AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0951230


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0951230 MtrunA17_Chr4g0067431 61.538 130 16 2 20 115 178 307 4.93e-46 151
Msa0951230 MtrunA17_Chr6g0467361 61.039 77 30 0 39 115 6 82 8.51e-31 105
Msa0951230 MtrunA17_Chr1g0163221 44.094 127 36 4 23 117 165 288 1.85e-22 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 14 sgRNAs with CRISPR-Local

Find 140 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCACAATAATTTAAAATT+TGG 0.142889 6_3:-41054084 Msa0951230:CDS
CATCCTGTGCAGATGTTTCT+TGG 0.182263 6_3:+41054218 None:intergenic
TGTTTCTTGGCAAATTCAAT+TGG 0.419212 6_3:+41054231 None:intergenic
TACCTCCTGCTGAAAATTTG+AGG 0.432319 6_3:+41054936 None:intergenic
AATAATCAATTTACACTAAG+TGG 0.456060 6_3:-41054126 Msa0951230:CDS
AGGTAGTTGTGATAATCTTA+AGG 0.476364 6_3:-41054918 Msa0951230:CDS
AATTTACACTAAGTGGTGGT+TGG 0.508389 6_3:-41054119 Msa0951230:CDS
GCACAGGATGGAAGGAAGAA+AGG 0.547170 6_3:-41054205 Msa0951230:CDS
AAACATCTGCACAGGATGGA+AGG 0.555297 6_3:-41054213 Msa0951230:CDS
TTGCCAAGAAACATCTGCAC+AGG 0.566543 6_3:-41054221 Msa0951230:CDS
TTGTTGATAAAGACATAACA+TGG 0.582622 6_3:-41054173 Msa0951230:CDS
TTTATGTTAAACAAATGCAA+AGG 0.598136 6_3:-41054048 Msa0951230:CDS
AATCAATTTACACTAAGTGG+TGG 0.617140 6_3:-41054123 Msa0951230:CDS
CAAGAAACATCTGCACAGGA+TGG 0.624347 6_3:-41054217 Msa0951230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTGACATTTTTTTTTT+TGG - chr6_3:41053515-41053534 Msa0951230:intron 10.0%
!!! TTATTTGACATTTTTTTTTT+TGG - chr6_3:41053515-41053534 Msa0951230:intron 10.0%
!!! TATTTGTGTCTTTTTTTTTT+AGG - chr6_3:41053299-41053318 Msa0951230:intron 15.0%
!! AATATATTAAAATGGAGTTA+TGG + chr6_3:41053837-41053856 None:intergenic 15.0%
!! AATAAATTACCTTCAAAATA+GGG + chr6_3:41054323-41054342 None:intergenic 15.0%
!! AAATAAATTACCTTCAAAAT+AGG + chr6_3:41054324-41054343 None:intergenic 15.0%
!!! AATTTATCTAAAGTAAAAGA+TGG + chr6_3:41054369-41054388 None:intergenic 15.0%
!! TTACTTTAGATAAATTCTAA+TGG - chr6_3:41054373-41054392 Msa0951230:intron 15.0%
!! TACTTTAGATAAATTCTAAT+GGG - chr6_3:41054374-41054393 Msa0951230:intron 15.0%
!!! TTTTTACTTTTATTTTGTGA+CGG - chr6_3:41054577-41054596 Msa0951230:intron 15.0%
!!! TATTTGTGTCTTTTTTTTTT+AGG - chr6_3:41053299-41053318 Msa0951230:intron 15.0%
!! AATATATTAAAATGGAGTTA+TGG + chr6_3:41053837-41053856 None:intergenic 15.0%
!! AATAAATTACCTTCAAAATA+GGG + chr6_3:41054323-41054342 None:intergenic 15.0%
!! AAATAAATTACCTTCAAAAT+AGG + chr6_3:41054324-41054343 None:intergenic 15.0%
!!! AATTTATCTAAAGTAAAAGA+TGG + chr6_3:41054369-41054388 None:intergenic 15.0%
!! TTACTTTAGATAAATTCTAA+TGG - chr6_3:41054373-41054392 Msa0951230:intron 15.0%
!! TACTTTAGATAAATTCTAAT+GGG - chr6_3:41054374-41054393 Msa0951230:intron 15.0%
