AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene22160

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene22160.t1 MTR_3g046760 90.076 131 13 0 15 145 25 155 1.70e-74 223
MS.gene22160.t1 MTR_4g096780 53.659 123 54 2 26 145 29 151 1.21e-35 124
MS.gene22160.t1 MTR_4g096780 53.659 123 54 2 26 145 29 151 4.26e-35 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene22160.t1 AT4G18260 54.717 106 47 1 41 145 52 157 8.90e-36 125
MS.gene22160.t1 AT2G30890 53.774 106 48 1 41 145 44 149 1.14e-35 124

Find 29 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATTAGGGGTTGCACTTTA+TGG 0.214906 3.4:+41816381 MS.gene22160:CDS
CTTTCTCCTTTGGGCTTCAA+TGG 0.240506 3.4:+41815187 MS.gene22160:CDS
ACAATAATCATCAAAGATTA+GGG 0.240819 3.4:+41816367 MS.gene22160:CDS
CATTACATGGCTTTCTCCTT+TGG 0.245393 3.4:+41815177 MS.gene22160:CDS
TTGCACTTTATGGTGTTATC+TGG 0.283526 3.4:+41816391 MS.gene22160:CDS
ATTACATGGCTTTCTCCTTT+GGG 0.302177 3.4:+41815178 MS.gene22160:CDS
AACAATAATCATCAAAGATT+AGG 0.323426 3.4:+41816366 MS.gene22160:CDS
AAACAATGACAACCACATTA+AGG 0.332306 3.4:+41814876 MS.gene22160:CDS
ATGGGATTCTTGATGCCTAT+TGG 0.346223 3.4:+41815206 MS.gene22160:CDS
GTAATTTCAAATTGAAGTCT+TGG 0.346934 3.4:-41815155 None:intergenic
ATGAATTGGTGTCGTATTAG+TGG 0.368785 3.4:-41814231 None:intergenic
CAATTTGAAATTACATTACA+TGG 0.377562 3.4:+41815164 MS.gene22160:CDS
TTTCTCCTTTGGGCTTCAAT+GGG 0.382298 3.4:+41815188 MS.gene22160:CDS
TCAAATATAGTTATATGAAT+TGG 0.387261 3.4:-41814245 None:intergenic
CTAATTGCAAGTATACCAAT+AGG 0.464337 3.4:-41815221 None:intergenic
TAGTTCATCACAAGAGCAAA+AGG 0.487022 3.4:+41814831 MS.gene22160:intron
GCTGTACTTCTTGCAACAGC+AGG 0.522233 3.4:+41816306 MS.gene22160:CDS
ATCTGGCTGCAAGTCCTAGT+TGG 0.526574 3.4:+41816408 MS.gene22160:CDS
AATAAAATTCTAAGCCACCT+TGG 0.535910 3.4:-41815266 None:intergenic
TGAATTGGTGTCGTATTAGT+GGG 0.537054 3.4:-41814230 None:intergenic
TTTGATGATTATTGTTGAAG+AGG 0.545214 3.4:-41816359 None:intergenic
TCAAATTTGATACCTTAATG+TGG 0.572931 3.4:-41814888 None:intergenic
CAAATAGAGAGGAGAATCCA+AGG 0.604953 3.4:+41815249 MS.gene22160:CDS
AATTAGATTATCAAATAGAG+AGG 0.630071 3.4:+41815238 MS.gene22160:CDS
AGAATCCCATTGAAGCCCAA+AGG 0.642048 3.4:-41815193 None:intergenic
GTGGTCGAATGATACCAACT+AGG 0.678006 3.4:-41816422 None:intergenic
TTGGTATCATTCGACCACGA+AGG 0.697962 3.4:+41816427 MS.gene22160:CDS
CAATAATCATCAAAGATTAG+GGG 0.720596 3.4:+41816368 MS.gene22160:CDS
ATAGAGAGGAGAATCCAAGG+TGG 0.833273 3.4:+41815252 MS.gene22160:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAATATTTAAATATAAT+TGG - chr3.4:41815418-41815437 None:intergenic 0.0%
