AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene058383

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene058383.t1 MTR_8g045490 76.923 156 15 1 1 135 1 156 3.28e-84 243
MS.gene058383.t1 MTR_8g045520 66.242 157 31 2 1 135 1 157 1.06e-70 209
MS.gene058383.t1 MTR_8g045400 66.000 150 31 1 1 130 1 150 2.96e-69 205
MS.gene058383.t1 MTR_8g045570 66.225 151 30 1 1 130 1 151 1.50e-68 203
MS.gene058383.t1 MTR_8g045695 62.420 157 36 3 1 135 1 156 1.78e-65 196
MS.gene058383.t1 MTR_8g045300 61.842 152 37 1 1 131 1 152 3.04e-65 195
MS.gene058383.t1 MTR_8g045555 62.252 151 36 1 1 130 1 151 3.23e-62 187
MS.gene058383.t1 MTR_8g045735 60.265 151 38 2 1 130 1 150 2.24e-61 186
MS.gene058383.t1 MTR_8g045640 59.236 157 41 3 1 135 1 156 4.12e-60 182
MS.gene058383.t1 MTR_8g045665 60.265 151 38 2 1 130 1 150 5.85e-60 182
MS.gene058383.t1 MTR_8g045560 58.278 151 41 2 1 130 1 150 7.56e-58 177
MS.gene058383.t1 MTR_1g030810 40.260 154 68 3 1 131 1 153 1.62e-31 110
MS.gene058383.t1 MTR_1g030820 35.714 154 75 3 1 131 1 153 3.75e-30 106
MS.gene058383.t1 MTR_1g030840 32.704 159 78 5 1 131 1 158 2.50e-18 76.6
MS.gene058383.t1 MTR_8g012550 27.703 148 83 4 6 131 8 153 2.63e-16 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene058383.t1 AT5G28010 31.373 153 81 4 3 132 15 166 1.02e-17 75.1
MS.gene058383.t1 AT5G28010 31.373 153 81 4 3 132 15 166 1.02e-17 75.1
MS.gene058383.t1 AT1G70890 30.719 153 82 4 3 132 7 158 9.81e-16 69.7
MS.gene058383.t1 AT1G70840 28.758 153 85 4 3 132 20 171 7.67e-15 67.8
MS.gene058383.t1 AT1G70830 29.412 153 84 4 3 132 22 173 3.05e-14 66.2
MS.gene058383.t1 AT1G23120 26.490 151 87 3 1 131 1 147 3.76e-14 65.5
MS.gene058383.t1 AT1G70830 29.412 153 84 4 3 132 22 173 5.24e-14 66.2
MS.gene058383.t1 AT1G23120 26.490 151 87 3 1 131 51 197 9.77e-14 65.5
MS.gene058383.t1 AT1G70830 29.412 153 84 4 3 132 22 173 1.17e-13 65.9
MS.gene058383.t1 AT1G70830 29.412 153 84 4 3 132 22 173 1.55e-13 66.2
MS.gene058383.t1 AT1G70830 28.105 153 86 4 3 132 184 335 5.55e-12 62.0
MS.gene058383.t1 AT1G23130 27.815 151 86 3 3 131 10 159 4.92e-13 62.8
MS.gene058383.t1 AT4G23670 29.139 151 85 3 1 130 1 150 1.47e-12 61.2
MS.gene058383.t1 AT1G70830 28.105 153 86 4 3 132 137 288 3.69e-12 62.0
MS.gene058383.t1 AT1G35260 27.397 146 81 4 6 128 5 148 1.32e-11 58.9
MS.gene058383.t1 AT1G70870 34.375 96 43 1 55 130 43 138 1.54e-11 58.2
MS.gene058383.t1 AT4G23680 26.490 151 89 3 1 130 1 150 8.65e-11 56.6

Find 23 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGGCTACATGGAACATTT+TGG 0.264766 3.2:-2671259 MS.gene058383:CDS
ATGGCACTGCTGCTGCTAAA+TGG 0.314913 3.2:-2671324 MS.gene058383:CDS
GTCTTCACCTTCATGAAGTT+TGG 0.318017 3.2:+2672692 None:intergenic
GGTGAGCTCAGTACTGAAAT+TGG 0.365883 3.2:-2672801 MS.gene058383:CDS
AAATGTTCCATGTAGCCATT+TGG 0.413070 3.2:+2671262 None:intergenic
AAACACTGGACTTATGTCAT+AGG 0.490184 3.2:-2672648 MS.gene058383:intron
AGATATTGATGAGCACTATA+AGG 0.500590 3.2:-2671383 MS.gene058383:CDS
TGACCCTCCAAATGGCTACA+TGG 0.521176 3.2:-2671269 MS.gene058383:CDS
GAGGATATTGACCCTCCAAA+TGG 0.540200 3.2:-2671277 MS.gene058383:CDS
TGTTCCATGTAGCCATTTGG+AGG 0.542543 3.2:+2671265 None:intergenic
AACACTTATAAGTTCTTCGG+TGG 0.555536 3.2:-2671406 MS.gene058383:intron
TATGATGAACTCTTTCACAA+AGG 0.564152 3.2:+2672715 None:intergenic
AACTTCATGAAGGTGAAGAC+TGG 0.571497 3.2:-2672689 MS.gene058383:CDS
GAAGTAATTGATAAGAGTGA+TGG 0.579637 3.2:-2671343 MS.gene058383:CDS
ATAATTCATAACAGATGGCA+AGG 0.593174 3.2:-2671480 MS.gene058383:intron
CATCATACCAAACTTCATGA+AGG 0.595182 3.2:-2672699 MS.gene058383:CDS
TATTGATGCTTATCTAGCCA+AGG 0.607429 3.2:-2671221 MS.gene058383:CDS
GTTCCATGTAGCCATTTGGA+GGG 0.622662 3.2:+2671266 None:intergenic
ACAGTGATTCAGTTAAACAC+TGG 0.626084 3.2:-2672662 MS.gene058383:CDS
CAGATTGTAGAACTTGTCAG+AGG 0.636689 3.2:+2672767 None:intergenic
TGAATATGAAAAGATCAATG+AGG 0.646793 3.2:-2671296 MS.gene058383:CDS
AGATTGTAGAACTTGTCAGA+GGG 0.675294 3.2:+2672768 None:intergenic
TTCTAAGAAATGGTGCTCTG+TGG 0.703436 3.2:-2672822 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATTTGTCAAAAAAAAAA+GGG + chr3.2:2672064-2672083 None:intergenic 10.0%
!! TTATATTTGTCAAAAAAAAA+AGG + chr3.2:2672065-2672084 None:intergenic 10.0%
!!! AAAAATAATAGGTTATTTTT+TGG - chr3.2:2672393-2672412 MS.gene058383:intron 10.0%
!!! CTTTTAGATTTTTTTATTTT+TGG + chr3.2:2671701-2671720 None:intergenic 10.0%
!!! TTATTATTCAATTTTTTGTT+TGG - chr3.2:2672113-2672132 MS.gene058383:intron 10.0%
!! AGTAAAATAATAAGATGATT+TGG + chr3.2:2671427-2671446 None:intergenic 15.0%
!!! AAATATTTTAAGGTAAACAA+CGG + chr3.2:2672095-2672114 None:intergenic 15.0%
!!! AAATGTTGATCATTTTTAAT+TGG - chr3.2:2671492-2671511 MS.gene058383:intron 15.0%
!!! AATCATCTTATTATTTTACT+TGG - chr3.2:2671427-2671446 MS.gene058383:intron 15.0%
!!! GATTCATATTTTTTTTTGAA+TGG + chr3.2:2671978-2671997 None:intergenic 15.0%
!!! TTAGCAAGTTTTATTTTTTT+TGG - chr3.2:2671754-2671773 MS.gene058383:intron 15.0%
!!! TTTTGGTCAAAAAAAATAAT+AGG - chr3.2:2672410-2672429 MS.gene058383:intron 15.0%
!! AAAAACACTTATAAGTTCTT+CGG - chr3.2:2672608-2672627 MS.gene058383:intron 20.0%
!! AGGTTATTTGTAGAAAAAAA+AGG - chr3.2:2672430-2672449 MS.gene058383:intron 20.0%
!!! AAATAATAAGATGATTTGGT+TGG + chr3.2:2671423-2671442 None:intergenic 20.0%
!!! TGATCAACATTTTTGTTTTA+AGG + chr3.2:2671484-2671503 None:intergenic 20.0%
!!! TTTTATTTGAATGTTTGCTT+TGG - chr3.2:2671575-2671594 MS.gene058383:intron 20.0%
! TGAATATGAAAAGATCAATG+AGG - chr3.2:2672721-2672740 MS.gene058383:CDS 25.0%
!! TTGGTCTATATAAAGAGTTT+TGG + chr3.2:2671682-2671701 None:intergenic 25.0%
!!! GTTTTATTTTTTTTGGTGAC+CGG - chr3.2:2671761-2671780 MS.gene058383:intron 25.0%
!!! TTTTATTTTTTTTGGTGACC+GGG - chr3.2:2671762-2671781 MS.gene058383:intron 25.0%
AACCATACTACTAGACTATT+AGG + chr3.2:2672330-2672349 None:intergenic 30.0%
AGATATTGATGAGCACTATA+AGG - chr3.2:2672634-2672653 MS.gene058383:intron 30.0%
ATAATTCATAACAGATGGCA+AGG - chr3.2:2672537-2672556 MS.gene058383:intron 30.0%
CCATCATAATTCATAACAGA+TGG - chr3.2:2672532-2672551 MS.gene058383:intron 30.0%
CCATCTGTTATGAATTATGA+TGG + chr3.2:2672535-2672554 None:intergenic 30.0%
GAAGTAATTGATAAGAGTGA+TGG - chr3.2:2672674-2672693 MS.gene058383:CDS 30.0%
TAGAGACAGACAATAACTTA+TGG - chr3.2:2672298-2672317 MS.gene058383:intron 30.0%
TATGATGAACTCTTTCACAA+AGG + chr3.2:2671305-2671324 None:intergenic 30.0%
TGTTATGAATTATGATGGCA+CGG + chr3.2:2672530-2672549 None:intergenic 30.0%
! TCATTAACCTATTTGCTACA+TGG - chr3.2:2672349-2672368 MS.gene058383:intron 30.0%
! TTATAGAGCTATCTTTTCCT+TGG + chr3.2:2672816-2672835 None:intergenic 30.0%
!!! TTTATTTTTTTTGGTGACCG+GGG - chr3.2:2671763-2671782 MS.gene058383:intron 30.0%
AAACACTGGACTTATGTCAT+AGG - chr3.2:2671369-2671388 MS.gene058383:CDS 35.0%
AAATGTTCCATGTAGCCATT+TGG + chr3.2:2672758-2672777 None:intergenic 35.0%
AACACTTATAAGTTCTTCGG+TGG - chr3.2:2672611-2672630 MS.gene058383:intron 35.0%
AATAGAGAGAAGAAGAGAGA+AGG - chr3.2:2672204-2672223 MS.gene058383:intron 35.0%
ACAGTGATTCAGTTAAACAC+TGG - chr3.2:2671355-2671374 MS.gene058383:CDS 35.0%
AGATTGTAGAACTTGTCAGA+GGG + chr3.2:2671252-2671271 None:intergenic 35.0%
AGCCTAATAGTCTAGTAGTA+TGG - chr3.2:2672325-2672344 MS.gene058383:intron 35.0%
CATCATACCAAACTTCATGA+AGG - chr3.2:2671318-2671337 MS.gene058383:CDS 35.0%
GTTATGAATTATGATGGCAC+GGG + chr3.2:2672529-2672548 None:intergenic 35.0%
TATTGATGCTTATCTAGCCA+AGG - chr3.2:2672796-2672815 MS.gene058383:CDS 35.0%
! AATGGCTACATGGAACATTT+TGG - chr3.2:2672758-2672777 MS.gene058383:CDS 35.0%
! TAACATTTTGCCTATGTAGG+TGG + chr3.2:2671659-2671678 None:intergenic 35.0%
! TGGTAACATTTTGCCTATGT+AGG + chr3.2:2671662-2671681 None:intergenic 35.0%
AACTTCATGAAGGTGAAGAC+TGG - chr3.2:2671328-2671347 MS.gene058383:CDS 40.0%
AAGGAGAGGAAGAGAGAATA+GGG - chr3.2:2672223-2672242 MS.gene058383:intron 40.0%
ACACAAAAGACCACCTACAT+AGG - chr3.2:2671646-2671665 MS.gene058383:intron 40.0%
CAGATTGTAGAACTTGTCAG+AGG + chr3.2:2671253-2671272 None:intergenic 40.0%
GTCTTCACCTTCATGAAGTT+TGG + chr3.2:2671328-2671347 None:intergenic 40.0%
TGGATGTCCATGTAGCAAAT+AGG + chr3.2:2672359-2672378 None:intergenic 40.0%
! TGAGCTTAACTCAGTTGGTA+GGG + chr3.2:2671799-2671818 None:intergenic 40.0%
AGAGAAGAAGAGAGAAGGAG+AGG - chr3.2:2672209-2672228 MS.gene058383:intron 45.0%
CCAACTGAGTTAAGCTCACA+AGG - chr3.2:2671801-2671820 MS.gene058383:intron 45.0%
CCTTGTGAGCTTAACTCAGT+TGG + chr3.2:2671804-2671823 None:intergenic 45.0%
GAAGGAGAGGAAGAGAGAAT+AGG - chr3.2:2672222-2672241 MS.gene058383:intron 45.0%
GAGGATATTGACCCTCCAAA+TGG - chr3.2:2672740-2672759 MS.gene058383:CDS 45.0%
GTGAGCTTAACTCAGTTGGT+AGG + chr3.2:2671800-2671819 None:intergenic 45.0%
GTTCCATGTAGCCATTTGGA+GGG + chr3.2:2672754-2672773 None:intergenic 45.0%
TGTTCCATGTAGCCATTTGG+AGG + chr3.2:2672755-2672774 None:intergenic 45.0%
! GGTGAGCTCAGTACTGAAAT+TGG - chr3.2:2671216-2671235 MS.gene058383:CDS 45.0%
!! ATAAAAAATTATGAATTATT+TGG - chr3.2:2672009-2672028 MS.gene058383:intron 5.0%
!! ATAATATTCATAAAAATAAT+AGG - chr3.2:2672382-2672401 MS.gene058383:intron 5.0%
!! TAAAAAATTATGAATTATTT+GGG - chr3.2:2672010-2672029 MS.gene058383:intron 5.0%
!!! ATTGAATAATAAATATTTTA+AGG + chr3.2:2672105-2672124 None:intergenic 5.0%
!!! ATTTTTATGAATATTATAAA+TGG + chr3.2:2672379-2672398 None:intergenic 5.0%
ATGGCACTGCTGCTGCTAAA+TGG - chr3.2:2672693-2672712 MS.gene058383:CDS 50.0%
GGTAGGGACAATGTAAACCC+CGG + chr3.2:2671783-2671802 None:intergenic 50.0%
TGACCCTCCAAATGGCTACA+TGG - chr3.2:2672748-2672767 MS.gene058383:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 2671204 2672835 2671204 ID=MS.gene058383
chr3.2 mRNA 2671204 2672835 2671204 ID=MS.gene058383.t1;Parent=MS.gene058383
chr3.2 exon 2672649 2672835 2672649 ID=MS.gene058383.t1.exon1;Parent=MS.gene058383.t1
chr3.2 CDS 2672649 2672835 2672649 ID=cds.MS.gene058383.t1;Parent=MS.gene058383.t1
chr3.2 exon 2671481 2671488 2671481 ID=MS.gene058383.t1.exon2;Parent=MS.gene058383.t1
chr3.2 CDS 2671481 2671488 2671481 ID=cds.MS.gene058383.t1;Parent=MS.gene058383.t1
chr3.2 exon 2671204 2671416 2671204 ID=MS.gene058383.t1.exon3;Parent=MS.gene058383.t1
chr3.2 CDS 2671204 2671416 2671204 ID=cds.MS.gene058383.t1;Parent=MS.gene058383.t1
Gene Sequence

>MS.gene058383

ATGGTGCTCTGTGGTGAGCTCAGTACTGAAATTGGAATCAAAACACCCTCTGACAAGTTCTACAATCTGTTCATAACAGAACTTCATGAAGTGCAAAACCTTTGTGAAAGAGTTCATCATACCAAACTTCATGAAGGTGAAGACTGGCATCACAGTGATTCAGTTAAACACTGGACTTATGTCATAGGTAATTATGTTTCTAATTCAATTAACTTGCCAACCAAATCATCTTATTATTTTACTTGGATTTTTCTATCATTAAGTTTGTTTGAAGTTTCCTTAAAACAAAAATGTTGATCATTTTTAATTGGTTTATGTGTGATTTTCGTCTAATACAAATATATTTTCTCTATTTAAATGTTCTATCATTTTTTTATTTGAATGTTTGCTTTGGTAGTTCAAAAAATAATTCAAGTAATAAATAATCAATATAATTAACTACACACAAAAGACCACCTACATAGGCAAAATGTTACCAAAACTCTTTATATAGACCAAAAATAAAAAAATCTAAAAGCAAAAGCAAACTAGATAAATACTGAGATATTAATTAGCAAGTTTTATTTTTTTTGGTGACCGGGGTTTACATTGTCCCTACCAACTGAGTTAAGCTCACAAGGACAATTTTAGCAAGTTTTAAGTACAATGTTAAAAATAATTTGATAGATTTAATTTGTAAATATTGTTAATATAGATTATGAGATCTCAAAATATATTCTATAAATAAAAAGTAATGAAAAGAACTATATAACAATTATGAATTATTTACTGCCATTCAAAAAAAAATATGAATCATTTACTGTAAATAAAAAATTATGAATTATTTGGGAGATTAAAATTAATCATATAAAGAATAACCCTTTTTTTTTTGACAAATATAAAGAATAACCGTTGTTTACCTTAAAATATTTATTATTCAATTTTTTGTTTGGAAAATTATTTATTAGAAAAAAGAAAACAATATAATTGTTATAAAACTCATAGAATAATAATTAATAAGAATAGAGAGAAGAAGAGAGAAGGAGAGGAAGAGAGAATAGGGCATTCTATTATTCTCATATGTGCACAAGTATGTTACATGTAAACTTTATTTATAGAGACAGACAATAACTTATGGAACAAGCCTAATAGTCTAGTAGTATGGTTCATTAACCTATTTGCTACATGGACATCCATTTATAATATTCATAAAAATAATAGGTTATTTTTTGGTCAAAAAAAATAATAGGTTATTTGTAGAAAAAAAAGGCTTGCATTTTTCTATAGTTATTTTTACAAGTGCATTTTTCTATAGTTGTTTTCATTTTTATCTGTATTAATTGCCCGTGCCATCATAATTCATAACAGATGGCAAGGTACACACATGTCATGAGAGTGTTGAAGAAGTTGATGAACTGAACAAAAAAAAACACTTATAAGTTCTTCGGTGGAGATATTGATGAGCACTATAAGGTCTTTAAGCTCATTCTTGAAGTAATTGATAAGAGTGATGGCACTGCTGCTGCTAAATGGACTATTGAATATGAAAAGATCAATGAGGATATTGACCCTCCAAATGGCTACATGGAACATTTTGGCAAATGCACTCGAGATATTGATGCTTATCTAGCCAAGGAAAAGATAGCTCTATAA
Protein sequence

>MS.gene058383.t1

MVLCGELSTEIGIKTPSDKFYNLFITELHEVQNLCERVHHTKLHEGEDWHHSDSVKHWTYVIDGKFFGGDIDEHYKVFKLILEVIDKSDGTAAAKWTIEYEKINEDIDPPNGYMEHFGKCTRDIDAYLAKEKIAL