!!! TTTTTACTTTTATTTTGTGA+CGG - chr6_3:41054577-41054596 Msa0951230:intron 15.0%
!! ACTAATGAAATTGACTAAAT+GGG + chr6_3:41053628-41053647 None:intergenic 20.0%
!! TACTAATGAAATTGACTAAA+TGG + chr6_3:41053629-41053648 None:intergenic 20.0%
!!! TTTTTTTTCAAGTAGTATAG+TGG + chr6_3:41053726-41053745 None:intergenic 20.0%
!! CATGACAATTAATCTAATTA+AGG + chr6_3:41053769-41053788 None:intergenic 20.0%
!! AACTCAGAATAAATACAAAA+AGG + chr6_3:41054027-41054046 None:intergenic 20.0%
!! AATAATCAATTTACACTAAG+TGG - chr6_3:41054167-41054186 Msa0951230:CDS 20.0%
!!! ATTTTAAATTATTGTGAGCT+CGG + chr6_3:41054208-41054227 None:intergenic 20.0%
!!! GCTCACAATAATTTAAAATT+TGG - chr6_3:41054209-41054228 Msa0951230:CDS 20.0%
!! TTTATGTTAAACAAATGCAA+AGG - chr6_3:41054245-41054264 Msa0951230:intron 20.0%
!!! TTTTCTTACATATTGGAATA+GGG + chr6_3:41054488-41054507 None:intergenic 20.0%
!!! TTTTTCTTACATATTGGAAT+AGG + chr6_3:41054489-41054508 None:intergenic 20.0%
!!! ACTCATTTTTTCTTACATAT+TGG + chr6_3:41054495-41054514 None:intergenic 20.0%
!! TCTATTAAGTTCATCAATTT+AGG + chr6_3:41054521-41054540 None:intergenic 20.0%
!!! TTTTGTTAGAACAAAGTAAA+TGG + chr6_3:41054675-41054694 None:intergenic 20.0%
!! ACTAATGAAATTGACTAAAT+GGG + chr6_3:41053628-41053647 None:intergenic 20.0%
!! TACTAATGAAATTGACTAAA+TGG + chr6_3:41053629-41053648 None:intergenic 20.0%
!!! TTTTTTTTCAAGTAGTATAG+TGG + chr6_3:41053726-41053745 None:intergenic 20.0%
!! CATGACAATTAATCTAATTA+AGG + chr6_3:41053769-41053788 None:intergenic 20.0%
!! AACTCAGAATAAATACAAAA+AGG + chr6_3:41054027-41054046 None:intergenic 20.0%
!! AATAATCAATTTACACTAAG+TGG - chr6_3:41054167-41054186 Msa0951230:CDS 20.0%
!!! ATTTTAAATTATTGTGAGCT+CGG + chr6_3:41054208-41054227 None:intergenic 20.0%
!!! GCTCACAATAATTTAAAATT+TGG - chr6_3:41054209-41054228 Msa0951230:CDS 20.0%
!! TTTATGTTAAACAAATGCAA+AGG - chr6_3:41054245-41054264 Msa0951230:intron 20.0%
!!! TTTTCTTACATATTGGAATA+GGG + chr6_3:41054488-41054507 None:intergenic 20.0%
!!! TTTTTCTTACATATTGGAAT+AGG + chr6_3:41054489-41054508 None:intergenic 20.0%
!!! ACTCATTTTTTCTTACATAT+TGG + chr6_3:41054495-41054514 None:intergenic 20.0%
!! TCTATTAAGTTCATCAATTT+AGG + chr6_3:41054521-41054540 None:intergenic 20.0%
!!! TTTTGTTAGAACAAAGTAAA+TGG + chr6_3:41054675-41054694 None:intergenic 20.0%
! TTAAGAAATTCTAACTCAGT+TGG - chr6_3:41053573-41053592 Msa0951230:intron 25.0%
! GATTAATTGTCATGTACTAA+TGG - chr6_3:41053775-41053794 Msa0951230:intron 25.0%
! ATAAATACAAAAAGGCCAAA+TGG + chr6_3:41054019-41054038 None:intergenic 25.0%
! TTTATTCTGAGTTGTATTAC+AGG - chr6_3:41054034-41054053 Msa0951230:CDS 25.0%
!! TTGTTGATAAAGACATAACA+TGG - chr6_3:41054120-41054139 Msa0951230:CDS 25.0%
! TAAAGAGAGCAAATTAAGAT+TGG - chr6_3:41054861-41054880 Msa0951230:intron 25.0%
