AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0638480


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0638480 MtrunA17_Chr4g0049791 98.824 85 1 0 1 85 1 85 3.18e-58 172
Msa0638480 MtrunA17_Chr2g0279651 85.882 85 12 0 1 85 1 85 7.55e-51 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0638480 AT4G33640.1 80.769 78 15 0 1 78 1 78 1.13e-41 132
Msa0638480 AT4G33640.2 80.769 78 15 0 1 78 67 144 3.49e-41 132

Find 31 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTTGATTCACAAACTAAA+TGG 0.258730 4_3:-34003063 None:intergenic
TGCATTTACTAAAACAGATT+TGG 0.294396 4_3:+34003234 Msa0638480:three_prime_UTR
TGCATTGTGAAGGTCACATT+TGG 0.398089 4_3:+34002727 Msa0638480:intron
AGTTGATGCTTAAATTTCAA+TGG 0.407398 4_3:-34003190 None:intergenic
CCTGCTGCTGCTAACTGATT+CGG 0.442731 4_3:+34002901 Msa0638480:exon
GAGTGATTTCCACATTATCA+TGG 0.446001 4_3:-34002867 None:intergenic
GTGTGTTTAAAGTTTCTGTT+CGG 0.456320 4_3:-34001898 None:intergenic
GAACACTCTTTCACGATGAT+CGG 0.491735 4_3:+34002749 Msa0638480:CDS
AAGAGGAGGTTGAAAAGCTG+AGG 0.496528 4_3:+34001983 Msa0638480:CDS
CCGAATCAGTTAGCAGCAGC+AGG 0.502169 4_3:-34002901 None:intergenic
CAGTTAGCAGCAGCAGGAGC+AGG 0.504867 4_3:-34002895 None:intergenic
GTTAGTGATTCAAGCAGTAA+AGG 0.512252 4_3:-34002945 None:intergenic
CTTGGAAATGTTCAAGCAGA+TGG 0.516658 4_3:+34002021 Msa0638480:CDS
CACTTCGTAAATAATAGTAT+AGG 0.525059 4_3:-34003158 None:intergenic
AGGGAAGAAATCAAGAGGCT+TGG 0.527446 4_3:+34002003 Msa0638480:CDS
CTTAAATTTCAATGGTTCTG+TGG 0.531142 4_3:-34003182 None:intergenic
GCTAACTGATTCGGTTGTGA+AGG 0.539593 4_3:+34002910 Msa0638480:exon
TGTGAAGATGAACGTAGAAG+AGG 0.563453 4_3:+34001966 Msa0638480:exon
GAAGATGAACGTAGAAGAGG+AGG 0.565552 4_3:+34001969 Msa0638480:exon
AGAGGAGGTTGAAAAGCTGA+GGG 0.572997 4_3:+34001984 Msa0638480:CDS
ATAGTATAGGATAAACATGA+AGG 0.579841 4_3:-34003145 None:intergenic
CTATACTATTATTTACGAAG+TGG 0.588267 4_3:+34003159 Msa0638480:three_prime_UTR
AATATATTTGAAGCACTCGT+CGG 0.601303 4_3:+34002778 Msa0638480:CDS
TCAAGCAGATGGTTCTTGCA+AGG 0.604584 4_3:+34002032 Msa0638480:CDS
CTAACTGATTCGGTTGTGAA+GGG 0.617075 4_3:+34002911 Msa0638480:exon
AGCTGAGGGAAGAAATCAAG+AGG 0.626324 4_3:+34001998 Msa0638480:CDS
GACGGTGAACTACTGTTGCA+AGG 0.632747 4_3:+34002841 Msa0638480:CDS
GATGTTGTAATATATGCATG+TGG 0.675462 4_3:+34003003 Msa0638480:three_prime_UTR
