AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene74981

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene74981.t1 MTR_2g029270 100.000 85 0 0 15 99 2 86 1.05e-59 177
MS.gene74981.t1 MTR_1g111970 100.000 85 0 0 15 99 2 86 1.05e-59 177
MS.gene74981.t1 MTR_2g015680 98.824 85 1 0 15 99 2 86 2.40e-59 176
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene74981.t1 AT3G61110 96.471 85 3 0 15 99 2 86 1.07e-58 175
MS.gene74981.t1 AT2G45710 95.181 83 4 0 15 97 2 84 1.01e-55 167
MS.gene74981.t1 AT5G47930 96.386 83 3 0 15 97 2 84 2.73e-55 166
MS.gene74981.t1 AT3G61111 83.529 85 14 0 15 99 2 86 1.29e-48 149
MS.gene74981.t1 AT3G61111 80.488 41 8 0 15 55 2 42 1.07e-17 71.2

Find 31 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTTGCCGCCGGTTGGC+TGG 0.271725 1.3:-75950291 None:intergenic
TCCACAGCCCTCTCAACTTT+GGG 0.311830 1.3:-75949023 None:intergenic
TAACAGAGGGGTGCTCCTTC+AGG 0.320285 1.3:+75950317 MS.gene74981:CDS
ATCTCCTAACTCATTCTTCA+TGG 0.338607 1.3:+75949433 MS.gene74981:CDS
TCAAGAGATCGATGTCGTTT+TGG 0.351397 1.3:-75949358 None:intergenic
TTCCACAGCCCTCTCAACTT+TGG 0.365114 1.3:-75949024 None:intergenic
AATACCATGAAGAATGAGTT+AGG 0.426658 1.3:-75949437 None:intergenic
CTTACATGTTGAAGCATCCT+TGG 0.445045 1.3:-75949570 None:intergenic
AGCCAACCGGCGGCAAAGCA+AGG 0.463038 1.3:+75950293 MS.gene74981:CDS
ACGGTATTGTGCCAGCCAAC+CGG 0.474939 1.3:+75950280 MS.gene74981:CDS
AGCCTTGCTTTGCCGCCGGT+TGG 0.478403 1.3:-75950295 None:intergenic
CACCAGCGGAGCTTGAGAAA+AGG 0.496318 1.3:+75949384 MS.gene74981:CDS
GGGGTGCTCCTTCAGGAAGA+AGG 0.503456 1.3:+75950324 MS.gene74981:CDS
TCTCAAACAGTCGTGGTTTG+CGG 0.511373 1.3:+75950247 MS.gene74981:CDS
TGTTAGCCTTGCTTTGCCGC+CGG 0.526081 1.3:-75950299 None:intergenic
TTATAGGATGTCAAATGCCA+AGG 0.569104 1.3:+75949553 MS.gene74981:intron
GGGTGCTCCTTCAGGAAGAA+GGG 0.579020 1.3:+75950325 MS.gene74981:CDS
GGCAAAGCAAGGCTAACAGA+GGG 0.582316 1.3:+75950304 MS.gene74981:CDS
GATGGGACCCAAAGTTGAGA+GGG 0.597213 1.3:+75949016 None:intergenic
ACCCAAAGTTGAGAGGGCTG+TGG 0.599911 1.3:+75949022 MS.gene74981:CDS
CTAATCACCCTTCTTCCTGA+AGG 0.602303 1.3:-75950332 None:intergenic
AGATGGGACCCAAAGTTGAG+AGG 0.608186 1.3:+75949015 None:intergenic
TAGCCACTCTCAAACAGTCG+TGG 0.620995 1.3:+75950240 MS.gene74981:CDS
GGCTGTGGAATCAAATGTGG+AGG 0.628873 1.3:+75949037 MS.gene74981:CDS