! TTAAGAAATTCTAACTCAGT+TGG - chr6_3:41053573-41053592 Msa0951230:intron 25.0%
! GATTAATTGTCATGTACTAA+TGG - chr6_3:41053775-41053794 Msa0951230:intron 25.0%
! ATAAATACAAAAAGGCCAAA+TGG + chr6_3:41054019-41054038 None:intergenic 25.0%
! TTTATTCTGAGTTGTATTAC+AGG - chr6_3:41054034-41054053 Msa0951230:CDS 25.0%
!! TTGTTGATAAAGACATAACA+TGG - chr6_3:41054120-41054139 Msa0951230:CDS 25.0%
! TAAAGAGAGCAAATTAAGAT+TGG - chr6_3:41054861-41054880 Msa0951230:intron 25.0%
AGGTAGTTGTGATAATCTTA+AGG - chr6_3:41053375-41053394 Msa0951230:intron 30.0%
! CTCTTTCAATGTATGTCTTT+TGG + chr6_3:41053474-41053493 None:intergenic 30.0%
ATACATTGAAAGAGATCACT+TGG - chr6_3:41053480-41053499 Msa0951230:intron 30.0%
AATGAAATTGACTAAATGGG+TGG + chr6_3:41053625-41053644 None:intergenic 30.0%
!!! TCACTTTTTATAACGTGAAG+AGG + chr6_3:41053695-41053714 None:intergenic 30.0%
TCTACATGATGTATTGTGAT+TGG - chr6_3:41053882-41053901 Msa0951230:intron 30.0%
TTCACACACACATATACATA+TGG + chr6_3:41053975-41053994 None:intergenic 30.0%
GTTAGAAAATTGCATCCATT+TGG - chr6_3:41054001-41054020 Msa0951230:intron 30.0%
TGTTTCTTGGCAAATTCAAT+TGG + chr6_3:41054065-41054084 None:intergenic 30.0%
AATCAATTTACACTAAGTGG+TGG - chr6_3:41054170-41054189 Msa0951230:CDS 30.0%
AGATGGCAATTGAAAAATAG+CGG + chr6_3:41054352-41054371 None:intergenic 30.0%
TAAAGTCAAAGAATGTCAAG+AGG + chr6_3:41054403-41054422 None:intergenic 30.0%
TGCATTGAATACACAAGTTA+CGG + chr6_3:41054442-41054461 None:intergenic 30.0%
!! GGTTTGTTAACGAATGTTTA+AGG + chr6_3:41054654-41054673 None:intergenic 30.0%
AGGTAGTTGTGATAATCTTA+AGG - chr6_3:41053375-41053394 Msa0951230:intron 30.0%
! CTCTTTCAATGTATGTCTTT+TGG + chr6_3:41053474-41053493 None:intergenic 30.0%
ATACATTGAAAGAGATCACT+TGG - chr6_3:41053480-41053499 Msa0951230:intron 30.0%
AATGAAATTGACTAAATGGG+TGG + chr6_3:41053625-41053644 None:intergenic 30.0%
!!! TCACTTTTTATAACGTGAAG+AGG + chr6_3:41053695-41053714 None:intergenic 30.0%
TCTACATGATGTATTGTGAT+TGG - chr6_3:41053882-41053901 Msa0951230:intron 30.0%
TTCACACACACATATACATA+TGG + chr6_3:41053975-41053994 None:intergenic 30.0%
GTTAGAAAATTGCATCCATT+TGG - chr6_3:41054001-41054020 Msa0951230:intron 30.0%
TGTTTCTTGGCAAATTCAAT+TGG + chr6_3:41054065-41054084 None:intergenic 30.0%
AATCAATTTACACTAAGTGG+TGG - chr6_3:41054170-41054189 Msa0951230:CDS 30.0%
AGATGGCAATTGAAAAATAG+CGG + chr6_3:41054352-41054371 None:intergenic 30.0%
TAAAGTCAAAGAATGTCAAG+AGG + chr6_3:41054403-41054422 None:intergenic 30.0%
TGCATTGAATACACAAGTTA+CGG + chr6_3:41054442-41054461 None:intergenic 30.0%
!! GGTTTGTTAACGAATGTTTA+AGG + chr6_3:41054654-41054673 None:intergenic 30.0%
! GATTTCCTCAAATTTTCAGC+AGG - chr6_3:41053352-41053371 Msa0951230:intron 35.0%
! ATGTCTTTTGGATCACACAA+AGG + chr6_3:41053462-41053481 None:intergenic 35.0%
