AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004091


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004091.t1 MTR_4g063060 98.693 153 1 1 1 153 1 152 1.17e-103 293
MS.gene004091.t1 MTR_2g096340 96.689 151 5 0 3 153 4 154 4.98e-101 286
MS.gene004091.t1 MTR_2g096340 96.644 149 5 0 5 153 13 161 2.55e-99 282
MS.gene004091.t1 MTR_7g023260 92.053 151 12 0 3 153 4 154 1.65e-67 202
MS.gene004091.t1 MTR_4g007840 94.595 37 2 0 117 153 36 72 1.95e-18 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004091.t1 AT3G55280 87.662 154 18 1 1 153 1 154 2.30e-70 209
MS.gene004091.t1 AT3G55280 87.662 154 18 1 1 153 1 154 2.30e-70 209
MS.gene004091.t1 AT2G39460 89.844 128 13 0 26 153 27 154 1.19e-66 199
MS.gene004091.t1 AT2G39460 89.844 128 13 0 26 153 27 154 1.19e-66 199
MS.gene004091.t1 AT3G55280 92.373 118 9 0 36 153 31 148 2.54e-66 199

Find 41 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATCCCTTGTTTGTGTCTT+TGG 0.162619 4.2:+42098102 None:intergenic
GCTTTCAATGCCTGTGCCTT+TGG 0.265621 4.2:+42098201 None:intergenic
GGCACTGATGCGAGGATATT+TGG 0.276630 4.2:+42098074 None:intergenic
TATCCCTTGTTTGTGTCTTT+GGG 0.296408 4.2:+42098103 None:intergenic
CAACCTAACATAGGCCTTCT+TGG 0.308307 4.2:+42097395 None:intergenic
GCACTGATGCGAGGATATTT+GGG 0.324549 4.2:+42098075 None:intergenic
TAGTGGTCAAGCTTGTTTCT+TGG 0.344862 4.2:+42098048 None:intergenic
ACATCCAATGCATCGTAATC+AGG 0.425991 4.2:+42097369 None:intergenic
CAATGCCTGTGCCTTTGGAT+CGG 0.450132 4.2:+42098206 None:intergenic
AGGTGTTAACCTTCTTCGCC+TGG 0.454264 4.2:+42097890 None:intergenic
GCTGCCAAGGCAGTCAAGTC+AGG 0.480557 4.2:-42098180 MS.gene004091:CDS
GTCAAGCTTGTTTCTTGGTG+TGG 0.490928 4.2:+42098053 None:intergenic
GTACCAAGAAGGCCTATGTT+AGG 0.503933 4.2:-42097398 MS.gene004091:CDS
CATAAATGCTCACCTGATCA+AGG 0.508831 4.2:+42097870 None:intergenic
GGAACTTCAAAATCTGATAG+TGG 0.511992 4.2:+42098031 None:intergenic
TTGTTTGTGTCTTTGGGCGA+TGG 0.513342 4.2:+42098109 None:intergenic
AATTGAGGATAACAACACTT+TGG 0.518687 4.2:-42097980 MS.gene004091:CDS
ATAGGCCTTCTTGGTACCAT+CGG 0.519310 4.2:+42097404 None:intergenic
TTGGATGTAGCAAACAAGAT+TGG 0.522533 4.2:-42097354 MS.gene004091:CDS
GAAGAAAATGTATGACATCC+AGG 0.526017 4.2:-42097908 MS.gene004091:CDS
TGTGCCTGACTTGACTGCCT+TGG 0.530575 4.2:+42098176 None:intergenic
AGAAGGTTAACACCTTGATC+AGG 0.531796 4.2:-42097882 MS.gene004091:intron
AGGCACAGCTATTAAGAAGA+AGG 0.535277 4.2:-42098160 MS.gene004091:CDS
GACACCTGATTACGATGCAT+TGG 0.535533 4.2:-42097373 MS.gene004091:CDS
TAGGCCTTCTTGGTACCATC+GGG 0.543529 4.2:+42097405 None:intergenic
CAAAGACACAAACAAGGGAT+AGG 0.544147 4.2:-42098101 MS.gene004091:CDS
GTATGACATCCAGGCGAAGA+AGG 0.560881 4.2:-42097899 MS.gene004091:CDS
TTAATCTGTTGCAGGCCCGA+TGG 0.562967 4.2:-42097420 MS.gene004091:intron
ACAGGCATTGAAAGCTGCCA+AGG 0.571400 4.2:-42098193 MS.gene004091:CDS
GAAGACCGATCCAAAGGCAC+AGG 0.572296 4.2:-42098211 MS.gene004091:CDS
GTCCGCAATGAAGAAAATTG+AGG 0.580232 4.2:-42097995 MS.gene004091:CDS
CAGGCCCGATGGTACCAAGA+AGG 0.589470 4.2:-42097409 MS.gene004091:CDS
TTGCGGACTCAGTGGTGAGT+GGG 0.598322 4.2:+42098010 None:intergenic
TTCTAAGAAGACCGATCCAA+AGG 0.610830 4.2:-42098217 MS.gene004091:CDS
ATTGCGGACTCAGTGGTGAG+TGG 0.611075 4.2:+42098009 None:intergenic
TTTCTTCATTGCGGACTCAG+TGG 0.615852 4.2:+42098002 None:intergenic
CACTGATGCGAGGATATTTG+GGG 0.617729 4.2:+42098076 None:intergenic
CTTGGTGTGGCACTGATGCG+AGG 0.626082 4.2:+42098066 None:intergenic
ATCAGGTGTCAACCTAACAT+AGG 0.641379 4.2:+42097386 None:intergenic
ATCGCCCAAAGACACAAACA+AGG 0.648974 4.2:-42098107 MS.gene004091:CDS
TCGCCCAAAGACACAAACAA+GGG 0.727590 4.2:-42098106 MS.gene004091:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTAACTATAATTTATCTT+TGG + chr4.2:42097928-42097947 None:intergenic 10.0%
!!! TATTTTAATCAAATAATGCA+TGG - chr4.2:42098311-42098330 MS.gene004091:intron 15.0%
!!! TTTTTACTAACAAAAATGAA+TGG + chr4.2:42097427-42097446 None:intergenic 15.0%
!! AATCAAATCATACATGAAAA+TGG + chr4.2:42097543-42097562 None:intergenic 20.0%
!! AGCATATGATATATCATTAA+GGG + chr4.2:42098199-42098218 None:intergenic 20.0%
!! ATTAAAATATACTGAACCAA+AGG + chr4.2:42098300-42098319 None:intergenic 20.0%
!! ATTATTATTATAGTTCAGCA+TGG - chr4.2:42099179-42099198 MS.gene004091:intron 20.0%
!!! AGCTTAAATGAAAACAATTT+TGG + chr4.2:42097707-42097726 None:intergenic 20.0%
!!! ATTGTTTTCATTTAAGCTTT+AGG - chr4.2:42097709-42097728 MS.gene004091:intron 20.0%
!!! TCATGTATGATTTGATTTTA+AGG - chr4.2:42097546-42097565 MS.gene004091:intron 20.0%
! AGAAAATTGAAGTTACCTTT+AGG + chr4.2:42097353-42097372 None:intergenic 25.0%
! ATCAAATAATGCATGGAATT+AGG - chr4.2:42098318-42098337 MS.gene004091:intron 25.0%
! CAGCATATGATATATCATTA+AGG + chr4.2:42098200-42098219 None:intergenic 25.0%
! GATTTACAAATTTGAGCTTA+TGG + chr4.2:42097810-42097829 None:intergenic 25.0%
