AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43847

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43847.t1 MTR_2g095840 95.714 70 3 0 90 159 301 370 3.04e-42 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43847.t1 AT3G45770 68.056 72 23 0 88 159 226 297 9.73e-28 105
MS.gene43847.t1 AT3G45770 70.000 70 21 0 90 159 306 375 1.70e-27 105

Find 45 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTTTCCTTGAGGGGTTTC+TGG 0.067739 2.2:+6073700 MS.gene43847:CDS
TTTGATTCAGGAGTGGATTT+AGG 0.162281 2.2:+6073398 MS.gene43847:intron
AAGCCGAAACTGGGTGCTTT+TGG 0.267600 2.2:+6073549 MS.gene43847:CDS
TGCTGTGTTGAAATCATTAA+AGG 0.283167 2.2:-6073989 None:intergenic
TTGATTCAGGAGTGGATTTA+GGG 0.293449 2.2:+6073399 MS.gene43847:intron
TTGTTAGCCCAAGCCGAAAC+TGG 0.300640 2.2:+6073539 MS.gene43847:CDS
AAGAATGATAGACAGGCTTT+TGG 0.340065 2.2:+6073764 MS.gene43847:CDS
ATAAGTCATGATATTTGCTT+TGG 0.349489 2.2:-6073576 None:intergenic
AAGCCTGTCTATCATTCTTC+TGG 0.360636 2.2:-6073760 None:intergenic
TAGAATTTGATCACTTGCTT+TGG 0.368534 2.2:-6074045 None:intergenic
GGGGTTTCTGGTTGCAGAAT+TGG 0.370660 2.2:+6073712 MS.gene43847:CDS
TGTCCAAAAGCACCCAGTTT+CGG 0.402634 2.2:-6073552 None:intergenic
GCACTCGAACCTTGGACATA+TGG 0.415440 2.2:+6073480 MS.gene43847:CDS
AAAGCACCCAGTTTCGGCTT+GGG 0.418170 2.2:-6073546 None:intergenic
TCCGTCCTGCACTCGAACCT+TGG 0.429087 2.2:+6073472 MS.gene43847:CDS
ATTTGATCACTTGCTTTGGT+TGG 0.429211 2.2:-6074041 None:intergenic
GATAAAGCTCTAGGAAAACT+TGG 0.442938 2.2:+6074015 MS.gene43847:CDS
TGTTGGCTCTACAGAAGATT+AGG 0.455318 2.2:+6073077 MS.gene43847:CDS
TGGCTGAGTGGCTAGTAGCT+TGG 0.465092 2.2:-6073512 None:intergenic
AATTGGTTGAGCGAAGATAA+AGG 0.470768 2.2:+6073729 MS.gene43847:CDS
GCTGTGTTGAAATCATTAAA+GGG 0.472835 2.2:-6073988 None:intergenic
AGTTTGGGCTTCAGTAGTGT+TGG 0.480384 2.2:+6073060 MS.gene43847:CDS
TTTGCAGGAACTTTCCTTGA+GGG 0.490724 2.2:+6073692 MS.gene43847:intron
AAAAGCACCCAGTTTCGGCT+TGG 0.492090 2.2:-6073547 None:intergenic
TAATGATTTCAACACAGCAT+TGG 0.494087 2.2:+6073993 MS.gene43847:CDS
GGCTATCATCAGCAAAGAAT+AGG 0.507986 2.2:+6073098 MS.gene43847:CDS
AGGCCAGAAGAATGATAGAC+AGG 0.508083 2.2:+6073757 MS.gene43847:CDS
TATGTCCAAGGTTCGAGTGC+AGG 0.525928 2.2:-6073477 None:intergenic
CGGCTTGGGCTAACAAGGTG+TGG 0.542199 2.2:-6073532 None:intergenic
GCTGTAGAACTAATCCTTCG+AGG 0.554504 2.2:+6073439 MS.gene43847:CDS
ACAGCATTGGATAAAGCTCT+AGG 0.556139 2.2:+6074006 MS.gene43847:CDS
TGTTAGCCCAAGCCGAAACT+GGG 0.568501 2.2:+6073540 MS.gene43847:CDS
AGTTTCGGCTTGGGCTAACA+AGG 0.576938 2.2:-6073537 None:intergenic
TTGCAGGAACTTTCCTTGAG+GGG 0.580175 2.2:+6073693 MS.gene43847:intron
ATTTAGGGTATCCTCACGGT+TGG 0.598828 2.2:+6073414 MS.gene43847:CDS
GAGCGAAGATAAAGGTGAAG+AGG 0.615630 2.2:+6073737 MS.gene43847:CDS
ACTCATTAACCATATGTCCA+AGG 0.617270 2.2:-6073489 None:intergenic
ATAAAGCTCTAGGAAAACTT+GGG 0.620470 2.2:+6074016 MS.gene43847:CDS
ATTTGCAGGAACTTTCCTTG+AGG 0.633105 2.2:+6073691 MS.gene43847:intron
CGGATACTGTACATCCTCGA+AGG 0.637626 2.2:-6073453 None:intergenic
TCCAAGGTTCGAGTGCAGGA+CGG 0.640854 2.2:-6073473 None:intergenic
GCTAACAAGGTGTGGCTGAG+TGG 0.654655 2.2:-6073524 None:intergenic
CTGCAACCAGAAACCCCTCA+AGG 0.657662 2.2:-6073706 None:intergenic
GTGGATTTAGGGTATCCTCA+CGG 0.686295 2.2:+6073410 MS.gene43847:CDS
TTCTACAGCTACCAACCGTG+AGG 0.725140 2.2:-6073425 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAAAAATTAGTAACCA+AGG + chr2.2:6073186-6073205 MS.gene43847:intron 15.0%
!! ATCATAGGATAAGAAAAATA+TGG + chr2.2:6073833-6073852 MS.gene43847:intron 20.0%
!! TATAAGCATGTATTATTGAA+AGG - chr2.2:6073613-6073632 None:intergenic 20.0%
!! TCATAGGATAAGAAAAATAT+GGG + chr2.2:6073834-6073853 MS.gene43847:intron 20.0%
!! TGATTTATTAAATGTAACCA+TGG + chr2.2:6073655-6073674 MS.gene43847:intron 20.0%
!!! AAACTTATTACTTGCATTTT+GGG + chr2.2:6073162-6073181 MS.gene43847:intron 20.0%
!!! AAATATGTGATTTAAAACCA+TGG - chr2.2:6073675-6073694 None:intergenic 20.0%
!!! TATTTTTCTTATCCTATGAT+AGG - chr2.2:6073833-6073852 None:intergenic 20.0%
! AAATGCAAGTAATAAGTTTC+AGG - chr2.2:6073161-6073180 None:intergenic 25.0%
! AATGCAAGTAATAAGTTTCA+GGG - chr2.2:6073160-6073179 None:intergenic 25.0%
! ATAAGTCATGATATTTGCTT+TGG - chr2.2:6073579-6073598 None:intergenic 25.0%
! ATGTATTTCAAAGTTTAGGT+GGG + chr2.2:6073221-6073240 MS.gene43847:intron 25.0%
! CAATCAGTTGAAATATTAAC+TGG + chr2.2:6073936-6073955 MS.gene43847:intron 25.0%
!! GAAACTTATTACTTGCATTT+TGG + chr2.2:6073161-6073180 MS.gene43847:intron 25.0%
!!! ACCTAAACTTTGAAATACAT+GGG - chr2.2:6073221-6073240 None:intergenic 25.0%
!!! GTTTTAAATCACATATTTGC+AGG + chr2.2:6073677-6073696 MS.gene43847:intron 25.0%
AGCTTGCAAAGATTATGAAA+TGG + chr2.2:6073260-6073279 MS.gene43847:intron 30.0%
AGGATAAGAAAAATATGGGA+GGG + chr2.2:6073838-6073857 MS.gene43847:intron 30.0%
CAAATATCATGACTTATCTG+TGG + chr2.2:6073582-6073601 MS.gene43847:intron 30.0%
CATGTATTTCAAAGTTTAGG+TGG + chr2.2:6073220-6073239 MS.gene43847:intron 30.0%
GAATAGGTGTGATATCATAA+TGG + chr2.2:6073114-6073133 MS.gene43847:intron 30.0%