AATTTACACTAAGTGGTGGT+TGG - chr6_3:41054174-41054193 Msa0951230:CDS 35.0%
!!! TGCTATTTTCTCTCTCGAAA+AGG - chr6_3:41054286-41054305 Msa0951230:intron 35.0%
! CTACATGTGTTGTGTTTCTA+TGG + chr6_3:41054740-41054759 None:intergenic 35.0%
!!! GCTTCAGTTCTCTTTTTTTG+AGG - chr6_3:41054813-41054832 Msa0951230:intron 35.0%
! GATTTCCTCAAATTTTCAGC+AGG - chr6_3:41053352-41053371 Msa0951230:intron 35.0%
! ATGTCTTTTGGATCACACAA+AGG + chr6_3:41053462-41053481 None:intergenic 35.0%
AATTTACACTAAGTGGTGGT+TGG - chr6_3:41054174-41054193 Msa0951230:CDS 35.0%
!!! TGCTATTTTCTCTCTCGAAA+AGG - chr6_3:41054286-41054305 Msa0951230:intron 35.0%
! CTACATGTGTTGTGTTTCTA+TGG + chr6_3:41054740-41054759 None:intergenic 35.0%
!!! GCTTCAGTTCTCTTTTTTTG+AGG - chr6_3:41054813-41054832 Msa0951230:intron 35.0%
! TTCCTCAAATTTTCAGCAGG+AGG - chr6_3:41053355-41053374 Msa0951230:intron 40.0%
TACCTCCTGCTGAAAATTTG+AGG + chr6_3:41053360-41053379 None:intergenic 40.0%
AAATTGACTAAATGGGTGGC+AGG + chr6_3:41053621-41053640 None:intergenic 40.0%
CGAGAGAGAAAATAGCAACT+TGG + chr6_3:41054283-41054302 None:intergenic 40.0%
TTACACTACCACTATTGACG+AGG + chr6_3:41054895-41054914 None:intergenic 40.0%
! TTCCTCAAATTTTCAGCAGG+AGG - chr6_3:41053355-41053374 Msa0951230:intron 40.0%
TACCTCCTGCTGAAAATTTG+AGG + chr6_3:41053360-41053379 None:intergenic 40.0%
AAATTGACTAAATGGGTGGC+AGG + chr6_3:41053621-41053640 None:intergenic 40.0%
CGAGAGAGAAAATAGCAACT+TGG + chr6_3:41054283-41054302 None:intergenic 40.0%
TTACACTACCACTATTGACG+AGG + chr6_3:41054895-41054914 None:intergenic 40.0%
CAGGAGATAGGAGTTTCTTG+GGG + chr6_3:41053602-41053621 None:intergenic 45.0%
GCAGGAGATAGGAGTTTCTT+GGG + chr6_3:41053603-41053622 None:intergenic 45.0%
TTGCCAAGAAACATCTGCAC+AGG - chr6_3:41054072-41054091 Msa0951230:CDS 45.0%
CATCCTGTGCAGATGTTTCT+TGG + chr6_3:41054078-41054097 None:intergenic 45.0%
CAAGAAACATCTGCACAGGA+TGG - chr6_3:41054076-41054095 Msa0951230:CDS 45.0%
AAACATCTGCACAGGATGGA+AGG - chr6_3:41054080-41054099 Msa0951230:CDS 45.0%
!! ACGAGCACTCCCTATTTTGA+AGG - chr6_3:41054311-41054330 Msa0951230:intron 45.0%
ACTACCACTATTGACGAGGT+CGG + chr6_3:41054891-41054910 None:intergenic 45.0%
CAGGAGATAGGAGTTTCTTG+GGG + chr6_3:41053602-41053621 None:intergenic 45.0%
GCAGGAGATAGGAGTTTCTT+GGG + chr6_3:41053603-41053622 None:intergenic 45.0%
TTGCCAAGAAACATCTGCAC+AGG - chr6_3:41054072-41054091 Msa0951230:CDS 45.0%
CATCCTGTGCAGATGTTTCT+TGG + chr6_3:41054078-41054097 None:intergenic 45.0%
CAAGAAACATCTGCACAGGA+TGG - chr6_3:41054076-41054095 Msa0951230:CDS 45.0%
AAACATCTGCACAGGATGGA+AGG - chr6_3:41054080-41054099 Msa0951230:CDS 45.0%
!! ACGAGCACTCCCTATTTTGA+AGG - chr6_3:41054311-41054330 Msa0951230:intron 45.0%
ACTACCACTATTGACGAGGT+CGG + chr6_3:41054891-41054910 None:intergenic 45.0%