GCAAGGAGTCCATGATAATG+TGG 0.676630 4_3:+34002858 Msa0638480:CDS
TGTAATATATGCATGTGGAG+AGG 0.735312 4_3:+34003008 Msa0638480:three_prime_UTR
CGTAAAGTAGTTGCATACGA+CGG 0.749247 4_3:+34002823 Msa0638480:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATAAATATAAAAAGCTTTT+AGG + chr4_3:34001875-34001894 Msa0638480:five_prime_UTR 10.0%
!! TAATAAACAAATTAATGTAT+AGG - chr4_3:34002344-34002363 None:intergenic 10.0%
!!! AATAAATATAAAAAGCTTTT+AGG + chr4_3:34001875-34001894 Msa0638480:five_prime_UTR 10.0%
!! TAATAAACAAATTAATGTAT+AGG - chr4_3:34002344-34002363 None:intergenic 10.0%
!!! AATTTGTTTATTATAAACCA+TGG + chr4_3:34002351-34002370 Msa0638480:intron 15.0%
!! ATAATTGTAATTAAATGTGT+TGG + chr4_3:34002513-34002532 Msa0638480:intron 15.0%
!!! AATTTGTTTATTATAAACCA+TGG + chr4_3:34002351-34002370 Msa0638480:intron 15.0%
!! ATAATTGTAATTAAATGTGT+TGG + chr4_3:34002513-34002532 Msa0638480:intron 15.0%
!! GAATCAAGTTCTTAATTAAA+AGG - chr4_3:34002138-34002157 None:intergenic 20.0%
!! TTTCATATGATATTTCGTAA+TGG - chr4_3:34002271-34002290 None:intergenic 20.0%
!!! AAGTATTGATATGATGTTTA+GGG - chr4_3:34002478-34002497 None:intergenic 20.0%
!!! TAAGTATTGATATGATGTTT+AGG - chr4_3:34002479-34002498 None:intergenic 20.0%
!! GAATCAAGTTCTTAATTAAA+AGG - chr4_3:34002138-34002157 None:intergenic 20.0%
!! TTTCATATGATATTTCGTAA+TGG - chr4_3:34002271-34002290 None:intergenic 20.0%
!!! AAGTATTGATATGATGTTTA+GGG - chr4_3:34002478-34002497 None:intergenic 20.0%
!!! TAAGTATTGATATGATGTTT+AGG - chr4_3:34002479-34002498 None:intergenic 20.0%
!!! AAGAAAGACTTTCTTGTTTT+TGG + chr4_3:34001924-34001943 Msa0638480:five_prime_UTR 25.0%
!! GAAAATGTATATGGTTTGTA+AGG - chr4_3:34002091-34002110 None:intergenic 25.0%
! ATGCATCATGAAAATGTATA+TGG - chr4_3:34002100-34002119 None:intergenic 25.0%
! TTCAGATCTAGATATATTGA+TGG + chr4_3:34002155-34002174 Msa0638480:intron 25.0%
! TCAGATCTAGATATATTGAT+GGG + chr4_3:34002156-34002175 Msa0638480:intron 25.0%
! TAATGTATAGGTAGATACAT+TGG - chr4_3:34002332-34002351 None:intergenic 25.0%
! TTGTTTATTATAAACCATGG+AGG + chr4_3:34002354-34002373 Msa0638480:intron 25.0%
!!! CATATCAGTTTTATATGGAA+TGG - chr4_3:34002399-34002418 None:intergenic 25.0%
! CATTCCATATAAAACTGATA+TGG + chr4_3:34002397-34002416 Msa0638480:intron 25.0%
!!! AATTTGCTGAAATAGTACTA+TGG + chr4_3:34002573-34002592 Msa0638480:intron 25.0%
! AAATATGTAATGCATTGTGA+AGG + chr4_3:34002717-34002736 Msa0638480:intron 25.0%
! CATTTGATTCACAAACTAAA+TGG - chr4_3:34003066-34003085 None:intergenic 25.0%
! ATAGTATAGGATAAACATGA+AGG - chr4_3:34003148-34003167 None:intergenic 25.0%
! CACTTCGTAAATAATAGTAT+AGG - chr4_3:34003161-34003180 None:intergenic 25.0%
! CTATACTATTATTTACGAAG+TGG + chr4_3:34003159-34003178 Msa0638480:three_prime_UTR 25.0%
!! AGTTGATGCTTAAATTTCAA+TGG - chr4_3:34003193-34003212 None:intergenic 25.0%
! TGCATTTACTAAAACAGATT+TGG + chr4_3:34003234-34003253 Msa0638480:three_prime_UTR 25.0%
!!! AAGAAAGACTTTCTTGTTTT+TGG + chr4_3:34001924-34001943 Msa0638480:five_prime_UTR 25.0%
!! GAAAATGTATATGGTTTGTA+AGG - chr4_3:34002091-34002110 None:intergenic 25.0%
! ATGCATCATGAAAATGTATA+TGG - chr4_3:34002100-34002119 None:intergenic 25.0%
! TTCAGATCTAGATATATTGA+TGG + chr4_3:34002155-34002174 Msa0638480:intron 25.0%
! TCAGATCTAGATATATTGAT+GGG + chr4_3:34002156-34002175 Msa0638480:intron 25.0%
! TAATGTATAGGTAGATACAT+TGG - chr4_3:34002332-34002351 None:intergenic 25.0%
! TTGTTTATTATAAACCATGG+AGG + chr4_3:34002354-34002373 Msa0638480:intron 25.0%
!!! CATATCAGTTTTATATGGAA+TGG - chr4_3:34002399-34002418 None:intergenic 25.0%
! CATTCCATATAAAACTGATA+TGG + chr4_3:34002397-34002416 Msa0638480:intron 25.0%
!!! AATTTGCTGAAATAGTACTA+TGG + chr4_3:34002573-34002592 Msa0638480:intron 25.0%
! AAATATGTAATGCATTGTGA+AGG + chr4_3:34002717-34002736 Msa0638480:intron 25.0%
! CATTTGATTCACAAACTAAA+TGG - chr4_3:34003066-34003085 None:intergenic 25.0%
! ATAGTATAGGATAAACATGA+AGG - chr4_3:34003148-34003167 None:intergenic 25.0%
! CACTTCGTAAATAATAGTAT+AGG - chr4_3:34003161-34003180 None:intergenic 25.0%
! CTATACTATTATTTACGAAG+TGG + chr4_3:34003159-34003178 Msa0638480:three_prime_UTR 25.0%
!! AGTTGATGCTTAAATTTCAA+TGG - chr4_3:34003193-34003212 None:intergenic 25.0%
! TGCATTTACTAAAACAGATT+TGG + chr4_3:34003234-34003253 Msa0638480:three_prime_UTR 25.0%
! GTGTGTTTAAAGTTTCTGTT+CGG - chr4_3:34001901-34001920 None:intergenic 30.0%
!!! AAAGACTTTCTTGTTTTTGG+TGG + chr4_3:34001927-34001946 Msa0638480:five_prime_UTR 30.0%
TTCTTGCAAGGTATAACAAA+AGG + chr4_3:34002044-34002063 Msa0638480:intron 30.0%
! TGATGGGTATTTATTGAATG+TGG + chr4_3:34002172-34002191 Msa0638480:intron 30.0%
! TGGTCACTTTCTTATTCTTA+TGG + chr4_3:34002192-34002211 Msa0638480:intron 30.0%
