AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1226150


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1226150 MtrunA17_Chr6g0488451 89.759 166 17 0 2 167 138 303 6.84e-107 310
Msa1226150 MtrunA17_Chr7g0256351 70.186 161 47 1 2 161 142 302 7.97e-74 226
Msa1226150 MtrunA17_Chr6g0488421 37.864 103 49 2 2 90 39 140 3.14e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1226150 AT5G56780.1 40.000 155 89 2 2 152 153 307 2.01e-27 107

Find 28 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCAACATACTTGATTTAAT+TGG 0.224850 8_1:+91926524 None:intergenic
TAAAATTTGTGGAGTGAATT+TGG 0.231337 8_1:-91926372 Msa1226150:CDS
GTTGTATCTTGAACTATCTT+AGG 0.344160 8_1:+91926419 None:intergenic
AGTGAAGGGTAGAAGTGATT+TGG 0.349328 8_1:+91926565 None:intergenic
TCGGATTTGTTATCTTTCAT+AGG 0.354876 8_1:+91926503 None:intergenic
GGAATTTGAACACGCGAGAT+AGG 0.386624 8_1:+91926453 None:intergenic
TGTTTGCAAGGCATCTCCCT+TGG 0.436980 8_1:+91926715 None:intergenic
GAGAAGAGTGGTAAAATTTG+TGG 0.450994 8_1:-91926383 Msa1226150:CDS
GCTGCCATTGTCTGCTTCAT+CGG 0.453379 8_1:+91926484 None:intergenic
ATCTGAAAATGTTCTTGTGC+TGG 0.457395 8_1:+91926592 None:intergenic
GTTAGGTGTCATGAACATAA+AGG 0.469142 8_1:-91926308 Msa1226150:CDS
TGAGTACATTTGATTATGCT+TGG 0.471865 8_1:-91926679 Msa1226150:CDS
GCTTGGAACACAATTAATAA+CGG 0.491690 8_1:-91926662 Msa1226150:CDS
CAGTTGAAATTCTGTTTGCA+AGG 0.502089 8_1:+91926703 None:intergenic
CCTTCACTCAAAAGAAAGTA+GGG 0.503569 8_1:-91926550 Msa1226150:CDS
CCCTTCACTCAAAAGAAAGT+AGG 0.510670 8_1:-91926551 Msa1226150:CDS
GAGCATTTCAAGAATATCAC+CGG 0.525607 8_1:+91926628 None:intergenic
CTATCTTAGGACGCGACCGG+TGG 0.570672 8_1:+91926432 None:intergenic
AATAACGGTCCACGGCGTCC+CGG 0.572061 8_1:-91926647 Msa1226150:CDS
CTCGCGTGTTCAAATTCCAC+CGG 0.598427 8_1:-91926448 Msa1226150:CDS
GAACTATCTTAGGACGCGAC+CGG 0.598468 8_1:+91926429 None:intergenic
TTCTATTTGTACAAAGACGC+CGG 0.623541 8_1:-91926342 Msa1226150:CDS
AGAATATCACCGGGACGCCG+TGG 0.625598 8_1:+91926638 None:intergenic
GTTGAACAGATGCAAACCAA+GGG 0.638402 8_1:-91926731 Msa1226150:intron
ACACAATTAATAACGGTCCA+CGG 0.642408 8_1:-91926655 Msa1226150:CDS
TGTTGAACAGATGCAAACCA+AGG 0.647561 8_1:-91926732 Msa1226150:intron
AGCATTTCAAGAATATCACC+GGG 0.651967 8_1:+91926629 None:intergenic
AAATCCGATGAAGCAGACAA+TGG 0.675612 8_1:-91926488 Msa1226150:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATTAGAAGCTTTAATAAT+TGG - chr8_1:91926271-91926290 Msa1226150:CDS 15.0%
!! AATCTAATAGAATAAACAAT+TGG - chr8_1:91926450-91926469 Msa1226150:CDS 15.0%
!!! GCATTTATATTTAATCTTTT+GGG + chr8_1:91926966-91926985 None:intergenic 15.0%
!!! TGCATTTATATTTAATCTTT+TGG + chr8_1:91926967-91926986 None:intergenic 15.0%
!!! ATATTAGAAGCTTTAATAAT+TGG - chr8_1:91926271-91926290 Msa1226150:CDS 15.0%
!! AATCTAATAGAATAAACAAT+TGG - chr8_1:91926450-91926469 Msa1226150:CDS 15.0%
!!! GCATTTATATTTAATCTTTT+GGG + chr8_1:91926966-91926985 None:intergenic 15.0%
!!! TGCATTTATATTTAATCTTT+TGG + chr8_1:91926967-91926986 None:intergenic 15.0%
!! TTAACAAGAAAAGTAAACAA+CGG - chr8_1:91926299-91926318 Msa1226150:CDS 20.0%
!! TGTTTATTCTATTAGATTAG+AGG + chr8_1:91926448-91926467 None:intergenic 20.0%
!!! TTTTCCAATTGTTTATAGAT+GGG - chr8_1:91926537-91926556 Msa1226150:CDS 20.0%
!! CAAAATGAACATATACAATA+TGG + chr8_1:91926679-91926698 None:intergenic 20.0%
!! ATAATATGTATCTCAAATCA+TGG + chr8_1:91926708-91926727 None:intergenic 20.0%
!! TTAATTAAGAGCTAAGTTAT+AGG - chr8_1:91926788-91926807 Msa1226150:intron 20.0%
!! TTAACAAGAAAAGTAAACAA+CGG - chr8_1:91926299-91926318 Msa1226150:CDS 20.0%
!! TGTTTATTCTATTAGATTAG+AGG + chr8_1:91926448-91926467 None:intergenic 20.0%
!!! TTTTCCAATTGTTTATAGAT+GGG - chr8_1:91926537-91926556 Msa1226150:CDS 20.0%
!! CAAAATGAACATATACAATA+TGG + chr8_1:91926679-91926698 None:intergenic 20.0%
!! ATAATATGTATCTCAAATCA+TGG + chr8_1:91926708-91926727 None:intergenic 20.0%
!! TTAATTAAGAGCTAAGTTAT+AGG - chr8_1:91926788-91926807 Msa1226150:intron 20.0%
! AAATTAAGAGACATGATTCA+AGG - chr8_1:91926514-91926533 Msa1226150:CDS 25.0%
!! GTTTTCCAATTGTTTATAGA+TGG - chr8_1:91926536-91926555 Msa1226150:CDS 25.0%
! TCAACTTATTAAGATCAAGA+TGG - chr8_1:91926599-91926618 Msa1226150:CDS 25.0%
!! TATGAAGTAAGTATTTTCTC+TGG - chr8_1:91926843-91926862 Msa1226150:intron 25.0%
! TAAAATTTGTGGAGTGAATT+TGG - chr8_1:91927408-91927427 Msa1226150:intron 25.0%
! AAATTAAGAGACATGATTCA+AGG - chr8_1:91926514-91926533 Msa1226150:CDS 25.0%
!! GTTTTCCAATTGTTTATAGA+TGG - chr8_1:91926536-91926555 Msa1226150:CDS 25.0%
! TCAACTTATTAAGATCAAGA+TGG - chr8_1:91926599-91926618 Msa1226150:CDS 25.0%
!! TATGAAGTAAGTATTTTCTC+TGG - chr8_1:91926843-91926862 Msa1226150:intron 25.0%
! TAAAATTTGTGGAGTGAATT+TGG - chr8_1:91927408-91927427 Msa1226150:intron 25.0%
!! ATGATTCTAGCTTCTTTCAT+TGG - chr8_1:91926401-91926420 Msa1226150:CDS 30.0%
GTATTAAGAGACATGATTCA+AGG + chr8_1:91926480-91926499 None:intergenic 30.0%
AATGCATAGAATGTACTTAC+AGG + chr8_1:91926565-91926584 None:intergenic 30.0%
GAACATATACAATATGGTCA+AGG + chr8_1:91926673-91926692 None:intergenic 30.0%
TAAGAGCTAAGTTATAGGTT+TGG - chr8_1:91926793-91926812 Msa1226150:intron 30.0%
CACATTTGCATCTTACATAA+AGG - chr8_1:91926985-91927004 Msa1226150:intron 30.0%
TGAGTACATTTGATTATGCT+TGG - chr8_1:91927101-91927120 Msa1226150:intron 30.0%
GCTTGGAACACAATTAATAA+CGG - chr8_1:91927118-91927137 Msa1226150:intron 30.0%
GGCAACATACTTGATTTAAT+TGG + chr8_1:91927259-91927278 None:intergenic 30.0%
!! TCGGATTTGTTATCTTTCAT+AGG + chr8_1:91927280-91927299 None:intergenic 30.0%
GTTGTATCTTGAACTATCTT+AGG + chr8_1:91927364-91927383 None:intergenic 30.0%
! AATTTTACCACTCTTCTCAA+CGG + chr8_1:91927395-91927414 None:intergenic 30.0%
!! ATGATTCTAGCTTCTTTCAT+TGG - chr8_1:91926401-91926420 Msa1226150:CDS 30.0%
GTATTAAGAGACATGATTCA+AGG + chr8_1:91926480-91926499 None:intergenic 30.0%
AATGCATAGAATGTACTTAC+AGG + chr8_1:91926565-91926584 None:intergenic 30.0%
GAACATATACAATATGGTCA+AGG + chr8_1:91926673-91926692 None:intergenic 30.0%
TAAGAGCTAAGTTATAGGTT+TGG - chr8_1:91926793-91926812 Msa1226150:intron 30.0%
CACATTTGCATCTTACATAA+AGG - chr8_1:91926985-91927004 Msa1226150:intron 30.0%
TGAGTACATTTGATTATGCT+TGG - chr8_1:91927101-91927120 Msa1226150:intron 30.0%
GCTTGGAACACAATTAATAA+CGG - chr8_1:91927118-91927137 Msa1226150:intron 30.0%
GGCAACATACTTGATTTAAT+TGG + chr8_1:91927259-91927278 None:intergenic 30.0%
!! TCGGATTTGTTATCTTTCAT+AGG + chr8_1:91927280-91927299 None:intergenic 30.0%
GTTGTATCTTGAACTATCTT+AGG + chr8_1:91927364-91927383 None:intergenic 30.0%
! AATTTTACCACTCTTCTCAA+CGG + chr8_1:91927395-91927414 None:intergenic 30.0%
!! TTCTAGCTTCTTTCATTGGA+AGG - chr8_1:91926405-91926424 Msa1226150:CDS 35.0%
ATACAATATGGTCAAGGCAA+TGG + chr8_1:91926667-91926686 None:intergenic 35.0%
AGTTATAGGTTTGGAAGTCT+AGG - chr8_1:91926802-91926821 Msa1226150:intron 35.0%
CAGTTGAAATTCTGTTTGCA+AGG + chr8_1:91927080-91927099 None:intergenic 35.0%
ACACAATTAATAACGGTCCA+CGG - chr8_1:91927125-91927144 Msa1226150:intron 35.0%
AGCATTTCAAGAATATCACC+GGG + chr8_1:91927154-91927173 None:intergenic 35.0%
GAGCATTTCAAGAATATCAC+CGG + chr8_1:91927155-91927174 None:intergenic 35.0%
ATCTGAAAATGTTCTTGTGC+TGG + chr8_1:91927191-91927210 None:intergenic 35.0%
!! CCTACTTTCTTTTGAGTGAA+GGG + chr8_1:91927232-91927251 None:intergenic 35.0%
CCTTCACTCAAAAGAAAGTA+GGG - chr8_1:91927230-91927249 Msa1226150:intron 35.0%
GAGAAGAGTGGTAAAATTTG+TGG - chr8_1:91927397-91927416 Msa1226150:intron 35.0%
TTCTATTTGTACAAAGACGC+CGG - chr8_1:91927438-91927457 Msa1226150:intron 35.0%
! GTTAGGTGTCATGAACATAA+AGG - chr8_1:91927472-91927491 Msa1226150:intron 35.0%
TCCAAGTCAGAATCAAAAAG+AGG - chr8_1:91927511-91927530 Msa1226150:intron 35.0%
!! TCCTCTTTTTGATTCTGACT+TGG + chr8_1:91927515-91927534 None:intergenic 35.0%
CAAAAAGAGGAAATGCTTGT+AGG - chr8_1:91927524-91927543 Msa1226150:intron 35.0%
!! TTCTAGCTTCTTTCATTGGA+AGG - chr8_1:91926405-91926424 Msa1226150:CDS 35.0%
ATACAATATGGTCAAGGCAA+TGG + chr8_1:91926667-91926686 None:intergenic 35.0%
AGTTATAGGTTTGGAAGTCT+AGG - chr8_1:91926802-91926821 Msa1226150:intron 35.0%
CAGTTGAAATTCTGTTTGCA+AGG + chr8_1:91927080-91927099 None:intergenic 35.0%
ACACAATTAATAACGGTCCA+CGG - chr8_1:91927125-91927144 Msa1226150:intron 35.0%
AGCATTTCAAGAATATCACC+GGG + chr8_1:91927154-91927173 None:intergenic 35.0%
GAGCATTTCAAGAATATCAC+CGG + chr8_1:91927155-91927174 None:intergenic 35.0%
ATCTGAAAATGTTCTTGTGC+TGG + chr8_1:91927191-91927210 None:intergenic 35.0%
!! CCTACTTTCTTTTGAGTGAA+GGG + chr8_1:91927232-91927251 None:intergenic 35.0%
CCTTCACTCAAAAGAAAGTA+GGG - chr8_1:91927230-91927249 Msa1226150:intron 35.0%
GAGAAGAGTGGTAAAATTTG+TGG - chr8_1:91927397-91927416 Msa1226150:intron 35.0%
TTCTATTTGTACAAAGACGC+CGG - chr8_1:91927438-91927457 Msa1226150:intron 35.0%
! GTTAGGTGTCATGAACATAA+AGG - chr8_1:91927472-91927491 Msa1226150:intron 35.0%
TCCAAGTCAGAATCAAAAAG+AGG - chr8_1:91927511-91927530 Msa1226150:intron 35.0%
!! TCCTCTTTTTGATTCTGACT+TGG + chr8_1:91927515-91927534 None:intergenic 35.0%
CAAAAAGAGGAAATGCTTGT+AGG - chr8_1:91927524-91927543 Msa1226150:intron 35.0%
AACATTTGTGTCGTGTCTCA+TGG + chr8_1:91926352-91926371 None:intergenic 40.0%
GGAGCCCATCTATAAACAAT+TGG + chr8_1:91926544-91926563 None:intergenic 40.0%
TGTTGAACAGATGCAAACCA+AGG - chr8_1:91927048-91927067 Msa1226150:intron 40.0%
GTTGAACAGATGCAAACCAA+GGG - chr8_1:91927049-91927068 Msa1226150:intron 40.0%
AGTGAAGGGTAGAAGTGATT+TGG + chr8_1:91927218-91927237 None:intergenic 40.0%
CCCTTCACTCAAAAGAAAGT+AGG - chr8_1:91927229-91927248 Msa1226150:intron 40.0%
!! CCCTACTTTCTTTTGAGTGA+AGG + chr8_1:91927233-91927252 None:intergenic 40.0%
AAATCCGATGAAGCAGACAA+TGG - chr8_1:91927292-91927311 Msa1226150:intron 40.0%
! GATTTTTCCGTTGAGAAGAG+TGG - chr8_1:91927385-91927404 Msa1226150:intron 40.0%
!!! CACCTAACTCTTTTTTCGAC+CGG + chr8_1:91927460-91927479 None:intergenic 40.0%
AACATTTGTGTCGTGTCTCA+TGG + chr8_1:91926352-91926371 None:intergenic 40.0%
GGAGCCCATCTATAAACAAT+TGG + chr8_1:91926544-91926563 None:intergenic 40.0%
TGTTGAACAGATGCAAACCA+AGG - chr8_1:91927048-91927067 Msa1226150:intron 40.0%
GTTGAACAGATGCAAACCAA+GGG - chr8_1:91927049-91927068 Msa1226150:intron 40.0%
AGTGAAGGGTAGAAGTGATT+TGG + chr8_1:91927218-91927237 None:intergenic 40.0%
CCCTTCACTCAAAAGAAAGT+AGG - chr8_1:91927229-91927248 Msa1226150:intron 40.0%
!! CCCTACTTTCTTTTGAGTGA+AGG + chr8_1:91927233-91927252 None:intergenic 40.0%
AAATCCGATGAAGCAGACAA+TGG - chr8_1:91927292-91927311 Msa1226150:intron 40.0%
! GATTTTTCCGTTGAGAAGAG+TGG - chr8_1:91927385-91927404 Msa1226150:intron 40.0%
!!! CACCTAACTCTTTTTTCGAC+CGG + chr8_1:91927460-91927479 None:intergenic 40.0%
GGAATTTGAACACGCGAGAT+AGG + chr8_1:91927330-91927349 None:intergenic 45.0%