!!! TACTTAATTTTTTTTTTTTT+TGG - chr6_3:41053328-41053347 Msa0951230:intron 5.0%
!! TAAGAAATAATATATTAAAA+TGG + chr6_3:41053845-41053864 None:intergenic 5.0%
!! TAAATAAAAAAGAATTTATT+TGG + chr6_3:41054553-41054572 None:intergenic 5.0%
!! TAAAAAATTATTCATTAAAA+AGG + chr6_3:41054610-41054629 None:intergenic 5.0%
!!! TACTTAATTTTTTTTTTTTT+TGG - chr6_3:41053328-41053347 Msa0951230:intron 5.0%
!! TAAGAAATAATATATTAAAA+TGG + chr6_3:41053845-41053864 None:intergenic 5.0%
!! TAAATAAAAAAGAATTTATT+TGG + chr6_3:41054553-41054572 None:intergenic 5.0%
!! TAAAAAATTATTCATTAAAA+AGG + chr6_3:41054610-41054629 None:intergenic 5.0%
GGCAGGAGATAGGAGTTTCT+TGG + chr6_3:41053604-41053623 None:intergenic 50.0%
CTAAATGGGTGGCAGGAGAT+AGG + chr6_3:41053614-41053633 None:intergenic 50.0%
GCACAGGATGGAAGGAAGAA+AGG - chr6_3:41054088-41054107 Msa0951230:CDS 50.0%
AGAACCGACCTCGTCAATAG+TGG - chr6_3:41054884-41054903 Msa0951230:intron 50.0%
GGCAGGAGATAGGAGTTTCT+TGG + chr6_3:41053604-41053623 None:intergenic 50.0%
CTAAATGGGTGGCAGGAGAT+AGG + chr6_3:41053614-41053633 None:intergenic 50.0%
GCACAGGATGGAAGGAAGAA+AGG - chr6_3:41054088-41054107 Msa0951230:CDS 50.0%
AGAACCGACCTCGTCAATAG+TGG - chr6_3:41054884-41054903 Msa0951230:intron 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 41053275 41055040 41053275 ID=Msa0951230;Name=Msa0951230
chr6_3 mRNA 41053275 41055040 41053275 ID=Msa0951230-mRNA-1;Parent=Msa0951230;Name=Msa0951230-mRNA-1;_AED=0.48;_eAED=0.52;_QI=0|0|0|0.75|0|0|4|0|124
chr6_3 exon 41055012 41055040 41055012 ID=Msa0951230-mRNA-1:exon:9826;Parent=Msa0951230-mRNA-1
chr6_3 exon 41054907 41054994 41054907 ID=Msa0951230-mRNA-1:exon:9825;Parent=Msa0951230-mRNA-1
chr6_3 exon 41054032 41054259 41054032 ID=Msa0951230-mRNA-1:exon:9824;Parent=Msa0951230-mRNA-1
chr6_3 exon 41053275 41053304 41053275 ID=Msa0951230-mRNA-1:exon:9823;Parent=Msa0951230-mRNA-1
chr6_3 CDS 41055012 41055040 41055012 ID=Msa0951230-mRNA-1:cds;Parent=Msa0951230-mRNA-1
chr6_3 CDS 41054907 41054994 41054907 ID=Msa0951230-mRNA-1:cds;Parent=Msa0951230-mRNA-1
chr6_3 CDS 41054032 41054259 41054032 ID=Msa0951230-mRNA-1:cds;Parent=Msa0951230-mRNA-1
chr6_3 CDS 41053275 41053304 41053275 ID=Msa0951230-mRNA-1:cds;Parent=Msa0951230-mRNA-1
Gene Sequence

>Msa0951230

ATGTTTCATTTTATATATTTTTTCTATTTGTGTTACTACTTAATTTTTTTTTTTTTTGGTGATTTCCTCAAATTTTCAGCAGGAGGTAGTTGTGATAATCTTAAGGAGCGAAGCAAAGTCATACCAATTGAATTTGCCAAGAAACATCTGCACAGGATGGAAGGAAGAAAGGTTACTCTTTTTGTTGATAAAGACATAACATGGAATGTTGATTTGAATGTCACTTCAAATAATCAATTTACACTAAGTGGTGGTTGGAGTAAATTCCGAGCTCACAATAATTTAAAATTTGGTGATATCTGTGTCTTTATGTTAAACAAATGCAAAGGAAAAGTTTCATTCCAACAAATTCACATGCTGACTTTGACATATTAA

Protein sequence

>Msa0951230

MFHFIYFFYLCYYLIFFFFGDFLKFSAGGSCDNLKERSKVIPIEFAKKHLHRMEGRKVTLFVDKDITWNVDLNVTSNNQFTLSGGWSKFRAHNNLKFGDICVFMLNKCKGKVSFQQIHMLTLTY*