!! CTAGCCATATCAGTTTTATA+TGG - chr4_3:34002404-34002423 None:intergenic 30.0%
! CTATATCTTCAGTTGATTCA+TGG - chr4_3:34002608-34002627 None:intergenic 30.0%
TATAGTGAGTGATGGTTAAT+TGG + chr4_3:34002623-34002642 Msa0638480:intron 30.0%
! AATATATTTGAAGCACTCGT+CGG + chr4_3:34002778-34002797 Msa0638480:CDS 30.0%
!!! GAATCACTAACCTGTTTTTA+TGG + chr4_3:34002957-34002976 Msa0638480:three_prime_UTR 30.0%
GATGTTGTAATATATGCATG+TGG + chr4_3:34003003-34003022 Msa0638480:three_prime_UTR 30.0%
! CTTAAATTTCAATGGTTCTG+TGG - chr4_3:34003185-34003204 None:intergenic 30.0%
! GTGTGTTTAAAGTTTCTGTT+CGG - chr4_3:34001901-34001920 None:intergenic 30.0%
!!! AAAGACTTTCTTGTTTTTGG+TGG + chr4_3:34001927-34001946 Msa0638480:five_prime_UTR 30.0%
TTCTTGCAAGGTATAACAAA+AGG + chr4_3:34002044-34002063 Msa0638480:intron 30.0%
! TGATGGGTATTTATTGAATG+TGG + chr4_3:34002172-34002191 Msa0638480:intron 30.0%
! TGGTCACTTTCTTATTCTTA+TGG + chr4_3:34002192-34002211 Msa0638480:intron 30.0%
!! CTAGCCATATCAGTTTTATA+TGG - chr4_3:34002404-34002423 None:intergenic 30.0%
! CTATATCTTCAGTTGATTCA+TGG - chr4_3:34002608-34002627 None:intergenic 30.0%
TATAGTGAGTGATGGTTAAT+TGG + chr4_3:34002623-34002642 Msa0638480:intron 30.0%
! AATATATTTGAAGCACTCGT+CGG + chr4_3:34002778-34002797 Msa0638480:CDS 30.0%
!!! GAATCACTAACCTGTTTTTA+TGG + chr4_3:34002957-34002976 Msa0638480:three_prime_UTR 30.0%
GATGTTGTAATATATGCATG+TGG + chr4_3:34003003-34003022 Msa0638480:three_prime_UTR 30.0%
! CTTAAATTTCAATGGTTCTG+TGG - chr4_3:34003185-34003204 None:intergenic 30.0%
TCTTATGGATCTAGATCACA+AGG + chr4_3:34002207-34002226 Msa0638480:intron 35.0%
ACTGAAGATATAGTGAGTGA+TGG + chr4_3:34002615-34002634 Msa0638480:intron 35.0%
GTTAATGCGCATATGTGAAT+TGG + chr4_3:34002653-34002672 Msa0638480:intron 35.0%
GAGTGATTTCCACATTATCA+TGG - chr4_3:34002870-34002889 None:intergenic 35.0%
GTTAGTGATTCAAGCAGTAA+AGG - chr4_3:34002948-34002967 None:intergenic 35.0%
TGTAATATATGCATGTGGAG+AGG + chr4_3:34003008-34003027 Msa0638480:three_prime_UTR 35.0%
TCTTATGGATCTAGATCACA+AGG + chr4_3:34002207-34002226 Msa0638480:intron 35.0%
ACTGAAGATATAGTGAGTGA+TGG + chr4_3:34002615-34002634 Msa0638480:intron 35.0%
GTTAATGCGCATATGTGAAT+TGG + chr4_3:34002653-34002672 Msa0638480:intron 35.0%
GAGTGATTTCCACATTATCA+TGG - chr4_3:34002870-34002889 None:intergenic 35.0%
GTTAGTGATTCAAGCAGTAA+AGG - chr4_3:34002948-34002967 None:intergenic 35.0%