GATTATGAAATGGTTGTATG+AGG + chr2.2:6073270-6073289 MS.gene43847:intron 30.0%
GCTGTGTTGAAATCATTAAA+GGG - chr2.2:6073991-6074010 None:intergenic 30.0%
GGGTATAAAAATTGCAAAAG+AGG - chr2.2:6073140-6073159 None:intergenic 30.0%
TAATGATTTCAACACAGCAT+TGG + chr2.2:6073993-6074012 MS.gene43847:CDS 30.0%
TAGAATTTGATCACTTGCTT+TGG - chr2.2:6074048-6074067 None:intergenic 30.0%
TAGGATAAGAAAAATATGGG+AGG + chr2.2:6073837-6073856 MS.gene43847:intron 30.0%
TCCCATGTATTTCAAAGTTT+AGG + chr2.2:6073217-6073236 MS.gene43847:intron 30.0%
TGCTGTGTTGAAATCATTAA+AGG - chr2.2:6073992-6074011 None:intergenic 30.0%
!! ATAAAGCTCTAGGAAAACTT+GGG + chr2.2:6074016-6074035 MS.gene43847:CDS 30.0%
!! CACCTAAACTTTGAAATACA+TGG - chr2.2:6073222-6073241 None:intergenic 30.0%
AATTGGTTGAGCGAAGATAA+AGG + chr2.2:6073729-6073748 MS.gene43847:CDS 35.0%
ACTCATTAACCATATGTCCA+AGG - chr2.2:6073492-6073511 None:intergenic 35.0%
ATTTGATCACTTGCTTTGGT+TGG - chr2.2:6074044-6074063 None:intergenic 35.0%
GATTGAGAGAAAAGAGAGTA+AGG - chr2.2:6073921-6073940 None:intergenic 35.0%
TACATGGGACTTATATACCT+TGG - chr2.2:6073206-6073225 None:intergenic 35.0%
! AAGAATGATAGACAGGCTTT+TGG + chr2.2:6073764-6073783 MS.gene43847:CDS 35.0%
! AGAATGATAGACAGGCTTTT+GGG + chr2.2:6073765-6073784 MS.gene43847:CDS 35.0%
! TTGATTCAGGAGTGGATTTA+GGG + chr2.2:6073399-6073418 MS.gene43847:intron 35.0%
! TTTGATTCAGGAGTGGATTT+AGG + chr2.2:6073398-6073417 MS.gene43847:intron 35.0%
!! GATAAAGCTCTAGGAAAACT+TGG + chr2.2:6074015-6074034 MS.gene43847:CDS 35.0%
!! TCTGAATCATGTTGCTTTAC+TGG + chr2.2:6073308-6073327 MS.gene43847:intron 35.0%
!!! CTCTTTTTTTGATTCAGGAG+TGG + chr2.2:6073391-6073410 MS.gene43847:intron 35.0%
AAGCCTGTCTATCATTCTTC+TGG - chr2.2:6073763-6073782 None:intergenic 40.0%
ATTGTGCTGAGGAACAAAAC+CGG + chr2.2:6073367-6073386 MS.gene43847:intron 40.0%
ATTTGCAGGAACTTTCCTTG+AGG + chr2.2:6073691-6073710 MS.gene43847:intron 40.0%
CAATTCCATCCTGCAAGATA+AGG - chr2.2:6073965-6073984 None:intergenic 40.0%
CCTGAATCAAAAAAAGAGCC+CGG - chr2.2:6073389-6073408 None:intergenic 40.0%
GATTCAGAGACGAAAGTTAC+AGG - chr2.2:6073296-6073315 None:intergenic 40.0%
GGCTATCATCAGCAAAGAAT+AGG + chr2.2:6073098-6073117 MS.gene43847:CDS 40.0%
GTATGTCTCGTACCTATCAT+AGG + chr2.2:6073818-6073837 MS.gene43847:intron 40.0%
TGGATAAAGTTCAGTGCAAC+TGG + chr2.2:6073344-6073363 MS.gene43847:intron 40.0%
TTTGCAGGAACTTTCCTTGA+GGG + chr2.2:6073692-6073711 MS.gene43847:intron 40.0%
! ACAGCATTGGATAAAGCTCT+AGG + chr2.2:6074006-6074025 MS.gene43847:CDS 40.0%
!! CTTTTGGGTCTTGTACAAGA+TGG + chr2.2:6073780-6073799 MS.gene43847:CDS 40.0%
!! TGTTGGCTCTACAGAAGATT+AGG + chr2.2:6073077-6073096 MS.gene43847:CDS 40.0%
AACTTTCCTTGAGGGGTTTC+TGG + chr2.2:6073700-6073719 MS.gene43847:CDS 45.0%
ACTTTATCCACTGCGAAGAC+AGG - chr2.2:6073334-6073353 None:intergenic 45.0%
AGGCCAGAAGAATGATAGAC+AGG + chr2.2:6073757-6073776 MS.gene43847:CDS 45.0%
AGTTTGGGCTTCAGTAGTGT+TGG + chr2.2:6073060-6073079 MS.gene43847:CDS 45.0%
GAGCGAAGATAAAGGTGAAG+AGG + chr2.2:6073737-6073756 MS.gene43847:CDS 45.0%
GCTGTAGAACTAATCCTTCG+AGG + chr2.2:6073439-6073458 MS.gene43847:CDS 45.0%
TTGCAGGAACTTTCCTTGAG+GGG + chr2.2:6073693-6073712 MS.gene43847:intron 45.0%
TTGTGCTGAGGAACAAAACC+GGG + chr2.2:6073368-6073387 MS.gene43847:intron 45.0%
! ATTTAGGGTATCCTCACGGT+TGG + chr2.2:6073414-6073433 MS.gene43847:CDS 45.0%
! GTGGATTTAGGGTATCCTCA+CGG + chr2.2:6073410-6073429 MS.gene43847:CDS 45.0%
!! TGTCCAAAAGCACCCAGTTT+CGG - chr2.2:6073555-6073574 None:intergenic 45.0%
!!! CCGGGCTCTTTTTTTGATTC+AGG + chr2.2:6073386-6073405 MS.gene43847:intron 45.0%
AACTGGTCGCCTTATCTTGC+AGG + chr2.2:6073953-6073972 MS.gene43847:intron 50.0%
AGTGCAACTGGATTGTGCTG+AGG + chr2.2:6073356-6073375 MS.gene43847:intron 50.0%
AGTTTAGGTGGGAAAGCCTC+TGG + chr2.2:6073232-6073251 MS.gene43847:intron 50.0%
CGGATACTGTACATCCTCGA+AGG - chr2.2:6073456-6073475 None:intergenic 50.0%
GCACTCGAACCTTGGACATA+TGG + chr2.2:6073480-6073499 MS.gene43847:CDS 50.0%
GTTTAGGTGGGAAAGCCTCT+GGG + chr2.2:6073233-6073252 MS.gene43847:intron 50.0%
TATGTCCAAGGTTCGAGTGC+AGG - chr2.2:6073480-6073499 None:intergenic 50.0%
TGTTAGCCCAAGCCGAAACT+GGG + chr2.2:6073540-6073559 MS.gene43847:CDS 50.0%
TTCTACAGCTACCAACCGTG+AGG - chr2.2:6073428-6073447 None:intergenic 50.0%
TTGTTAGCCCAAGCCGAAAC+TGG + chr2.2:6073539-6073558 MS.gene43847:CDS 50.0%
! AAAGCACCCAGTTTCGGCTT+GGG - chr2.2:6073549-6073568 None:intergenic 50.0%
! AAGCCGAAACTGGGTGCTTT+TGG + chr2.2:6073549-6073568 MS.gene43847:CDS 50.0%
!! AAAAGCACCCAGTTTCGGCT+TGG - chr2.2:6073550-6073569 None:intergenic 50.0%
!! AGTTTCGGCTTGGGCTAACA+AGG - chr2.2:6073540-6073559 None:intergenic 50.0%
!! GGGGTTTCTGGTTGCAGAAT+TGG + chr2.2:6073712-6073731 MS.gene43847:CDS 50.0%
CTGCAACCAGAAACCCCTCA+AGG - chr2.2:6073709-6073728 None:intergenic 55.0%
GCTAACAAGGTGTGGCTGAG+TGG - chr2.2:6073527-6073546 None:intergenic 55.0%
GGTCGCCTTATCTTGCAGGA+TGG + chr2.2:6073957-6073976 MS.gene43847:intron 55.0%
TCCAAGGTTCGAGTGCAGGA+CGG - chr2.2:6073476-6073495 None:intergenic 55.0%
TGGCTGAGTGGCTAGTAGCT+TGG - chr2.2:6073515-6073534 None:intergenic 55.0%