! TACAAATTATCTCAAATGTC+AGG + chr4.2:42098916-42098935 None:intergenic 25.0%
! TGATGAGCAAAAAAAAAGTT+AGG - chr4.2:42097605-42097624 MS.gene004091:intron 25.0%
! TGCTGATAAGAAAAAGATTA+AGG - chr4.2:42098714-42098733 MS.gene004091:intron 25.0%
!! GATTAATACTGATTATCCAT+AGG - chr4.2:42098274-42098293 MS.gene004091:intron 25.0%
!! TTCTAGTTGAATATGTGTTT+AGG - chr4.2:42099096-42099115 MS.gene004091:intron 25.0%
!!! CATTATTTTCCACTGATTTA+AGG - chr4.2:42097378-42097397 MS.gene004091:CDS 25.0%
!!! CTGAAGAACTTCTAAAATTA+AGG - chr4.2:42097750-42097769 MS.gene004091:intron 25.0%
!!! CTTAATTTTAGAAGTTCTTC+AGG + chr4.2:42097752-42097771 None:intergenic 25.0%
!!! GCTGTTTTTATAAGCTATAT+TGG - chr4.2:42097968-42097987 MS.gene004091:CDS 25.0%
AATAAGTTGCTTATCCAAAC+AGG + chr4.2:42097851-42097870 None:intergenic 30.0%
AATTGAGGATAACAACACTT+TGG - chr4.2:42098672-42098691 MS.gene004091:intron 30.0%
AGAAAACAGAAAACCATTGT+TGG + chr4.2:42099030-42099049 None:intergenic 30.0%
ATGTCTGCAAAATATACTAC+TGG + chr4.2:42098941-42098960 None:intergenic 30.0%
ATTAAGGTGAAACTAGTGTA+TGG - chr4.2:42097766-42097785 MS.gene004091:intron 30.0%
ATTTATGCAGTTACTGTTCA+AGG - chr4.2:42098798-42098817 MS.gene004091:intron 30.0%
TTAGGCATTAATACCAACAA+TGG - chr4.2:42099014-42099033 MS.gene004091:intron 30.0%
TTGGAGAACTTATGAAAACA+AGG - chr4.2:42098066-42098085 MS.gene004091:CDS 30.0%
! ATCCTCAATTTTCTTCATTG+CGG + chr4.2:42098662-42098681 None:intergenic 30.0%
! TTCTAGTTGAATACGTGTTT+AGG - chr4.2:42098996-42099015 MS.gene004091:intron 30.0%
!!! TTTTTTGCTCATCATAACTC+AGG + chr4.2:42097599-42097618 None:intergenic 30.0%
AATTACGCTTACATCCTGTT+TGG - chr4.2:42097834-42097853 MS.gene004091:intron 35.0%
AGCACATAACCTTAAATCAG+TGG + chr4.2:42097390-42097409 None:intergenic 35.0%
GAAGAAAATGTATGACATCC+AGG - chr4.2:42098744-42098763 MS.gene004091:intron 35.0%
GCATAGTTATGCTATGATCA+GGG - chr4.2:42099118-42099137 MS.gene004091:intron 35.0%
GGAACTTCAAAATCTGATAG+TGG + chr4.2:42098624-42098643 None:intergenic 35.0%
TATATCATTAAGGGCCTGTT+TGG + chr4.2:42098190-42098209 None:intergenic 35.0%
TTGGATGTAGCAAACAAGAT+TGG - chr4.2:42099298-42099317 MS.gene004091:intron 35.0%
! ATACGTTTTGTGAGACTGTT+TGG + chr4.2:42098139-42098158 None:intergenic 35.0%
! CAGGATGTAAGCGTAATTTT+CGG + chr4.2:42097832-42097851 None:intergenic 35.0%
! TATCCCTTGTTTGTGTCTTT+GGG + chr4.2:42098552-42098571 None:intergenic 35.0%
! TCGACTTTTTAATCTGTTGC+AGG - chr4.2:42099224-42099243 MS.gene004091:intron 35.0%
!! AGACATACCGAACCATTTTT+GGG - chr4.2:42098955-42098974 MS.gene004091:intron 35.0%
AAACCGCCAAAACCCAAAAA+TGG + chr4.2:42098970-42098989 None:intergenic 40.0%
ACATCCAATGCATCGTAATC+AGG + chr4.2:42099286-42099305 None:intergenic 40.0%
ACCCTAACAAAACATGCGAA+GGG + chr4.2:42098889-42098908 None:intergenic 40.0%
ACTGATTATCCATAGGCCTT+TGG - chr4.2:42098281-42098300 MS.gene004091:intron 40.0%
AGAAGGTTAACACCTTGATC+AGG - chr4.2:42098770-42098789 MS.gene004091:intron 40.0%
AGGCACAGCTATTAAGAAGA+AGG - chr4.2:42098492-42098511 MS.gene004091:intron 40.0%
ATCAGGTGTCAACCTAACAT+AGG + chr4.2:42099269-42099288 None:intergenic 40.0%
CAAAGACACAAACAAGGGAT+AGG - chr4.2:42098551-42098570 MS.gene004091:intron 40.0%
CATAAATGCTCACCTGATCA+AGG + chr4.2:42098785-42098804 None:intergenic 40.0%
CTGCGCAAAAACATTGCATA+AGG + chr4.2:42098408-42098427 None:intergenic 40.0%
GAGTTTGTAAGCGACTGTTT+AGG - chr4.2:42097568-42097587 MS.gene004091:intron 40.0%
GCCAAAACCCAAAAATGGTT+CGG + chr4.2:42098965-42098984 None:intergenic 40.0%
GGCATAGTTATGCTATGATC+AGG - chr4.2:42099117-42099136 MS.gene004091:intron 40.0%
GTCCGCAATGAAGAAAATTG+AGG - chr4.2:42098657-42098676 MS.gene004091:intron 40.0%
TACCCTAACAAAACATGCGA+AGG + chr4.2:42098890-42098909 None:intergenic 40.0%
TATACTGAACCAAAGGCCTA+TGG + chr4.2:42098293-42098312 None:intergenic 40.0%
TCAAAGAAGCCAATCCAAAC+AGG - chr4.2:42098173-42098192 MS.gene004091:CDS 40.0%
! CAGACATACCGAACCATTTT+TGG - chr4.2:42098954-42098973 MS.gene004091:intron 40.0%
! CTATCCCTTGTTTGTGTCTT+TGG + chr4.2:42098553-42098572 None:intergenic 40.0%
! TAGTGGTCAAGCTTGTTTCT+TGG + chr4.2:42098607-42098626 None:intergenic 40.0%
! TTCTAAGAAGACCGATCCAA+AGG - chr4.2:42098435-42098454 MS.gene004091:intron 40.0%
!! ACCCTTCGCATGTTTTGTTA+GGG - chr4.2:42098885-42098904 MS.gene004091:intron 40.0%
!! CTTATGCAATGTTTTTGCGC+AGG - chr4.2:42098406-42098425 MS.gene004091:intron 40.0%
!! TACCCTTCGCATGTTTTGTT+AGG - chr4.2:42098884-42098903 MS.gene004091:intron 40.0%
!!! ACCGAACCATTTTTGGGTTT+TGG - chr4.2:42098961-42098980 MS.gene004091:intron 40.0%
!!! GAACCATTTTTGGGTTTTGG+CGG - chr4.2:42098964-42098983 MS.gene004091:intron 40.0%
ATAGGCCTTCTTGGTACCAT+CGG + chr4.2:42099251-42099270 None:intergenic 45.0%
ATCGCCCAAAGACACAAACA+AGG - chr4.2:42098545-42098564 MS.gene004091:intron 45.0%
CAACCTAACATAGGCCTTCT+TGG + chr4.2:42099260-42099279 None:intergenic 45.0%