TGTAATATATGCATGTGGAG+AGG + chr4_3:34003008-34003027 Msa0638480:three_prime_UTR 35.0%
TGTGAAGATGAACGTAGAAG+AGG + chr4_3:34001966-34001985 Msa0638480:exon 40.0%
CTTGGAAATGTTCAAGCAGA+TGG + chr4_3:34002021-34002040 Msa0638480:CDS 40.0%
CACAAGGTCATTCACAACAT+TGG + chr4_3:34002223-34002242 Msa0638480:intron 40.0%
TGCATTGTGAAGGTCACATT+TGG + chr4_3:34002727-34002746 Msa0638480:intron 40.0%
GAACACTCTTTCACGATGAT+CGG + chr4_3:34002749-34002768 Msa0638480:CDS 40.0%
CGTAAAGTAGTTGCATACGA+CGG + chr4_3:34002823-34002842 Msa0638480:CDS 40.0%
!! CTAACTGATTCGGTTGTGAA+GGG + chr4_3:34002911-34002930 Msa0638480:exon 40.0%
!!! CACTAACCTGTTTTTATGGC+TGG + chr4_3:34002961-34002980 Msa0638480:three_prime_UTR 40.0%
ATCACACCAGCCATAAAAAC+AGG - chr4_3:34002970-34002989 None:intergenic 40.0%
TGTGAAGATGAACGTAGAAG+AGG + chr4_3:34001966-34001985 Msa0638480:exon 40.0%
CTTGGAAATGTTCAAGCAGA+TGG + chr4_3:34002021-34002040 Msa0638480:CDS 40.0%
CACAAGGTCATTCACAACAT+TGG + chr4_3:34002223-34002242 Msa0638480:intron 40.0%
TGCATTGTGAAGGTCACATT+TGG + chr4_3:34002727-34002746 Msa0638480:intron 40.0%
GAACACTCTTTCACGATGAT+CGG + chr4_3:34002749-34002768 Msa0638480:CDS 40.0%
CGTAAAGTAGTTGCATACGA+CGG + chr4_3:34002823-34002842 Msa0638480:CDS 40.0%
!! CTAACTGATTCGGTTGTGAA+GGG + chr4_3:34002911-34002930 Msa0638480:exon 40.0%
!!! CACTAACCTGTTTTTATGGC+TGG + chr4_3:34002961-34002980 Msa0638480:three_prime_UTR 40.0%
ATCACACCAGCCATAAAAAC+AGG - chr4_3:34002970-34002989 None:intergenic 40.0%
GAAGATGAACGTAGAAGAGG+AGG + chr4_3:34001969-34001988 Msa0638480:exon 45.0%
AAGAGGAGGTTGAAAAGCTG+AGG + chr4_3:34001983-34002002 Msa0638480:CDS 45.0%
AGAGGAGGTTGAAAAGCTGA+GGG + chr4_3:34001984-34002003 Msa0638480:CDS 45.0%
AGCTGAGGGAAGAAATCAAG+AGG + chr4_3:34001998-34002017 Msa0638480:CDS 45.0%
AGGGAAGAAATCAAGAGGCT+TGG + chr4_3:34002003-34002022 Msa0638480:CDS 45.0%
TCAAGCAGATGGTTCTTGCA+AGG + chr4_3:34002032-34002051 Msa0638480:CDS 45.0%
! GCAAGGAGTCCATGATAATG+TGG + chr4_3:34002858-34002877 Msa0638480:CDS 45.0%
!! GCTAACTGATTCGGTTGTGA+AGG + chr4_3:34002910-34002929 Msa0638480:exon 45.0%
GAAGATGAACGTAGAAGAGG+AGG + chr4_3:34001969-34001988 Msa0638480:exon 45.0%
AAGAGGAGGTTGAAAAGCTG+AGG + chr4_3:34001983-34002002 Msa0638480:CDS 45.0%
AGAGGAGGTTGAAAAGCTGA+GGG + chr4_3:34001984-34002003 Msa0638480:CDS 45.0%