!!! TATTAATTTAACACTTATTT+TGG - chr3.4:41815450-41815469 None:intergenic 10.0%
!!! TTAAATAATAATCTTTTTGA+TGG + chr3.4:41816010-41816029 MS.gene22160:intron 10.0%
!! AATTATAATCTTTGTCAAAA+AGG - chr3.4:41815961-41815980 None:intergenic 15.0%
!! GAATAAATTAACTAAAAATG+TGG - chr3.4:41815893-41815912 None:intergenic 15.0%
!! TCAAATATAGTTATATGAAT+TGG - chr3.4:41814248-41814267 None:intergenic 15.0%
!! TTCTTAATGAAAAAAAATTG+AGG - chr3.4:41815083-41815102 None:intergenic 15.0%
!!! TAAGATGTTTTTTCTAATTT+TGG + chr3.4:41814336-41814355 MS.gene22160:intron 15.0%
!! AAAATATTGATAGATCCAAA+TGG - chr3.4:41815782-41815801 None:intergenic 20.0%
!! AAATATTGATAGATCCAAAT+GGG - chr3.4:41815781-41815800 None:intergenic 20.0%
!! AACAATAATCATCAAAGATT+AGG + chr3.4:41816366-41816385 MS.gene22160:CDS 20.0%
!! AATTAGATTATCAAATAGAG+AGG + chr3.4:41815238-41815257 MS.gene22160:CDS 20.0%
!! ACAATAATCATCAAAGATTA+GGG + chr3.4:41816367-41816386 MS.gene22160:CDS 20.0%
!! AGATTATAATTGATACTTTG+AGG + chr3.4:41815970-41815989 MS.gene22160:intron 20.0%
!! ATTTGAGTATTTGAATATGT+CGG - chr3.4:41814372-41814391 None:intergenic 20.0%
!! TAATGAAAAAAAATTGAGGA+AGG - chr3.4:41815079-41815098 None:intergenic 20.0%
!! TACATAAATAGGTCAATTAA+AGG - chr3.4:41815717-41815736 None:intergenic 20.0%
!! TTACTAATAAGATCATGTAA+TGG + chr3.4:41815926-41815945 MS.gene22160:intron 20.0%
!!! ACTAAAGTATAAAGTATCTT+AGG + chr3.4:41815666-41815685 MS.gene22160:intron 20.0%
!!! AGTTTGTCTTTTTAATATCA+AGG + chr3.4:41814982-41815001 MS.gene22160:intron 20.0%
!!! CAATTTGAAATTACATTACA+TGG + chr3.4:41815164-41815183 MS.gene22160:CDS 20.0%
!!! GTTTGTCTTTTTAATATCAA+GGG + chr3.4:41814983-41815002 MS.gene22160:intron 20.0%
! AATATTGATAGATCCAAATG+GGG - chr3.4:41815780-41815799 None:intergenic 25.0%
! ATCTTCCATATTGAAGATTA+AGG - chr3.4:41814931-41814950 None:intergenic 25.0%
! CAATAATCATCAAAGATTAG+GGG + chr3.4:41816368-41816387 MS.gene22160:CDS 25.0%
! CTATTTATGTAATAAAGCAG+TGG + chr3.4:41815726-41815745 MS.gene22160:intron 25.0%
! GTAATTTCAAATTGAAGTCT+TGG - chr3.4:41815158-41815177 None:intergenic 25.0%
! TATTAGTAACTAACAAGCTT+TGG - chr3.4:41815915-41815934 None:intergenic 25.0%
! TCAAATTTGATACCTTAATG+TGG - chr3.4:41814891-41814910 None:intergenic 25.0%
!! CACTGCTTTATTACATAAAT+AGG - chr3.4:41815728-41815747 None:intergenic 25.0%
!! CTATGTTCATACAATTTTTC+AGG + chr3.4:41815289-41815308 MS.gene22160:CDS 25.0%
!! TTTGATGATTATTGTTGAAG+AGG - chr3.4:41816362-41816381 None:intergenic 25.0%
!!! CATTGGTTAACTTTTAATGA+TGG + chr3.4:41815830-41815849 MS.gene22160:intron 25.0%
!!! GAATTTATTTTGTATTCTGC+TGG + chr3.4:41815368-41815387 MS.gene22160:intron 25.0%