GGAATTTGAACACGCGAGAT+AGG + chr8_1:91927330-91927349 None:intergenic 45.0%
! TGTTTGCAAGGCATCTCCCT+TGG + chr8_1:91927068-91927087 None:intergenic 50.0%
GCTGCCATTGTCTGCTTCAT+CGG + chr8_1:91927299-91927318 None:intergenic 50.0%
CTCGCGTGTTCAAATTCCAC+CGG - chr8_1:91927332-91927351 Msa1226150:intron 50.0%
GAACTATCTTAGGACGCGAC+CGG + chr8_1:91927354-91927373 None:intergenic 50.0%
CGCCGGTCGAAAAAAGAGTT+AGG - chr8_1:91927455-91927474 Msa1226150:intron 50.0%
! TGTTTGCAAGGCATCTCCCT+TGG + chr8_1:91927068-91927087 None:intergenic 50.0%
GCTGCCATTGTCTGCTTCAT+CGG + chr8_1:91927299-91927318 None:intergenic 50.0%
CTCGCGTGTTCAAATTCCAC+CGG - chr8_1:91927332-91927351 Msa1226150:intron 50.0%
GAACTATCTTAGGACGCGAC+CGG + chr8_1:91927354-91927373 None:intergenic 50.0%
CGCCGGTCGAAAAAAGAGTT+AGG - chr8_1:91927455-91927474 Msa1226150:intron 50.0%
AATAACGGTCCACGGCGTCC+CGG - chr8_1:91927133-91927152 Msa1226150:intron 60.0%
AGAATATCACCGGGACGCCG+TGG + chr8_1:91927145-91927164 None:intergenic 60.0%
CTATCTTAGGACGCGACCGG+TGG + chr8_1:91927351-91927370 None:intergenic 60.0%
AATAACGGTCCACGGCGTCC+CGG - chr8_1:91927133-91927152 Msa1226150:intron 60.0%
AGAATATCACCGGGACGCCG+TGG + chr8_1:91927145-91927164 None:intergenic 60.0%
CTATCTTAGGACGCGACCGG+TGG + chr8_1:91927351-91927370 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 91926250 91927552 91926250 ID=Msa1226150;Name=Msa1226150
chr8_1 mRNA 91926250 91927552 91926250 ID=Msa1226150-mRNA-1;Parent=Msa1226150;Name=Msa1226150-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|0|0|0.5|1|1|2|0|167
chr8_1 exon 91927544 91927552 91927544 ID=Msa1226150-mRNA-1:exon:33501;Parent=Msa1226150-mRNA-1
chr8_1 exon 91926250 91926744 91926250 ID=Msa1226150-mRNA-1:exon:33500;Parent=Msa1226150-mRNA-1
chr8_1 CDS 91927544 91927552 91927544 ID=Msa1226150-mRNA-1:cds;Parent=Msa1226150-mRNA-1
chr8_1 CDS 91926250 91926744 91926250 ID=Msa1226150-mRNA-1:cds;Parent=Msa1226150-mRNA-1
Gene Sequence

>Msa1226150

ATGGCAAAAATGCAAACCAAGGGAGATGCCTTGCAAACAGAATTTCAACTGTTGAGTACATTTGATTATGCTTGGAACACAATTAATAACGGTCCACGGCGTCCCGGTGATATTCTTGAAATGCTCAACAAAATATCTTCCAGCACAAGAACATTTTCAGATGTAGCCAAATCACTTCTACCCTTCACTCAAAAGAAAGTAGGGATACCAATTAAATCAAGTATGTTGCCTATGAAAGATAACAAATCCGATGAAGCAGACAATGGCAGCTACAATTTCCTATCTCGCGTGTTCAAATTCCACCGGTCGCGTCCTAAGATAGTTCAAGATACAACTGATTTTTCCGTTGAGAAGAGTGGTAAAATTTGTGGAGTGAATTTGGATAATAGTTCTATTTGTACAAAGACGCCGGTCGAAAAAAGAGTTAGGTGTCATGAACATAAAGGAATGAGAATAAGAACATCCAAGTCAGAATCAAAAAGAGGAAATGCTTGTAGGTACTAA

Protein sequence

>Msa1226150

MAKMQTKGDALQTEFQLLSTFDYAWNTINNGPRRPGDILEMLNKISSSTRTFSDVAKSLLPFTQKKVGIPIKSSMLPMKDNKSDEADNGSYNFLSRVFKFHRSRPKIVQDTTDFSVEKSGKICGVNLDNSSICTKTPVEKRVRCHEHKGMRIRTSKSESKRGNACRY*