AGCTGAGGGAAGAAATCAAG+AGG + chr4_3:34001998-34002017 Msa0638480:CDS 45.0%
AGGGAAGAAATCAAGAGGCT+TGG + chr4_3:34002003-34002022 Msa0638480:CDS 45.0%
TCAAGCAGATGGTTCTTGCA+AGG + chr4_3:34002032-34002051 Msa0638480:CDS 45.0%
! GCAAGGAGTCCATGATAATG+TGG + chr4_3:34002858-34002877 Msa0638480:CDS 45.0%
!! GCTAACTGATTCGGTTGTGA+AGG + chr4_3:34002910-34002929 Msa0638480:exon 45.0%
CGCATGATATCTCTCCTCCA+TGG - chr4_3:34002371-34002390 None:intergenic 50.0%
GACGGTGAACTACTGTTGCA+AGG + chr4_3:34002841-34002860 Msa0638480:CDS 50.0%
CCTGCTGCTGCTAACTGATT+CGG + chr4_3:34002901-34002920 Msa0638480:exon 50.0%
CGCATGATATCTCTCCTCCA+TGG - chr4_3:34002371-34002390 None:intergenic 50.0%
GACGGTGAACTACTGTTGCA+AGG + chr4_3:34002841-34002860 Msa0638480:CDS 50.0%
CCTGCTGCTGCTAACTGATT+CGG + chr4_3:34002901-34002920 Msa0638480:exon 50.0%
CCGAATCAGTTAGCAGCAGC+AGG - chr4_3:34002904-34002923 None:intergenic 55.0%
CCGAATCAGTTAGCAGCAGC+AGG - chr4_3:34002904-34002923 None:intergenic 55.0%
CAGTTAGCAGCAGCAGGAGC+AGG - chr4_3:34002898-34002917 None:intergenic 60.0%
CAGTTAGCAGCAGCAGGAGC+AGG - chr4_3:34002898-34002917 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 34001850 34003273 34001850 ID=Msa0638480;Name=Msa0638480
chr4_3 mRNA 34001850 34003273 34001850 ID=Msa0638480-mRNA-1;Parent=Msa0638480;Name=Msa0638480-mRNA-1;_AED=0.00;_eAED=0.00;_QI=123|1|1|1|1|1|2|355|86
chr4_3 exon 34001850 34002053 34001850 ID=Msa0638480-mRNA-1:exon:7708;Parent=Msa0638480-mRNA-1
chr4_3 exon 34002739 34003273 34002739 ID=Msa0638480-mRNA-1:exon:7709;Parent=Msa0638480-mRNA-1
chr4_3 five_prime_UTR 34001850 34001972 34001850 ID=Msa0638480-mRNA-1:five_prime_utr;Parent=Msa0638480-mRNA-1
chr4_3 CDS 34001973 34002053 34001973 ID=Msa0638480-mRNA-1:cds;Parent=Msa0638480-mRNA-1
chr4_3 CDS 34002739 34002918 34002739 ID=Msa0638480-mRNA-1:cds;Parent=Msa0638480-mRNA-1
chr4_3 three_prime_UTR 34002919 34003273 34002919 ID=Msa0638480-mRNA-1:three_prime_utr;Parent=Msa0638480-mRNA-1
Gene Sequence

>Msa0638480

ATGAACGTAGAAGAGGAGGTTGAAAAGCTGAGGGAAGAAATCAAGAGGCTTGGAAATGTTCAAGCAGATGGTTCTTGCAAGGTCACATTTGGAACACTCTTTCACGATGATCGGTGCGCAAATATATTTGAAGCACTCGTCGGTACACTAAGAGCTGCTAAAAAGCGTAAAGTAGTTGCATACGACGGTGAACTACTGTTGCAAGGAGTCCATGATAATGTGGAAATCACTCTTAATCCTGCTCCTGCTGCTGCTAACTGA

Protein sequence

>Msa0638480

MNVEEEVEKLREEIKRLGNVQADGSCKVTFGTLFHDDRCANIFEALVGTLRAAKKRKVVAYDGELLLQGVHDNVEITLNPAPAAAN*