CACTGATGCGAGGATATTTG+GGG + chr4.2:42098579-42098598 None:intergenic 45.0%
CATTAAGGGCCTGTTTGGAT+TGG + chr4.2:42098185-42098204 None:intergenic 45.0%
GACACCTGATTACGATGCAT+TGG - chr4.2:42099279-42099298 MS.gene004091:intron 45.0%
GTACCAAGAAGGCCTATGTT+AGG - chr4.2:42099254-42099273 MS.gene004091:intron 45.0%
TCGCCCAAAGACACAAACAA+GGG - chr4.2:42098546-42098565 MS.gene004091:intron 45.0%
TTGTTTGTGTCTTTGGGCGA+TGG + chr4.2:42098546-42098565 None:intergenic 45.0%
TTTCTTCATTGCGGACTCAG+TGG + chr4.2:42098653-42098672 None:intergenic 45.0%
! GCACTGATGCGAGGATATTT+GGG + chr4.2:42098580-42098599 None:intergenic 45.0%
! GTCAAGCTTGTTTCTTGGTG+TGG + chr4.2:42098602-42098621 None:intergenic 45.0%
AGGTGTTAACCTTCTTCGCC+TGG + chr4.2:42098765-42098784 None:intergenic 50.0%
CAATGCCTGTGCCTTTGGAT+CGG + chr4.2:42098449-42098468 None:intergenic 50.0%
GCTTTCAATGCCTGTGCCTT+TGG + chr4.2:42098454-42098473 None:intergenic 50.0%
GTATGACATCCAGGCGAAGA+AGG - chr4.2:42098753-42098772 MS.gene004091:intron 50.0%
TAGGCCTTCTTGGTACCATC+GGG + chr4.2:42099250-42099269 None:intergenic 50.0%
TTAATCTGTTGCAGGCCCGA+TGG - chr4.2:42099232-42099251 MS.gene004091:intron 50.0%
!! ACAGGCATTGAAAGCTGCCA+AGG - chr4.2:42098459-42098478 MS.gene004091:intron 50.0%
!! GGCACTGATGCGAGGATATT+TGG + chr4.2:42098581-42098600 None:intergenic 50.0%
ATTGCGGACTCAGTGGTGAG+TGG + chr4.2:42098646-42098665 None:intergenic 55.0%
TTGCGGACTCAGTGGTGAGT+GGG + chr4.2:42098645-42098664 None:intergenic 55.0%
! GAAGACCGATCCAAAGGCAC+AGG - chr4.2:42098441-42098460 MS.gene004091:intron 55.0%
! TGTGCCTGACTTGACTGCCT+TGG + chr4.2:42098479-42098498 None:intergenic 55.0%
CAGGCCCGATGGTACCAAGA+AGG - chr4.2:42099243-42099262 MS.gene004091:intron 60.0%
GCTGCCAAGGCAGTCAAGTC+AGG - chr4.2:42098472-42098491 MS.gene004091:intron 60.0%
!! CTTGGTGTGGCACTGATGCG+AGG + chr4.2:42098589-42098608 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 42097344 42099330 42097344 ID=MS.gene004091
chr4.2 mRNA 42097344 42099330 42097344 ID=MS.gene004091.t1;Parent=MS.gene004091
chr4.2 exon 42099318 42099330 42099318 ID=MS.gene004091.t1.exon1;Parent=MS.gene004091.t1
chr4.2 CDS 42099318 42099330 42099318 ID=cds.MS.gene004091.t1;Parent=MS.gene004091.t1
chr4.2 exon 42097883 42098246 42097883 ID=MS.gene004091.t1.exon2;Parent=MS.gene004091.t1
chr4.2 CDS 42097883 42098246 42097883 ID=cds.MS.gene004091.t1;Parent=MS.gene004091.t1
chr4.2 exon 42097344 42097428 42097344 ID=MS.gene004091.t1.exon3;Parent=MS.gene004091.t1
chr4.2 CDS 42097344 42097428 42097344 ID=cds.MS.gene004091.t1;Parent=MS.gene004091.t1
Gene Sequence

>MS.gene004091

ATGGCTCCTAAAGGTAACTTCAATTTTCTGATCTCATTATTTTCCACTGATTTAAGGTTATGTGCTATTTCAATTTTCAACCATTCATTTTTGTTAGTAAAAAATGTTTTTGTATAATTTAGATTGAACTTAATCAATATGTAATTAATCGAAAGAAAAATGTTCATATGTTAATTGTATAATTGTGTAAGTCATTCCATTTTCATGTATGATTTGATTTTAAGGAGTTTGTAAGCGACTGTTTAGGACTGTCCTGAGTTATGATGAGCAAAAAAAAAGTTAGGTTTTGCTCAGATAAATAGCTTAATTGAGTGCTCATGCTAGAATCGCTTATTAGCTATTTTTATAACAAAAGATACACCAAAATTGTTTTCATTTAAGCTTTAGGTTGTTTTCATAAGCTATCCTGAAGAACTTCTAAAATTAAGGTGAAACTAGTGTATGGACATGTCAAAAGCTGTTTCCATAAGCTCAAATTTGTAAATCCGAAAATTACGCTTACATCCTGTTTGGATAAGCAACTTATTTGCAGCTTATAGTACACACACTCATTCATAAGCTTACTTAAGCTATTTTTATAGCCAAAGATAAATTATAGTTAAATAGTTTTTCTATATGCTATAAGCTGTTTTTATAAGCTATATCGAAAAACTTATGAAAACAAGCTAAAAAATGTTTGTGAAAATTGTCATTTATGCTATAAGCTGTTTTTATAAGCTATATTGGAGAACTTATGAAAACAAGGTAAACAAAATTTGTGAAAATTGTCATAAGCTGTTTTCATAAGTTCGTCCAAACAGTCTCACAAAACGTATGCTAGTAGATAATCTCAAAGAAGCCAATCCAAACAGGCCCTTAATGATATATCATATGCTGTTTTTAAATAAGTTTTCTATTTAACTTGCAGAATTATTGCTTAATCTCTCATATGATTAATACTGATTATCCATAGGCCTTTGGTTCAGTATATTTTAATCAAATAATGCATGGAATTAGGAAGATTATTATATTACACAAAAAAAATAGTTAGAACTTTGTTTTTTTTTTCTTTTCTTCATGTGCCTTATGCAATGTTTTTGCGCAGGTGATGTTTCTAAGAAGACCGATCCAAAGGCACAGGCATTGAAAGCTGCCAAGGCAGTCAAGTCAGGCACAGCTATTAAGAAGAAGGCAAAGAAGATTAGAACAACTGTAACTTTCCATCGCCCAAAGACACAAACAAGGGATAGGAACCCCAAATATCCTCGCATCAGTGCCACACCAAGAAACAAGCTTGACCACTATCAGATTTTGAAGTTCCCACTCACCACTGAGTCCGCAATGAAGAAAATTGAGGATAACAACACTTTGGTTTTCATTGTTGACTTGCGTGCTGATAAGAAAAAGATTAAGGATGCAGTGAAGAAAATGTATGACATCCAGGCGAAGAAGGTTAACACCTTGATCAGGTGAGCATTTATGCAGTTACTGTTCAAGGCAAATTAATAATCTGATAAATGCTAATAACAGTTGTAGTCTAATTGTCAAATTCATACTGCACTACCCTTCGCATGTTTTGTTAGGGTAGTACCTGACATTTGAGATAATTTGTAGTCCAGTAGTATATTTTGCAGACATACCGAACCATTTTTGGGTTTTGGCGGTTTTTTGTTTTCTAGTTGAATACGTGTTTAGGCATTAATACCAACAATGGTTTTCTGTTTTCTAGTTGAATACGTGTTTAGGCATTAATACCAACAATGGTTTTCTGTTTTCTAGTTGAATATGTGTTTAGGCATAGTTATGCTATGATCAGGGAGATTGCATAGTTATGCTATGATCTGTACAATTTAATTATTATTATTATAGTTCAGCATGGTGATTTCAGACAATTTCTAAACTCGACTTTTTAATCTGTTGCAGGCCCGATGGTACCAAGAAGGCCTATGTTAGGTTGACACCTGATTACGATGCATTGGATGTAGCAAACAAGATTGGTATCATCTAA

Protein sequence

>MS.gene004091.t1

MAPKGDVSKKTDPKAQALKAAKAVKSGTAIKKKAKKIRTTVTFHRPKTQTRDRNPKYPRISATPRNKLDHYQILKFPLTTESAMKKIEDNNTLVFIVDLRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDYDALDVANKIGII