AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70428


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70428.t1 MTR_3g083080 42.073 164 73 5 6 152 30 188 4.61e-26 99.0
MS.gene70428.t1 MTR_3g082420 36.527 167 88 6 3 152 39 204 4.37e-24 94.4
MS.gene70428.t1 MTR_3g080680 40.000 180 77 7 1 152 5 181 8.42e-24 92.8
MS.gene70428.t1 MTR_3g083030 40.462 173 77 7 2 155 49 214 3.55e-22 89.4
MS.gene70428.t1 MTR_3g082340 34.524 168 90 6 4 152 39 205 3.17e-20 84.3
MS.gene70428.t1 MTR_3g083050 39.623 159 72 6 13 155 41 191 5.01e-20 83.2
MS.gene70428.t1 MTR_4g055800 34.706 170 83 6 11 164 127 284 1.13e-18 81.3
MS.gene70428.t1 MTR_8g461300 38.068 176 72 9 2 150 14 179 2.92e-17 75.9
MS.gene70428.t1 MTR_3g083150 39.252 107 57 4 50 151 91 194 2.59e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGTATTATATCACCTTTC+AGG 0.222077 3.1:-66148359 MS.gene70428:CDS
TGCGGTTGTGGTCCCAATTC+AGG 0.229825 3.1:+66148904 None:intergenic
AAGATCTTCGGTTAAGTTAA+TGG 0.250637 3.1:+66148592 None:intergenic
CAAAATGTTGAAACCTGAAT+TGG 0.269249 3.1:-66148917 None:intergenic
TCGTATTTCGATTGCGGTTG+TGG 0.305044 3.1:+66148892 None:intergenic
GCTATCGTGGAGTACGGATA+TGG 0.366721 3.1:-66146970 MS.gene70428:CDS
GTCAGCAATTAGTTCATCTA+TGG 0.376229 3.1:+66148789 None:intergenic
AGATCTTCGGTTAAGTTAAT+GGG 0.384715 3.1:+66148593 None:intergenic
CCATGCTATAACAACTTTCC+AGG 0.403448 3.1:-66148308 MS.gene70428:CDS
GTACGACGATGACGACTTTG+CGG 0.444713 3.1:-66148824 MS.gene70428:CDS
ACTGCTGTTGCCTGTGGTGG+TGG 0.453533 3.1:-66148385 MS.gene70428:CDS
AAAATGTTGAAACCTGAATT+GGG 0.454585 3.1:-66148916 MS.gene70428:CDS
GAATTACAATCAAAATAATC+AGG 0.466466 3.1:-66148531 MS.gene70428:intron
CCACATAACTCTAGAACGGC+TGG 0.510258 3.1:+66148626 None:intergenic
AAAGTCGTCATCGTCGTACA+TGG 0.527955 3.1:+66148828 None:intergenic
GAGAGTAGGACGAAGATCTT+CGG 0.537282 3.1:+66148580 None:intergenic
ACCACTGCTGTTGCCTGTGG+TGG 0.537702 3.1:-66148388 MS.gene70428:CDS
CATCATCCCATACTTCGGCC+TGG 0.538029 3.1:+66148290 None:intergenic
TCCGAATCGTATTTCGATTG+CGG 0.541557 3.1:+66148886 None:intergenic
ATTCAGGCTATCGTGGAGTA+CGG 0.559342 3.1:-66146976 MS.gene70428:intron
AGTTGTTATAGCATGGCTGT+TGG 0.561797 3.1:+66148315 None:intergenic
GTTATAGCATGGCTGTTGGA+AGG 0.561860 3.1:+66148319 None:intergenic
TCAGAGAGAGTAACGAGAGT+AGG 0.562238 3.1:+66148566 None:intergenic
ATACAAATCACCACCACCAC+AGG 0.565336 3.1:+66148375 None:intergenic
ACCGCAATCGAAATACGATT+CGG 0.566744 3.1:-66148887 MS.gene70428:CDS
CGACTTTGCGGAAGAGAGAG+AGG 0.588174 3.1:-66148812 MS.gene70428:CDS
CCTGGAAAGTTGTTATAGCA+TGG 0.593345 3.1:+66148308 None:intergenic
TGTACCACTGCTGTTGCCTG+TGG 0.600572 3.1:-66148391 MS.gene70428:CDS
CAGCAGTGGTACACTTGACA+AGG 0.618690 3.1:+66148401 None:intergenic
CCAGCCGTTCTAGAGTTATG+TGG 0.626689 3.1:-66148626 MS.gene70428:CDS
ACAGCCACATAACTCTAGAA+CGG 0.642024 3.1:+66148622 None:intergenic
ACCACCACAGGCAACAGCAG+TGG 0.646579 3.1:+66148387 None:intergenic
GGATGATAGATAGCATCGAA+CGG 0.667704 3.1:+66148647 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATCAAATACAATTTCAT+AGG + chr3.1:66147702-66147721 None:intergenic 15.0%
!! AATTGTTCTTCTTAATTATT+AGG - chr3.1:66147388-66147407 MS.gene70428:intron 15.0%
!! AATTTCATGAAGAAATAAAA+TGG + chr3.1:66147746-66147765 None:intergenic 15.0%
!! ATTGTTCTTCTTAATTATTA+GGG - chr3.1:66147389-66147408 MS.gene70428:intron 15.0%
!! AAAAATTAAACATGTAAGGA+TGG + chr3.1:66147641-66147660 None:intergenic 20.0%
!! CAAGAAAAATTAAACATGTA+AGG + chr3.1:66147645-66147664 None:intergenic 20.0%
!! GAATTACAATCAAAATAATC+AGG - chr3.1:66147303-66147322 MS.gene70428:intron 20.0%
!!! CTTACATGTTTAATTTTTCT+TGG - chr3.1:66147643-66147662 MS.gene70428:intron 20.0%
! CCATATAGATAATCAGAATT+CGG - chr3.1:66148202-66148221 MS.gene70428:intron 25.0%
! GAATATAAAAGTGATAGAAC+TGG + chr3.1:66148842-66148861 None:intergenic 25.0%
! GAGATAAGTTACAATGAATA+AGG + chr3.1:66148695-66148714 None:intergenic 25.0%
! GATTTATTACAACAAACTCT+GGG + chr3.1:66148786-66148805 None:intergenic 25.0%
! GGAAATACTGTAATAGAATA+AGG + chr3.1:66148674-66148693 None:intergenic 25.0%
! TAAAATCTAATACACTACCT+TGG - chr3.1:66147604-66147623 MS.gene70428:intron 25.0%
! TGATTTATTACAACAAACTC+TGG + chr3.1:66148787-66148806 None:intergenic 25.0%
! TTCATTGTAACTTATCTCTA+TGG - chr3.1:66148697-66148716 MS.gene70428:intron 25.0%
! TTTGTATTATATCACCTTTC+AGG - chr3.1:66147475-66147494 MS.gene70428:intron 25.0%
!! ACAAGAACTAATGGTAATTT+TGG + chr3.1:66148646-66148665 None:intergenic 25.0%
!! ACTGTGTTTTTCTCTTTATT+TGG - chr3.1:66147870-66147889 MS.gene70428:intron 25.0%
!! AGAATAAACCATAAAGCATT+TGG - chr3.1:66148381-66148400 MS.gene70428:CDS 25.0%
!! CTTATATTCCTTTTAGCAAT+GGG + chr3.1:66148363-66148382 None:intergenic 25.0%
!! GGTAGTGTATTAGATTTTAA+TGG + chr3.1:66147603-66147622 None:intergenic 25.0%
!! TCTCTCTTTTTCTCTTAATT+GGG - chr3.1:66148482-66148501 MS.gene70428:intron 25.0%
!! TCTTATATTCCTTTTAGCAA+TGG + chr3.1:66148364-66148383 None:intergenic 25.0%
!! TTGCTTTAACACTGAATTTT+TGG - chr3.1:66148099-66148118 MS.gene70428:intron 25.0%
!! TTTGTTTGTTGGAAATACTT+TGG - chr3.1:66147828-66147847 MS.gene70428:intron 25.0%
!!! AAATCATATTTTAGGAATGG+AGG + chr3.1:66148606-66148625 None:intergenic 25.0%
!!! AGGAAATCATATTTTAGGAA+TGG + chr3.1:66148609-66148628 None:intergenic 25.0%
!!! CTGTGTTTTTCTCTTTATTT+GGG - chr3.1:66147871-66147890 MS.gene70428:intron 25.0%
!!! GTTCTATCACTTTTATATTC+AGG - chr3.1:66148842-66148861 MS.gene70428:CDS 25.0%
!!! GTTTGTTGTAATAAATCAGA+AGG - chr3.1:66148789-66148808 MS.gene70428:CDS 25.0%
!!! TGTGTTTTTCTCTTTATTTG+GGG - chr3.1:66147872-66147891 MS.gene70428:intron 25.0%
AAGATCTTCGGTTAAGTTAA+TGG + chr3.1:66147245-66147264 None:intergenic 30.0%
AAGCATTACCAAATGCTTTA+TGG + chr3.1:66148392-66148411 None:intergenic 30.0%
ACATATCACAAATGTCTACA+GGG - chr3.1:66148412-66148431 MS.gene70428:CDS 30.0%
AGATCTTCGGTTAAGTTAAT+GGG + chr3.1:66147244-66147263 None:intergenic 30.0%
AGATTTATCAGAACAAACTC+TGG + chr3.1:66148736-66148755 None:intergenic 30.0%
ATAGATAGATTCGTACACTT+AGG + chr3.1:66147091-66147110 None:intergenic 30.0%
ATATTGCTACCGAATAAAAC+TGG + chr3.1:66148243-66148262 None:intergenic 30.0%
CCGAATTCTGATTATCTATA+TGG + chr3.1:66148205-66148224 None:intergenic 30.0%
CTTGTAATAAAAACAGGTTC+TGG + chr3.1:66147988-66148007 None:intergenic 30.0%
GATTTATCAGAACAAACTCT+GGG + chr3.1:66148735-66148754 None:intergenic 30.0%
GGATGGAATTATTATTACCA+AGG + chr3.1:66147624-66147643 None:intergenic 30.0%
GTAATAGTGTCTTATCACAA+GGG + chr3.1:66147924-66147943 None:intergenic 30.0%
TACATATCACAAATGTCTAC+AGG - chr3.1:66148411-66148430 MS.gene70428:CDS 30.0%
TCCTTGCTTGTAATAAAAAC+AGG + chr3.1:66147994-66148013 None:intergenic 30.0%
TCTTGGTTAATCAATCTTCT+TGG - chr3.1:66147660-66147679 MS.gene70428:intron 30.0%
TGATAACTGAACTTGTATCA+GGG - chr3.1:66148278-66148297 MS.gene70428:intron 30.0%
TTTGGCAAATCAAATTGTTG+TGG - chr3.1:66148117-66148136 MS.gene70428:intron 30.0%
TTTGTTGGAAATACTTTGGA+TGG - chr3.1:66147832-66147851 MS.gene70428:intron 30.0%
! CTCTCTCTTTTTCTCTTAAT+TGG - chr3.1:66148481-66148500 MS.gene70428:intron 30.0%
! TCAAACTAGACTTTGTTTGT+TGG - chr3.1:66147817-66147836 MS.gene70428:intron 30.0%
! TGCTGAGGAAATCATATTTT+AGG + chr3.1:66148614-66148633 None:intergenic 30.0%