CGGCAAAGCAAGGCTAACAG+AGG 0.648379 1.3:+75950303 MS.gene74981:CDS
GGTTTGCGGCAACTGTCAGA+CGG 0.650064 1.3:+75950261 MS.gene74981:CDS
AAACCACGACTGTTTGAGAG+TGG 0.670924 1.3:-75950243 None:intergenic
GAGGGCTGTGGAATCAAATG+TGG 0.673501 1.3:+75949034 MS.gene74981:CDS
CGATCTCTTGAACCCACCAG+CGG 0.674494 1.3:+75949370 MS.gene74981:CDS
GCAAAGCAAGGCTAACAGAG+GGG 0.682022 1.3:+75950305 MS.gene74981:CDS
GTATTGTGCCAGCCAACCGG+CGG 0.694777 1.3:+75950283 MS.gene74981:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAACAAATTACAAA+CGG - chr1.3:75949509-75949528 None:intergenic 10.0%
!!! TTATTATATTTCTATCATTT+AGG + chr1.3:75949941-75949960 MS.gene74981:intron 10.0%
!! AATTAACATATACATAACAA+TGG - chr1.3:75949478-75949497 None:intergenic 15.0%
!! ATGACTAAATTAATAGAATT+CGG - chr1.3:75949817-75949836 None:intergenic 15.0%
!! CAAACTTAATTAATCATAAT+TGG - chr1.3:75949314-75949333 None:intergenic 15.0%
!! TAAATGGAAAATCTATTTAA+AGG - chr1.3:75949140-75949159 None:intergenic 15.0%
!!! AAATTACTTTTTTATTCAAC+CGG - chr1.3:75949663-75949682 None:intergenic 15.0%
!! AAAAGACTGTAAATGTTAAA+TGG - chr1.3:75949156-75949175 None:intergenic 20.0%
!! AATTGAAACCAACTTATTAT+AGG + chr1.3:75950153-75950172 MS.gene74981:intron 20.0%
!! CATCAATTTAATCTATGTTA+GGG - chr1.3:75949855-75949874 None:intergenic 20.0%
!! GGTTTATTCAACTAAAAAAA+TGG - chr1.3:75949724-75949743 None:intergenic 20.0%
!! TAGTTCAATGACTAAATTTA+AGG - chr1.3:75949745-75949764 None:intergenic 20.0%
!! TGACTAAATTAATAGAATTC+GGG - chr1.3:75949816-75949835 None:intergenic 20.0%
!! TTATTATACTTATACAACTC+AGG - chr1.3:75949788-75949807 None:intergenic 20.0%
!! TTTATAATGGTTGAAATTTG+TGG + chr1.3:75950074-75950093 MS.gene74981:intron 20.0%
!!! AATTACTTTTTTATTCAACC+GGG - chr1.3:75949662-75949681 None:intergenic 20.0%
!!! ATATCATATCTTTTTCACAT+GGG + chr1.3:75949084-75949103 MS.gene74981:intron 20.0%
!!! TATATCATATCTTTTTCACA+TGG + chr1.3:75949083-75949102 MS.gene74981:intron 20.0%
!!! TATGCATATTTTTATCGTTT+AGG + chr1.3:75949880-75949899 MS.gene74981:intron 20.0%
!!! TTTCTCTTTGTATTTGTTAT+AGG + chr1.3:75949537-75949556 MS.gene74981:intron 20.0%
!!! TTTGACTTGTTAGTTTATAA+TGG + chr1.3:75950061-75950080 MS.gene74981:intron 20.0%
! AATCTCATAAAGAGTTTCTA+GGG + chr1.3:75949202-75949221 MS.gene74981:intron 25.0%
! CCATCAATTTAATCTATGTT+AGG - chr1.3:75949856-75949875 None:intergenic 25.0%
! CCTAACATAGATTAAATTGA+TGG + chr1.3:75949853-75949872 MS.gene74981:intron 25.0%
! TTTATAATTGTTGAAACCTG+TGG + chr1.3:75950199-75950218 MS.gene74981:intron 25.0%
!! AAATTTGACTTCTACTTTGA+AGG - chr1.3:75950125-75950144 None:intergenic 25.0%
!! AATTTGACTTCTACTTTGAA+GGG - chr1.3:75950124-75950143 None:intergenic 25.0%
!!! TTGATGATTTTGTTGTTTTC+AGG + chr1.3:75949331-75949350 MS.gene74981:intron 25.0%
AAACCAACAAGTCAAATCAA+AGG - chr1.3:75950182-75950201 None:intergenic 30.0%
AAACTCTTTATGAGATTGGA+AGG - chr1.3:75949199-75949218 None:intergenic 30.0%
AACTCTTTATGAGATTGGAA+GGG - chr1.3:75949198-75949217 None:intergenic 30.0%
AATACCATGAAGAATGAGTT+AGG - chr1.3:75949440-75949459 None:intergenic 30.0%
ACCAAAAATTCGACTTATAC+AGG - chr1.3:75950005-75950024 None:intergenic 30.0%
CAATCTCATAAAGAGTTTCT+AGG + chr1.3:75949201-75949220 MS.gene74981:intron 30.0%
CAATGTCACAATGATTGTTA+TGG + chr1.3:75949905-75949924 MS.gene74981:intron 30.0%
CTAGAAACTCTTTATGAGAT+TGG - chr1.3:75949203-75949222 None:intergenic 30.0%
TAAAGAAACAAAAGAGAGAG+TGG - chr1.3:75949268-75949287 None:intergenic 30.0%
TAATCATAATTGGAGCGATT+CGG - chr1.3:75949304-75949323 None:intergenic 30.0%
TTATATAGATACTAGAGACC+CGG + chr1.3:75949641-75949660 MS.gene74981:intron 30.0%
! CTTTGAAGGGAAAATAAATG+TGG - chr1.3:75950111-75950130 None:intergenic 30.0%
! TCCTGTATAAGTCGAATTTT+TGG + chr1.3:75950001-75950020 MS.gene74981:intron 30.0%
!! AAAGGTGTCCTATAATAAGT+TGG - chr1.3:75950164-75950183 None:intergenic 30.0%
ACTCTTTATGAGATTGGAAG+GGG - chr1.3:75949197-75949216 None:intergenic 35.0%
ATCTCCTAACTCATTCTTCA+TGG + chr1.3:75949433-75949452 MS.gene74981:CDS 35.0%
TTATAGGATGTCAAATGCCA+AGG + chr1.3:75949553-75949572 MS.gene74981:intron 35.0%
! TTTTTCACATGGGCTCTTAA+TGG + chr1.3:75949094-75949113 MS.gene74981:intron 35.0%
!! ACACCTTTGATTTGACTTGT+TGG + chr1.3:75950176-75950195 MS.gene74981:intron 35.0%
! CTTACATGTTGAAGCATCCT+TGG - chr1.3:75949573-75949592 None:intergenic 40.0%
!! TCAAGAGATCGATGTCGTTT+TGG - chr1.3:75949361-75949380 None:intergenic 40.0%
AAACCACGACTGTTTGAGAG+TGG - chr1.3:75950246-75950265 None:intergenic 45.0%
AGAGTGGTTAACCATTGTCG+AGG - chr1.3:75949252-75949271 None:intergenic 45.0%
CTAATCACCCTTCTTCCTGA+AGG - chr1.3:75950335-75950354 None:intergenic 45.0%
TCATCTCTCAACCTCGACAA+TGG + chr1.3:75949238-75949257 MS.gene74981:intron 45.0%
TCTCAAACAGTCGTGGTTTG+CGG + chr1.3:75950247-75950266 MS.gene74981:CDS 45.0%
! TACAGTAGTTCTGCAACCAC+AGG - chr1.3:75950218-75950237 None:intergenic 45.0%
! TCATAATTGGAGCGATTCGG+AGG - chr1.3:75949301-75949320 None:intergenic 45.0%
AAGGCGACACTCACTCACAT+TGG - chr1.3:75949121-75949140 None:intergenic 50.0%
AGGCGACACTCACTCACATT+GGG - chr1.3:75949120-75949139 None:intergenic 50.0%
GAGGGCTGTGGAATCAAATG+TGG + chr1.3:75949034-75949053 MS.gene74981:CDS 50.0%
GCAAAGCAAGGCTAACAGAG+GGG + chr1.3:75950305-75950324 MS.gene74981:CDS 50.0%
GGCAAAGCAAGGCTAACAGA+GGG + chr1.3:75950304-75950323 MS.gene74981:CDS 50.0%
GGCTGTGGAATCAAATGTGG+AGG + chr1.3:75949037-75949056 MS.gene74981:CDS 50.0%
TAGCCACTCTCAAACAGTCG+TGG + chr1.3:75950240-75950259 MS.gene74981:CDS 50.0%
TCCACAGCCCTCTCAACTTT+GGG - chr1.3:75949026-75949045 None:intergenic 50.0%
TTCCACAGCCCTCTCAACTT+TGG - chr1.3:75949027-75949046 None:intergenic 50.0%
! TTCCTTTTCTCAAGCTCCGC+TGG - chr1.3:75949389-75949408 None:intergenic 50.0%
! TTTTCTCAAGCTCCGCTGGT+GGG - chr1.3:75949385-75949404 None:intergenic 50.0%
ACCCAAAGTTGAGAGGGCTG+TGG + chr1.3:75949022-75949041 MS.gene74981:CDS 55.0%
ACGGTATTGTGCCAGCCAAC+CGG + chr1.3:75950280-75950299 MS.gene74981:CDS 55.0%
CACCAGCGGAGCTTGAGAAA+AGG + chr1.3:75949384-75949403 MS.gene74981:CDS 55.0%
CGATCTCTTGAACCCACCAG+CGG + chr1.3:75949370-75949389 MS.gene74981:CDS 55.0%
CGGCAAAGCAAGGCTAACAG+AGG + chr1.3:75950303-75950322 MS.gene74981:CDS 55.0%
GGGTGCTCCTTCAGGAAGAA+GGG + chr1.3:75950325-75950344 MS.gene74981:CDS 55.0%
GGTTTGCGGCAACTGTCAGA+CGG + chr1.3:75950261-75950280 MS.gene74981:CDS 55.0%
! CTTTTCTCAAGCTCCGCTGG+TGG - chr1.3:75949386-75949405 None:intergenic 55.0%
!! TAACAGAGGGGTGCTCCTTC+AGG + chr1.3:75950317-75950336 MS.gene74981:CDS 55.0%
!! TGTTAGCCTTGCTTTGCCGC+CGG - chr1.3:75950302-75950321 None:intergenic 55.0%
GTATTGTGCCAGCCAACCGG+CGG + chr1.3:75950283-75950302 MS.gene74981:CDS 60.0%
! GGGGTGCTCCTTCAGGAAGA+AGG + chr1.3:75950324-75950343 MS.gene74981:CDS 60.0%
AAGGGGCTGCGACTGCGAGA+AGG - chr1.3:75949180-75949199 None:intergenic 65.0%
AGCCAACCGGCGGCAAAGCA+AGG + chr1.3:75950293-75950312 MS.gene74981:CDS 65.0%
AGCCTTGCTTTGCCGCCGGT+TGG - chr1.3:75950298-75950317 None:intergenic 65.0%
! TTGCTTTGCCGCCGGTTGGC+TGG - chr1.3:75950294-75950313 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 75949017 75950354 75949017 ID=MS.gene74981