! TTACTGGCCTGTCTTCGCAG+TGG + chr2.2:6073324-6073343 MS.gene43847:intron 55.0%
CTTTGCAAGCTCCTGCCCAG+AGG - chr2.2:6073251-6073270 None:intergenic 60.0%
TCCGTCCTGCACTCGAACCT+TGG + chr2.2:6073472-6073491 MS.gene43847:CDS 60.0%
! CGGCTTGGGCTAACAAGGTG+TGG - chr2.2:6073535-6073554 None:intergenic 60.0%
AGGTGGGAAAGCCTCTGGGC+AGG + chr2.2:6073237-6073256 MS.gene43847:intron 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 6073046 6074068 6073046 ID=MS.gene43847
chr2.2 mRNA 6073046 6074068 6073046 ID=MS.gene43847.t1;Parent=MS.gene43847
chr2.2 exon 6073046 6073119 6073046 ID=MS.gene43847.t1.exon1;Parent=MS.gene43847.t1
chr2.2 CDS 6073046 6073119 6073046 ID=cds.MS.gene43847.t1;Parent=MS.gene43847.t1
chr2.2 exon 6073408 6073600 6073408 ID=MS.gene43847.t1.exon2;Parent=MS.gene43847.t1
chr2.2 CDS 6073408 6073600 6073408 ID=cds.MS.gene43847.t1;Parent=MS.gene43847.t1
chr2.2 exon 6073699 6073817 6073699 ID=MS.gene43847.t1.exon3;Parent=MS.gene43847.t1
chr2.2 CDS 6073699 6073817 6073699 ID=cds.MS.gene43847.t1;Parent=MS.gene43847.t1
chr2.2 exon 6073975 6074068 6073975 ID=MS.gene43847.t1.exon4;Parent=MS.gene43847.t1
chr2.2 CDS 6073975 6074068 6073975 ID=cds.MS.gene43847.t1;Parent=MS.gene43847.t1
Gene Sequence

>MS.gene43847

ATGATATCTTTTATAGTTTGGGCTTCAGTAGTGTTGGCTCTACAGAAGATTAGGCTATCATCAGCAAAGAATAGGTGTGATATCATAATGGCCTCTTTTGCAATTTTTATACCCTGAAACTTATTACTTGCATTTTGGGTATATTAAAAATTAGTAACCAAGGTATATAAGTCCCATGTATTTCAAAGTTTAGGTGGGAAAGCCTCTGGGCAGGAGCTTGCAAAGATTATGAAATGGTTGTATGAGGCCTGTAACTTTCGTCTCTGAATCATGTTGCTTTACTGGCCTGTCTTCGCAGTGGATAAAGTTCAGTGCAACTGGATTGTGCTGAGGAACAAAACCGGGCTCTTTTTTTGATTCAGGAGTGGATTTAGGGTATCCTCACGGTTGGTAGCTGTAGAACTAATCCTTCGAGGATGTACAGTATCCGTCCTGCACTCGAACCTTGGACATATGGTTAATGAGTCCAAGCTACTAGCCACTCAGCCACACCTTGTTAGCCCAAGCCGAAACTGGGTGCTTTTGGACATCCAAAGCAAATATCATGACTTATCTGTGGCATAACCTTTCAATAATACATGCTTATACTTTTTAATAGAAATAGCATTGTGATTTATTAAATGTAACCATGGTTTTAAATCACATATTTGCAGGAACTTTCCTTGAGGGGTTTCTGGTTGCAGAATTGGTTGAGCGAAGATAAAGGTGAAGAGGCCAGAAGAATGATAGACAGGCTTTTGGGTCTTGTACAAGATGGAAAGTTAAAATACAAGTATGTCTCGTACCTATCATAGGATAAGAAAAATATGGGAGGGATTTATATTCACTCTGAACAATCAATTGTTCATAAATTTTAAAATTTATAACGAAGTCCTTACTCTCTTTTCTCTCAATCAGTTGAAATATTAACTGGTCGCCTTATCTTGCAGGATGGAATTGACTCCCTTTAATGATTTCAACACAGCATTGGATAAAGCTCTAGGAAAACTTGGGAGCCAACCAAAGCAAGTGATCAAATTCTAA
Protein sequence

>MS.gene43847.t1

MISFIVWASVVLALQKIRLSSAKNRSGFRVSSRLVAVELILRGCTVSVLHSNLGHMVNESKLLATQPHLVSPSRNWVLLDIQSKYHDLSELSLRGFWLQNWLSEDKGEEARRMIDRLLGLVQDGKLKYKMELTPFNDFNTALDKALGKLGSQPKQVIKF