! TTGATAACTGAACTTGTATC+AGG - chr3.1:66148277-66148296 MS.gene70428:intron 30.0%
!! TAGCAAGTTTTAGCAATGAT+AGG + chr3.1:66147953-66147972 None:intergenic 30.0%
!!! ACCTGTTTTTATTACAAGCA+AGG - chr3.1:66147990-66148009 MS.gene70428:intron 30.0%
!!! TGCAAATCACCAGTTTTATT+CGG - chr3.1:66148231-66148250 MS.gene70428:intron 30.0%
AAAAGAATCATGTTGCAGTC+TGG - chr3.1:66148050-66148069 MS.gene70428:intron 35.0%
AAGGATAGCACAAGAACTAA+TGG + chr3.1:66148655-66148674 None:intergenic 35.0%
ACAAAGGCAGTATCAAATCT+AGG + chr3.1:66148446-66148465 None:intergenic 35.0%
ATCATCATCATCCCATACTT+CGG + chr3.1:66147552-66147571 None:intergenic 35.0%
CGTAATAGTGTCTTATCACA+AGG + chr3.1:66147925-66147944 None:intergenic 35.0%
GACCTGATATCAAACTACAA+AGG + chr3.1:66148462-66148481 None:intergenic 35.0%
GTCAGCAATTAGTTCATCTA+TGG + chr3.1:66147048-66147067 None:intergenic 35.0%
TAATTGGGCTTTCTTAGTGT+TGG - chr3.1:66148497-66148516 MS.gene70428:intron 35.0%
TGCCTTTGTAGTTTGATATC+AGG - chr3.1:66148457-66148476 MS.gene70428:intron 35.0%
TTTCTTTAGCAGTTGTGAGA+TGG + chr3.1:66148159-66148178 None:intergenic 35.0%
! CTTTTATATTCAGGCTATCG+TGG - chr3.1:66148851-66148870 MS.gene70428:CDS 35.0%
ACCGCAATCGAAATACGATT+CGG - chr3.1:66146947-66146966 MS.gene70428:CDS 40.0%
AGACGTAACCCATTGCTAAA+AGG - chr3.1:66148352-66148371 MS.gene70428:CDS 40.0%
AGTTGTTATAGCATGGCTGT+TGG + chr3.1:66147522-66147541 None:intergenic 40.0%
CCATGCTATAACAACTTTCC+AGG - chr3.1:66147526-66147545 MS.gene70428:intron 40.0%
CCTGGAAAGTTGTTATAGCA+TGG + chr3.1:66147529-66147548 None:intergenic 40.0%
CTAAAGAAAATGTTGCGCAG+GGG - chr3.1:66148170-66148189 MS.gene70428:intron 40.0%
GCTAAAGAAAATGTTGCGCA+GGG - chr3.1:66148169-66148188 MS.gene70428:intron 40.0%
TCCGAATCGTATTTCGATTG+CGG + chr3.1:66146951-66146970 None:intergenic 40.0%
TGCTAAAGAAAATGTTGCGC+AGG - chr3.1:66148168-66148187 MS.gene70428:intron 40.0%
! ACAGCCACATAACTCTAGAA+CGG + chr3.1:66147215-66147234 None:intergenic 40.0%
! GGATGATAGATAGCATCGAA+CGG + chr3.1:66147190-66147209 None:intergenic 40.0%
!! TTCTTCTGCTTTTGCCTGAA+AGG + chr3.1:66147492-66147511 None:intergenic 40.0%
AAAATGTTGCGCAGGGGATT+AGG - chr3.1:66148176-66148195 MS.gene70428:intron 45.0%
AAAGTCGTCATCGTCGTACA+TGG + chr3.1:66147009-66147028 None:intergenic 45.0%
AACTTTCCAGGCCGAAGTAT+GGG - chr3.1:66147538-66147557 MS.gene70428:intron 45.0%
ATACAAATCACCACCACCAC+AGG + chr3.1:66147462-66147481 None:intergenic 45.0%
ATTCAGGCTATCGTGGAGTA+CGG - chr3.1:66148858-66148877 MS.gene70428:CDS 45.0%
GAGAGTAGGACGAAGATCTT+CGG + chr3.1:66147257-66147276 None:intergenic 45.0%
GTTATAGCATGGCTGTTGGA+AGG + chr3.1:66147518-66147537 None:intergenic 45.0%
TCAGAGAGAGTAACGAGAGT+AGG + chr3.1:66147271-66147290 None:intergenic 45.0%
TCGTATTTCGATTGCGGTTG+TGG + chr3.1:66146945-66146964 None:intergenic 45.0%
! TGATGATGATGATGCTGACG+AGG - chr3.1:66147565-66147584 MS.gene70428:intron 45.0%
!!! TTTTGGCTTCAGAGTTGCTG+AGG + chr3.1:66148629-66148648 None:intergenic 45.0%
CAACTTTCCAGGCCGAAGTA+TGG - chr3.1:66147537-66147556 MS.gene70428:intron 50.0%
CAGCAGTGGTACACTTGACA+AGG + chr3.1:66147436-66147455 None:intergenic 50.0%
GCTATCGTGGAGTACGGATA+TGG - chr3.1:66148864-66148883 MS.gene70428:CDS 50.0%
GTACGACGATGACGACTTTG+CGG - chr3.1:66147010-66147029 MS.gene70428:intron 50.0%
!! CCACATAACTCTAGAACGGC+TGG + chr3.1:66147211-66147230 None:intergenic 50.0%
!! CCAGCCGTTCTAGAGTTATG+TGG - chr3.1:66147208-66147227 MS.gene70428:intron 50.0%
CATCATCCCATACTTCGGCC+TGG + chr3.1:66147547-66147566 None:intergenic 55.0%
CGACTTTGCGGAAGAGAGAG+AGG - chr3.1:66147022-66147041 MS.gene70428:intron 55.0%
TGCGGTTGTGGTCCCAATTC+AGG + chr3.1:66146933-66146952 None:intergenic 55.0%
TGTACCACTGCTGTTGCCTG+TGG - chr3.1:66147443-66147462 MS.gene70428:intron 55.0%
ACCACCACAGGCAACAGCAG+TGG + chr3.1:66147450-66147469 None:intergenic 60.0%
ACCACTGCTGTTGCCTGTGG+TGG - chr3.1:66147446-66147465 MS.gene70428:intron 60.0%
ACTGCTGTTGCCTGTGGTGG+TGG - chr3.1:66147449-66147468 MS.gene70428:intron 60.0%
! AACAGGTTCTGGCGCTGCTG+AGG + chr3.1:66147977-66147996 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 66146921 66148935 66146921 ID=MS.gene70428
chr3.1 mRNA 66146921 66148935 66146921 ID=MS.gene70428.t1;Parent=MS.gene70428
chr3.1 exon 66148762 66148935 66148762 ID=MS.gene70428.t1.exon1;Parent=MS.gene70428.t1
chr3.1 CDS 66148762 66148935 66148762 ID=cds.MS.gene70428.t1;Parent=MS.gene70428.t1
chr3.1 exon 66148532 66148669 66148532 ID=MS.gene70428.t1.exon2;Parent=MS.gene70428.t1
chr3.1 CDS 66148532 66148669 66148532 ID=cds.MS.gene70428.t1;Parent=MS.gene70428.t1
chr3.1 exon 66148303 66148446 66148303 ID=MS.gene70428.t1.exon3;Parent=MS.gene70428.t1
chr3.1 CDS 66148303 66148446 66148303 ID=cds.MS.gene70428.t1;Parent=MS.gene70428.t1
chr3.1 exon 66146921 66146992 66146921 ID=MS.gene70428.t1.exon4;Parent=MS.gene70428.t1
chr3.1 CDS 66146921 66146992 66146921 ID=cds.MS.gene70428.t1;Parent=MS.gene70428.t1
Gene Sequence

>MS.gene70428

ATGTTGAAACCTGAATTGGGACCACAACCGCAATCGAAATACGATTCGGAGTACGACGACGATGACGACTTTGCGAAATGCTTCTCCATGTACGACGATGACGACTTTGCGGAAGAGAGAGAGGCCATAGATGAACTAATTGCTGACTATACAGAGAAGTCTTGCAACCTAAGTGTACGAATCTATCTATCTATCTATTTCAATTTATTTTTAATTTTATCATGTTTCGCTCACTCTACTAATTTTGATGATTCTGTACAACACAGCCGTTCGATGCTATCTATCATCCAGCCGTTCTAGAGTTATGTGGCTGTGTCGTACCCATTAACTTAACCGAAGATCTTCGTCCTACTCTCGTTACTCTCTCTGAGCTTGCTTTGAAGAATTACAATCAAAATAATCAGGTACGTTACAGTGTTATATGTTATATGCTGTTTATTCAATTATTCATCAACTAAACTGATAATAATTGTTCTTCTTAATTATTAGGGTACAAGTTTTGTGTTTCATGACCTTGTCAAGTGTACCACTGCTGTTGCCTGTGGTGGTGGTGATTTGTATTATATCACCTTTCAGGCAAAAGCAGAAGAAGATCCTTCCAACAGCCATGCTATAACAACTTTCCAGGCCGAAGTATGGGATGATGATGATGATGATGCTGACGAGGTCATATCGTGTGCCATTAAAATCTAATACACTACCTTGGTAATAATAATTCCATCCTTACATGTTTAATTTTTCTTGGTTAATCAATCTTCTTGGAGATTAGTTTATAGTTCCTATGAAATTGTATTTGATTTTGATATTTATAACAAGCTTCAACCATTTTATTTCTTCATGAAATTCACAATTATGAAAACTTGAAGTTTTTTGTTCAATCATTTCTTGCTTTACTTTCAAACTAGACTTTGTTTGTTGGAAATACTTTGGATGGTGATAAATGAAAGAAACTGTGTTTTTCTCTTTATTTGGGGCTTTCTTCATGTTGTTAGATTTTTTTCCCTTGTGATAAGACACTATTACGTATTACCTATCATTGCTAAAACTTGCTATCCTCAGCAGCGCCAGAACCTGTTTTTATTACAAGCAAGGAAAGAAATTTTTATTTGCTTTGCTGTTTGTACGTTGAAAAAGAATCATGTTGCAGTCTGGTTTAAAAAGCTTTAAATTTATATTAGTTGCTTTAACACTGAATTTTTGGCAAATCAAATTGTTGTGGAGTCTGATTTTGTTAGCCATCTCACAACTGCTAAAGAAAATGTTGCGCAGGGGATTAGGTGACCATATAGATAATCAGAATTCGGTCAATATGCAAATCACCAGTTTTATTCGGTAGCAATATTACTATGCACATAATTGATAACTGAACTTGTATCAGGGTTTTAGTGTTAAGTTGATGTACTCACAGTAGTTAGACATATAGTACATTACAGACGTAACCCATTGCTAAAAGGAATATAAGAATAAACCATAAAGCATTTGGTAATGCTTACATATCACAAATGTCTACAGGGTGAACAGTCCTAGATTTGATACTGCCTTTGTAGTTTGATATCAGGTCTCTCTCTTTTTCTCTTAATTGGGCTTTCTTAGTGTTGGTAGACGTTGCACTGTAGTTAGACGCTGTTATAACTTATAACTTGTATGTTTGAATAATGTTGATATCTTGAAATATAATTTAACCTCCATTCCTAAAATATGATTTCCTCAGCAACTCTGAAGCCAAAATTACCATTAGTTCTTGTGCTATCCTTATTCTATTACAGTATTTCCTTATTCATTGTAACTTATCTCTATGGAAAGATAAATTTCCCAGAGTTTGTTCTGATAAATCTATCTTATCATGTTCGAAAGATAAATTTCCCAGAGTTTGTTGTAATAAATCAGAAGGATTATTCTAGTAATTAGCTATATCTGACCAGTTCTATCACTTTTATATTCAGGCTATCGTGGAGTACGGATATGGATTAGTTGCAGTCAGATTTTCATACAGTCAGTTCAGTCATATAGTCTGA

Protein sequence

>MS.gene70428.t1

MLKPELGPQPQSKYDSEYDDDDDFAKCFSMYDDDDFAEEREAIDELIADYTEKSCNLSPFDAIYHPAVLELCGCVVPINLTEDLRPTLVTLSELALKNYNQNNQGTSFVFHDLVKCTTAVACGGGDLYYITFQAKAEEDPSNSHAITTFQAEAIVEYGYGLVAVRFSYSQFSHIV