!!! TCTTTTTGATGGTAATATGA+AGG + chr3.4:41816021-41816040 MS.gene22160:intron 25.0%
!!! TTTTGAGTTTCTGTTAAAAC+AGG + chr3.4:41816278-41816297 MS.gene22160:intron 25.0%
AAACAATGACAACCACATTA+AGG + chr3.4:41814876-41814895 MS.gene22160:CDS 30.0%
AAAGACAAACTCTTAGCTAT+AGG - chr3.4:41814973-41814992 None:intergenic 30.0%
AAATCTCCACTAGCATTAAT+TGG + chr3.4:41814699-41814718 MS.gene22160:intron 30.0%
AAGCTGAAATATTTGTCCTT+AGG + chr3.4:41814422-41814441 MS.gene22160:intron 30.0%
AATAAAATTCTAAGCCACCT+TGG - chr3.4:41815269-41815288 None:intergenic 30.0%
AGATCATATGAAAGACATGA+TGG + chr3.4:41814738-41814757 MS.gene22160:intron 30.0%
ATTAAGATCAGTTGTCACAT+TGG + chr3.4:41815813-41815832 MS.gene22160:intron 30.0%
CAAAGAATGAGATCAATATG+AGG - chr3.4:41814489-41814508 None:intergenic 30.0%
CATGTCTTTCATATGATCTT+TGG - chr3.4:41814737-41814756 None:intergenic 30.0%
CTAAATGTAACCACATATGT+CGG + chr3.4:41816127-41816146 MS.gene22160:intron 30.0%
CTAATTGCAAGTATACCAAT+AGG - chr3.4:41815224-41815243 None:intergenic 30.0%
GATCATATGAAAGACATGAT+GGG + chr3.4:41814739-41814758 MS.gene22160:intron 30.0%
TATCTTAGGTAGATATTCTG+TGG + chr3.4:41815680-41815699 MS.gene22160:intron 30.0%
TCTTGCCTTAATCTTCAATA+TGG + chr3.4:41814923-41814942 MS.gene22160:intron 30.0%
TTAATGCTAGTGGAGATTTA+AGG - chr3.4:41814698-41814717 None:intergenic 30.0%
! AACTTTTAATGATGGCATGA+AGG + chr3.4:41815838-41815857 MS.gene22160:intron 30.0%
! AAGAAATGAACTTTGTTTGC+TGG - chr3.4:41814768-41814787 None:intergenic 30.0%
! ACTTTTAATGATGGCATGAA+GGG + chr3.4:41815839-41815858 MS.gene22160:intron 30.0%
! CAAGAGCAAAAGGAAATTTT+AGG + chr3.4:41814841-41814860 MS.gene22160:CDS 30.0%
AAACAAGACATGCTTGAAAG+AGG - chr3.4:41814792-41814811 None:intergenic 35.0%
ATGCTATATTAGTGTGTGAG+AGG - chr3.4:41814583-41814602 None:intergenic 35.0%
ATTACATGGCTTTCTCCTTT+GGG + chr3.4:41815178-41815197 MS.gene22160:CDS 35.0%
CAATCTCCAATTAATGCTAG+TGG - chr3.4:41814708-41814727 None:intergenic 35.0%
GAGAGTTTATTTACCCTTCA+TGG - chr3.4:41814449-41814468 None:intergenic 35.0%
GATTGTCTTGTCACATAGAT+AGG - chr3.4:41815515-41815534 None:intergenic 35.0%
TAGTTCATCACAAGAGCAAA+AGG + chr3.4:41814831-41814850 MS.gene22160:intron 35.0%
TCTTGTGATGAACTAACAAG+TGG - chr3.4:41814826-41814845 None:intergenic 35.0%
TGAGTTTCTGTTAAAACAGG+CGG + chr3.4:41816281-41816300 MS.gene22160:intron 35.0%
TGCTATATTAGTGTGTGAGA+GGG - chr3.4:41814582-41814601 None:intergenic 35.0%
! TAAAGCAGTGGTGAAAGTTT+TGG + chr3.4:41815738-41815757 MS.gene22160:intron 35.0%
!! AATTTTCTTGCTGTCTTCAC+AGG - chr3.4:41816075-41816094 None:intergenic 35.0%
!! ATGAATTGGTGTCGTATTAG+TGG - chr3.4:41814234-41814253 None:intergenic 35.0%
!! CACCTTGAAGAGTACTTTAT+GGG + chr3.4:41814635-41814654 MS.gene22160:intron 35.0%
!! TGAATTGGTGTCGTATTAGT+GGG - chr3.4:41814233-41814252 None:intergenic 35.0%
!! TTGCACTTTATGGTGTTATC+TGG + chr3.4:41816391-41816410 MS.gene22160:CDS 35.0%
AGATTAGGGGTTGCACTTTA+TGG + chr3.4:41816381-41816400 MS.gene22160:CDS 40.0%
ATGGGATTCTTGATGCCTAT+TGG + chr3.4:41815206-41815225 MS.gene22160:CDS 40.0%
ATTTACCCTTCATGGTCCTA+AGG - chr3.4:41814441-41814460 None:intergenic 40.0%
ATTTGTCCTTAGGACCATGA+AGG + chr3.4:41814432-41814451 MS.gene22160:intron 40.0%
CAAATAGAGAGGAGAATCCA+AGG + chr3.4:41815249-41815268 MS.gene22160:CDS 40.0%
CATTACATGGCTTTCTCCTT+TGG + chr3.4:41815177-41815196 MS.gene22160:CDS 40.0%
TTTCTCCTTTGGGCTTCAAT+GGG + chr3.4:41815188-41815207 MS.gene22160:CDS 40.0%
TTTGTCCTTAGGACCATGAA+GGG + chr3.4:41814433-41814452 MS.gene22160:intron 40.0%
! CTCCCATAAAGTACTCTTCA+AGG - chr3.4:41814640-41814659 None:intergenic 40.0%
!! CTTGAAGAGTACTTTATGGG+AGG + chr3.4:41814638-41814657 MS.gene22160:intron 40.0%
!! GCACCTTGAAGAGTACTTTA+TGG + chr3.4:41814634-41814653 MS.gene22160:intron 40.0%
!! GTGGTGAAAGTTTTGGTAGA+TGG + chr3.4:41815745-41815764 MS.gene22160:intron 40.0%
!! GTTTTGGTAGATGGTTACTC+TGG + chr3.4:41815754-41815773 MS.gene22160:intron 40.0%
AGAATCCCATTGAAGCCCAA+AGG - chr3.4:41815196-41815215 None:intergenic 45.0%
ATAGAGAGGAGAATCCAAGG+TGG + chr3.4:41815252-41815271 MS.gene22160:CDS 45.0%
ATGACACACACCGACATATG+TGG - chr3.4:41816140-41816159 None:intergenic 45.0%
CTTTCTCCTTTGGGCTTCAA+TGG + chr3.4:41815187-41815206 MS.gene22160:CDS 45.0%
GTGGTCGAATGATACCAACT+AGG - chr3.4:41816425-41816444 None:intergenic 45.0%
TTGGTATCATTCGACCACGA+AGG + chr3.4:41816427-41816446 MS.gene22160:CDS 45.0%
ATCTGGCTGCAAGTCCTAGT+TGG + chr3.4:41816408-41816427 MS.gene22160:CDS 50.0%
ATGGTTACTCTGGCCCCATT+TGG + chr3.4:41815764-41815783 MS.gene22160:intron 50.0%
GCTGTACTTCTTGCAACAGC+AGG + chr3.4:41816306-41816325 MS.gene22160:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 41814218 41816452 41814218 ID=MS.gene22160
chr3.4 mRNA 41814218 41816452 41814218 ID=MS.gene22160.t1;Parent=MS.gene22160
chr3.4 exon 41814218 41814276 41814218 ID=MS.gene22160.t1.exon1;Parent=MS.gene22160.t1
chr3.4 CDS 41814218 41814276 41814218 ID=cds.MS.gene22160.t1;Parent=MS.gene22160.t1
chr3.4 exon 41814834 41814897 41814834 ID=MS.gene22160.t1.exon2;Parent=MS.gene22160.t1
chr3.4 CDS 41814834 41814897 41814834 ID=cds.MS.gene22160.t1;Parent=MS.gene22160.t1
chr3.4 exon 41815149 41815310 41815149 ID=MS.gene22160.t1.exon3;Parent=MS.gene22160.t1
chr3.4 CDS 41815149 41815310 41815149 ID=cds.MS.gene22160.t1;Parent=MS.gene22160.t1
chr3.4 exon 41816300 41816452 41816300 ID=MS.gene22160.t1.exon4;Parent=MS.gene22160.t1
chr3.4 CDS 41816300 41816452 41816300 ID=cds.MS.gene22160.t1;Parent=MS.gene22160.t1
Gene Sequence

>MS.gene22160

ATGTCGATATCTCCCACTAATACGACACCAATTCATATAACTATATTTGATATCGAAGTGTTAGTGTCATCTTCGTCTGATTGTATTAGTATGTCATAAACTAACAAAACATACATTGTAAGATGTTTTTTCTAATTTTGGATGATAGTGACCGACATATTCAAATACTCAAATGCTGTTTACTCTTGAAAGAAACATAATTCTAAGCTGAAATATTTGTCCTTAGGACCATGAAGGGTAAATAAACTCTCTCATGAGCTTACTCTTACCTCATATTGATCTCATTCTTTGTTGAACTTGTGACAACTATTTAGTCGTTCTCTCTGACAATAAAGATAAGAGTGCTCACTTCTTAGTACAACCCTCTCACACACTAATATAGCATGAGAGAGAGAATGAGAGAGACAAAATGATAAGCACCTTGAAGAGTACTTTATGGGAGGCACATTCAATACTTGAAATGCTCTAGTATTGCAGCCTTAAATCTCCACTAGCATTAATTGGAGATTGTGTTGACCAAAGATCATATGAAAGACATGATGGGAATCCAGCAAACAAAGTTCATTTCTTTCCTCTTTCAAGCATGTCTTGTTTTGTTCTTATTTCCACTTGTTAGTTCATCACAAGAGCAAAAGGAAATTTTAGGCACTAATTCAACAAACAATGACAACCACATTAAGGTATCAAATTTGATTTTCATATTCTTCTTGCCTTAATCTTCAATATGGAAGATGTTCATATTTTTCTCATATCCTATAGCTAAGAGTTTGTCTTTTTAATATCAAGGGACATAGTTGAAATTCTTTTACAAATGATGTAAATTAATTATTAATGTCACTTTAATTAATTATAAATTTTCCTTCCTCAATTTTTTTTCATTAAGAAGTATTGTCTATGAAACTAACATATTTTTATTGTTTCATATATGAAGATGAGTCCAAGACTTCAATTTGAAATTACATTACATGGCTTTCTCCTTTGGGCTTCAATGGGATTCTTGATGCCTATTGGTATACTTGCAATTAGATTATCAAATAGAGAGGAGAATCCAAGGTGGCTTAGAATTTTATTCTATGTTCATACAATTTTTCAGGCAAGTATATTTAAATTAAAGTCTATATATTACTTTATAATTCTTTATCAGATTTAAGAATTTATTTTGTATTCTGCTGGCTGCTTTTTTTTTTTACTTGACATCCAATTATATTTAAATATTTATAGTTCTATCTCCAAAATAAGTGTTAAATTAATAACTTTTTAAAATAGTTCTATCAACTTTTAAGTTTTAAATCTACCTATCTATGTGACAAGACAATCATAAACATTAGTGTTAAAATTTAATTAATACAAATTTCAAAGTTTAATGCATAAGTTTTAAAAATGTCATACAATTAATAAAGAATCATAACTTTGAGAAAGAAAAAAAAGCTAGAGTTAGTGCAGAATAAACTAAAGTATAAAGTATCTTAGGTAGATATTCTGTGGTCATTTTTTAACCTTTAATTGACCTATTTATGTAATAAAGCAGTGGTGAAAGTTTTGGTAGATGGTTACTCTGGCCCCATTTGGATCTATCAATATTTTTTAAATACTTTATTAAGATCAGTTGTCACATTGGTTAACTTTTAATGATGGCATGAAGGGAAGATAAGATCATTAGAGTAGTAAGATTCCACATTTTTAGTTAATTTATTCCAAAGCTTGTTAGTTACTAATAAGATCATGTAATGGTGATTGCTTCCTTTTTGACAAAGATTATAATTGATACTTTGAGGACAAGAAAGACAATTTATTAAATAATAATCTTTTTGATGGTAATATGAAGGTTTTCTTCGTCTCATTTTTGAAGTACAGCCTGTGAAGACAGCAAGAAAATTATTCTGATGATTGTGTTACTTACTATTGATAACTAAATGTAACCACATATGTCGGTGTGTGTCATATACTAAGAGACATATTTAATCTAAAGTTTCAGTGTTGCATATAGAAAATAACTGATTTTTTTTTTTTTAAAACATTTTATTCATTGATTATATTTTCATGTTTAATGTGATGTATAATTTTGAGTTTCTGTTAAAACAGGCGGTTGCTGTACTTCTTGCAACAGCAGGAGCAATCATGTCAATAAAAAATTTCAACAACCTCTTCAACAATAATCATCAAAGATTAGGGGTTGCACTTTATGGTGTTATCTGGCTGCAAGTCCTAGTTGGTATCATTCGACCACGAAGGTAA
Protein sequence

>MS.gene22160.t1

MSISPTNTTPIHITIFDIEVSSQEQKEILGTNSTNNDNHIKMSPRLQFEITLHGFLLWASMGFLMPIGILAIRLSNREENPRWLRILFYVHTIFQAVAVLLATAGAIMSIKNFNNLFNNNHQRLGVALYGVIWLQVLVGIIRPRR