chr1.3 mRNA 75949017 75950354 75949017 ID=MS.gene74981.t1;Parent=MS.gene74981
chr1.3 exon 75949017 75949058 75949017 ID=MS.gene74981.t1.exon1;Parent=MS.gene74981.t1
chr1.3 CDS 75949017 75949058 75949017 ID=cds.MS.gene74981.t1;Parent=MS.gene74981.t1
chr1.3 exon 75949353 75949454 75949353 ID=MS.gene74981.t1.exon2;Parent=MS.gene74981.t1
chr1.3 CDS 75949353 75949454 75949353 ID=cds.MS.gene74981.t1;Parent=MS.gene74981.t1
chr1.3 exon 75949559 75949587 75949559 ID=MS.gene74981.t1.exon3;Parent=MS.gene74981.t1
chr1.3 CDS 75949559 75949587 75949559 ID=cds.MS.gene74981.t1;Parent=MS.gene74981.t1
chr1.3 exon 75950228 75950354 75950228 ID=MS.gene74981.t1.exon4;Parent=MS.gene74981.t1
chr1.3 CDS 75950228 75950354 75950228 ID=cds.MS.gene74981.t1;Parent=MS.gene74981.t1
Gene Sequence

>MS.gene74981

ATGGGACCCAAAGTTGAGAGGGCTGTGGAATCAAATGTGGAGGTACATTTTAGAAAAAACAATAGTTATATCATATCTTTTTCACATGGGCTCTTAATGGCCCAATGTGAGTGAGTGTCGCCTTTAAATAGATTTTCCATTTAACATTTACAGTCTTTTGCCTTCTCGCAGTCGCAGCCCCTTCCAATCTCATAAAGAGTTTCTAGGGTTTGCGATTTGATTCATCTCTCAACCTCGACAATGGTTAACCACTCTCTCTTTTGTTTCTTTACGTATATAAACCTCCGAATCGCTCCAATTATGATTAATTAAGTTTGATGATTTTGTTGTTTTCAGGTTCTCCAAAACGACATCGATCTCTTGAACCCACCAGCGGAGCTTGAGAAAAGGAAGCACAAGCTCAAGCGTCTCGTTCAATCTCCTAACTCATTCTTCATGGTATTCAATTTTTTTCATTTCCATTGTTATGTATATGTTAATTTTTTTATTCCGTTTGTAATTTGTTTTTTTTTTTTTTTTGTTTCTCTTTGTATTTGTTATAGGATGTCAAATGCCAAGGATGCTTCAACATGTAAGTCTCTAATTTATGTTATTTTATTTCTTTGAGAAATACATAGTTTTGTGTTATATAGATACTAGAGACCCGGTTGAATAAAAAAGTAATTTGTTATATAGTATAAGTAAAATTATTAATAATTATAAAACCATTTTTTTAGTTGAATAAACCTTAAATTTAGTCATTGAACTATCACTCTTTTCATTTTAGTTCCTGAGTTGTATAAGTATAATAAACAGTCCCGAATTCTATTAATTTAGTCATTTAATCTATGTTAATCCCTAACATAGATTAAATTGATGGATTTTATGCATATTTTTATCGTTTAGGAACAATGTCACAATGATTGTTATGGACTTCGCTACTGCTTATTATATTTCTATCATTTAGGTACAATGATAAATTATGATTTATGCTTCTAGTTCTTTTCCTGTATAAGTCGAATTTTTGGTAAAAATTGAAACAAACTTATTATAGAACAACATTGATTTGACTTGTTAGTTTATAATGGTTGAAATTTGTGGATGCAGAATTACCACATTTATTTTCCCTTCAAAGTAGAAGTCAAATTTTTGATAAAAATTGAAACCAACTTATTATAGGACACCTTTGATTTGACTTGTTGGTTTATAATTGTTGAAACCTGTGGTTGCAGAACTACTGTATTTAGCCACTCTCAAACAGTCGTGGTTTGCGGCAACTGTCAGACGGTATTGTGCCAGCCAACCGGCGGCAAAGCAAGGCTAACAGAGGGGTGCTCCTTCAGGAAGAAGGGTGATTAG
Protein sequence

>MS.gene74981.t1

MGPKVERAVESNVEVLQNDIDLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGNCQTVLCQPTGGKARLTEGCSFRKKGD