTCTTTGACAGAACCCT+TGG - chr2.1:63393951-63393970 MS.gene003140:intron 40.0%
!! GCTTTTGAAAACAGCCTGTA+TGG - chr2.1:63394272-63394291 MS.gene003140:CDS 40.0%
ACCCTTGGGAGTTCTCAATT+TGG - chr2.1:63393966-63393985 MS.gene003140:intron 45.0%
AGTTGTGCAAGGGAAAAGGT+TGG - chr2.1:63393552-63393571 MS.gene003140:CDS 45.0%
CACCAAATTGAGAACTCCCA+AGG + chr2.1:63393971-63393990 None:intergenic 45.0%
CGGTGAGCAAACATTAAGGA+AGG - chr2.1:63394557-63394576 MS.gene003140:intron 45.0%
CTGCAGAGACTAATGGTTGA+AGG + chr2.1:63394506-63394525 None:intergenic 45.0%
CTTCCGGTGAGCAAACATTA+AGG - chr2.1:63394553-63394572 MS.gene003140:intron 45.0%
GTAACAGACTGCAAAGACCA+AGG - chr2.1:63393885-63393904 MS.gene003140:intron 45.0%
! AAGCTATCACAGAGTGCTTG+TGG + chr2.1:63394256-63394275 None:intergenic 45.0%
!! AAGGGAAAAGGTTGGTGATC+CGG - chr2.1:63393560-63393579 MS.gene003140:CDS 45.0%
!! GATCACTGGTCTTGAAATCC+CGG + chr2.1:63393582-63393601 None:intergenic 45.0%
AGGCTTCGCGAAGTAGAATC+CGG - chr2.1:63394663-63394682 MS.gene003140:CDS 50.0%
!! AGGGAAAAGGTTGGTGATCC+GGG - chr2.1:63393561-63393580 MS.gene003140:CDS 50.0%
GCGCGGTTGTGCAGAATGTT+TGG - chr2.1:63394637-63394656 MS.gene003140:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 63393520 63394737 63393520 ID=MS.gene003140
chr2.1 mRNA 63393520 63394737 63393520 ID=MS.gene003140.t1;Parent=MS.gene003140
chr2.1 exon 63394627 63394737 63394627 ID=MS.gene003140.t1.exon1;Parent=MS.gene003140.t1
chr2.1 CDS 63394627 63394737 63394627 ID=cds.MS.gene003140.t1;Parent=MS.gene003140.t1
chr2.1 exon 63394270 63394365 63394270 ID=MS.gene003140.t1.exon2;Parent=MS.gene003140.t1
chr2.1 CDS 63394270 63394365 63394270 ID=cds.MS.gene003140.t1;Parent=MS.gene003140.t1
chr2.1 exon 63393520 63393813 63393520 ID=MS.gene003140.t1.exon3;Parent=MS.gene003140.t1
chr2.1 CDS 63393520 63393813 63393520 ID=cds.MS.gene003140.t1;Parent=MS.gene003140.t1
Gene Sequence

>MS.gene003140

ATGAGTGAACAATTAGGGCAGCTAAAGGTCATAGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTTGTTCTCAAATTAGGAAATCAGGTAACTAAAATTTATTATTTCATTTTCATCTTAGGTTTGTTTATCTTCACATTAAGGACATATTTGGATCAACAGTGGGTAGCTAATTGCTAAAAAAACACCTGTTGGCATGTTAAGTGTATTTAAATACTATATAAGTACTCATGTTATGAGATTAAGTCCACATTAAACTTAGAAGATGCATTAAACTTATACTACTAGTAAGTAAACTAGTCTGTTTTAACCTCAATATTAAATGATTCATTCATTAAACTGTAACAGACTGCAAAGACCAAGGTCATTAATAGCTGTTTGAATCCGGTTTGGAATGAAGAGCTGAATTTCTCTTTGACAGAACCCTTGGGAGTTCTCAATTTGGTGAGTCTCCTCACATTTACAATGCCTTGTTTATTGGTCTTTAATGCTTGGAAGGTACTCTAGTTGATGTATATTTTACTGTGGTTTTGAGTTATATTGATCAATTTTGAAACCATAGAGTTTAATGCACTATATATTAGCTTGGAAGGTACTCTACATGTTTTATATAGGACTGTTTAGAATGGCTTATTTGAGTTTATCTAATAGGCTTGGAAGAGTTTATGAAAATGACATGACATATTCATAAGCTGTTTTCAGCTTATTTCCACAAGCACTCTGTGATAGCTTTTGAAAACAGCCTGTATGGAAACAATTGTCTTTATTTATCCCTTTGCTATAGAAATAACTTAACATGAGCACTTATATGATCAACTTTTATGTTATATGCGCTTAATTAGTTTTTTGTTTATATCTGAGAGGGCCTATATTTATAACTGAGTTGCATTTTGAATATAGGAAGTGTTTGATAAAGATCTTTTGAAAGCTGATGACAAAATGGGAAATGCATTTATCAACCTTCAACCATTAGTCTCTGCAGCTAGATTAAGAGACATTTTAAGAGTCTCTTCCGGTGAGCAAACATTAAGGAAGGTTATACCCGACTCTGAAAATTGTCTTGTACGCGAAAGCAGTATCAATTGTGTTAACGGCGCGGTTGTGCAGAATGTTTGGTTAAGGCTTCGCGAAGTAGAATCCGGAGAGATAGAATTGACACTCAAGTTGACCACACCTGTTGTTACTTCAAAATAG
Protein sequence

>MS.gene003140.t1

MSEQLGQLKVIVVQGKRLVIRDFKTSDPYVVLKLGNQTAKTKVINSCLNPVWNEELNFSLTEPLGVLNLEVFDKDLLKADDKMGNAFINLQPLVSAARLRDILRVSSGEQTLRKVIPDSENCLVRESSINCVNGAVVQNVWLRLREVESGEIELTLKLTTPVVTSK