AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394260 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394260 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394260 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394260 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1394260 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1394260 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1394260 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394260 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1394260 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 tig0021785:-98533 Msa1394260:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 tig0021785:+98271 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 tig0021785:+98567 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 tig0021785:-98616 Msa1394260:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 tig0021785:-98668 Msa1394260:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 tig0021785:-98575 Msa1394260:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 tig0021785:+98568 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 tig0021785:-98213 Msa1394260:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 tig0021785:+98500 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 tig0021785:+98265 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 tig0021785:+98610 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 tig0021785:-98659 Msa1394260:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 tig0021785:+98282 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 tig0021785:-98212 Msa1394260:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 tig0021785:-98684 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 tig0021785:-98554 Msa1394260:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 tig0021785:+98505 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 tig0021785:+98506 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 tig0021785:-98555 Msa1394260:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 tig0021785:-98571 Msa1394260:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 tig0021785:+98504 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 tig0021785:+98204 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 tig0021785:-98677 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 tig0021785:-98576 Msa1394260:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 tig0021785:+98572 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 tig0021785:+98571 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 tig0021785:-98211 Msa1394260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - tig0021785:98406-98425 Msa1394260:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + tig0021785:98596-98615 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + tig0021785:98597-98616 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + tig0021785:98355-98374 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - tig0021785:98409-98428 Msa1394260:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + tig0021785:98510-98529 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - tig0021785:98213-98232 Msa1394260:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + tig0021785:98222-98241 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + tig0021785:98332-98351 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - tig0021785:98356-98375 Msa1394260:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + tig0021785:98382-98401 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + tig0021785:98461-98480 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - tig0021785:98296-98315 Msa1394260:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + tig0021785:98327-98346 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + tig0021785:98328-98347 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - tig0021785:98338-98357 Msa1394260:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + tig0021785:98368-98387 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + tig0021785:98456-98475 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - tig0021785:98456-98475 Msa1394260:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + tig0021785:98462-98481 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - tig0021785:98460-98479 Msa1394260:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + tig0021785:98550-98569 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + tig0021785:98561-98580 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + tig0021785:98567-98586 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - tig0021785:98253-98272 Msa1394260:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + tig0021785:98264-98283 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + tig0021785:98265-98284 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + tig0021785:98326-98345 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - tig0021785:98373-98392 Msa1394260:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + tig0021785:98437-98456 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + tig0021785:98444-98463 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - tig0021785:98500-98519 Msa1394260:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + tig0021785:98506-98525 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + tig0021785:98507-98526 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + tig0021785:98628-98647 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - tig0021785:98254-98273 Msa1394260:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - tig0021785:98274-98293 Msa1394260:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - tig0021785:98275-98294 Msa1394260:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - tig0021785:98429-98448 Msa1394260:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - tig0021785:98499-98518 Msa1394260:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - tig0021785:98616-98635 Msa1394260:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - tig0021785:98617-98636 Msa1394260:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - tig0021785:98618-98637 Msa1394260:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + tig0021785:98260-98279 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - tig0021785:98470-98489 Msa1394260:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - tig0021785:98161-98180 Msa1394260:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + tig0021785:98261-98280 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - tig0021785:98258-98277 Msa1394260:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - tig0021785:98478-98497 Msa1394260:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - tig0021785:98170-98189 Msa1394260:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 98159 98692 98159 ID=Msa1394260;Name=Msa1394260
tig0021785 mRNA 98159 98692 98159 ID=Msa1394260-mRNA-1;Parent=Msa1394260;Name=Msa1394260-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
tig0021785 exon 98515 98692 98515 ID=Msa1394260-mRNA-1:exon:14247;Parent=Msa1394260-mRNA-1
tig0021785 exon 98159 98309 98159 ID=Msa1394260-mRNA-1:exon:14246;Parent=Msa1394260-mRNA-1
tig0021785 five_prime_UTR 98676 98692 98676 ID=Msa1394260-mRNA-1:five_prime_utr;Parent=Msa1394260-mRNA-1
tig0021785 CDS 98515 98675 98515 ID=Msa1394260-mRNA-1:cds;Parent=Msa1394260-mRNA-1
tig0021785 CDS 98159 98309 98159 ID=Msa1394260-mRNA-1:cds;Parent=Msa1394260-mRNA-1
Gene Sequence

>Msa1394260

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1394260

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN