AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1271210


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1271210 MtrunA17_Chr1g0211321 98.246 57 1 0 1 57 1 57 3.32e-35 115
Msa1271210 MtrunA17_Chr8g0335151 98.246 57 1 0 1 57 1 57 3.43e-35 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1271210 AT4G01710.1 80.392 51 10 0 7 57 4 54 1.99e-21 81.3
Msa1271210 AT5G65274.1 68.421 57 18 0 1 57 1 57 2.73e-20 78.6

Find 21 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTGCTTGGCGCCACATTTC+AGG 0.193741 8_3:+4665578 Msa1271210:three_prime_UTR
GTTATCATCTTAAAGTCATT+TGG 0.299618 8_3:-4665751 None:intergenic
CACGTCTTCATTAGAAGTAT+TGG 0.344651 8_3:-4665559 None:intergenic
TGACTTTAAGATGATAACTT+AGG 0.368044 8_3:+4665756 Msa1271210:three_prime_UTR
AACTTAGGGCCTGTTTGAAT+TGG 0.368227 8_3:+4665771 Msa1271210:three_prime_UTR
GTGTTCAATTCTTGTAATGA+TGG 0.427929 8_3:-4665200 None:intergenic
TCAAATAAACCAATTCAAAC+AGG 0.457612 8_3:-4665780 None:intergenic
GAAAATCACTCTGATTTGTA+TGG 0.460107 8_3:+4665138 Msa1271210:exon
GCCCTTAAAACTGCACTTGA+AGG 0.464123 8_3:+4665373 Msa1271210:CDS
ATCACTCTGATTTGTATGGC+AGG 0.487625 8_3:+4665142 Msa1271210:exon
GACTTTAAGATGATAACTTA+GGG 0.493477 8_3:+4665757 Msa1271210:three_prime_UTR
TTCGGGAAAATTGAAGCTGA+AGG 0.511039 8_3:+4665059 Msa1271210:five_prime_UTR
ACAGACACAAACACGAACAT+TGG 0.536902 8_3:-4665693 None:intergenic
ACTTCTAATGAAGACGTGCT+TGG 0.541424 8_3:+4665564 Msa1271210:three_prime_UTR
ATTTGTATGGCAGGATCAGA+AGG 0.546400 8_3:+4665151 Msa1271210:exon
GACTAGTGATGAACGTTGCA+AGG 0.550130 8_3:+4665408 Msa1271210:CDS
TGTTACATACTGTTTGAGCA+AGG 0.595063 8_3:-4665242 None:intergenic
GCAACGTTCATCACTAGTCA+TGG 0.601987 8_3:-4665404 None:intergenic
TTCATCACTAGTCATGGCAT+AGG 0.655247 8_3:-4665398 None:intergenic
TTGAATGTGATCACATATGT+CGG 0.662659 8_3:-4665610 None:intergenic
GGTGTCAGACACCTGAAATG+TGG 0.678895 8_3:-4665589 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGCATAAAAATAGTAAAA+GGG - chr8_3:4665447-4665466 None:intergenic 15.0%
!! AAATGCATAAAAATAGTAAA+AGG - chr8_3:4665448-4665467 None:intergenic 15.0%
!!! TTTCTTTTTCTAATAGATAT+TGG + chr8_3:4665650-4665669 Msa1271210:three_prime_UTR 15.0%
!! AATGCATAAAAATAGTAAAA+GGG - chr8_3:4665447-4665466 None:intergenic 15.0%
!! AAATGCATAAAAATAGTAAA+AGG - chr8_3:4665448-4665467 None:intergenic 15.0%
!!! TTTCTTTTTCTAATAGATAT+TGG + chr8_3:4665650-4665669 Msa1271210:three_prime_UTR 15.0%
!! ATGCATAAAAATAGTAAAAG+GGG - chr8_3:4665446-4665465 None:intergenic 20.0%
!!! TTTTGTGCTTTTATTTCATT+TGG + chr8_3:4665496-4665515 Msa1271210:three_prime_UTR 20.0%
!!! TTTGTGCTTTTATTTCATTT+GGG + chr8_3:4665497-4665516 Msa1271210:three_prime_UTR 20.0%
!!! ATTTTAGAGTTTTGTACAAT+TGG + chr8_3:4665723-4665742 Msa1271210:three_prime_UTR 20.0%
!! ATGCATAAAAATAGTAAAAG+GGG - chr8_3:4665446-4665465 None:intergenic 20.0%
!!! TTTTGTGCTTTTATTTCATT+TGG + chr8_3:4665496-4665515 Msa1271210:three_prime_UTR 20.0%
!!! TTTGTGCTTTTATTTCATTT+GGG + chr8_3:4665497-4665516 Msa1271210:three_prime_UTR 20.0%
!!! ATTTTAGAGTTTTGTACAAT+TGG + chr8_3:4665723-4665742 Msa1271210:three_prime_UTR 20.0%
!! AGAAAAGCAAAACATTTTCT+CGG + chr8_3:4665085-4665104 Msa1271210:five_prime_UTR 25.0%
!! CAATTTTAGATATAAACCAG+TGG + chr8_3:4665348-4665367 Msa1271210:intron 25.0%
! GTTATCATCTTAAAGTCATT+TGG - chr8_3:4665754-4665773 None:intergenic 25.0%
!!! TGACTTTAAGATGATAACTT+AGG + chr8_3:4665756-4665775 Msa1271210:three_prime_UTR 25.0%
!!! GACTTTAAGATGATAACTTA+GGG + chr8_3:4665757-4665776 Msa1271210:three_prime_UTR 25.0%
!! AGAAAAGCAAAACATTTTCT+CGG + chr8_3:4665085-4665104 Msa1271210:five_prime_UTR 25.0%
!! CAATTTTAGATATAAACCAG+TGG + chr8_3:4665348-4665367 Msa1271210:intron 25.0%
! GTTATCATCTTAAAGTCATT+TGG - chr8_3:4665754-4665773 None:intergenic 25.0%
!!! TGACTTTAAGATGATAACTT+AGG + chr8_3:4665756-4665775 Msa1271210:three_prime_UTR 25.0%
!!! GACTTTAAGATGATAACTTA+GGG + chr8_3:4665757-4665776 Msa1271210:three_prime_UTR 25.0%
! GAAAAGCAAAACATTTTCTC+GGG + chr8_3:4665086-4665105 Msa1271210:five_prime_UTR 30.0%
! GAAAATCACTCTGATTTGTA+TGG + chr8_3:4665138-4665157 Msa1271210:exon 30.0%
GTGTTCAATTCTTGTAATGA+TGG - chr8_3:4665203-4665222 None:intergenic 30.0%
AAAAATAGTAAAAGGGGCTA+AGG - chr8_3:4665440-4665459 None:intergenic 30.0%
TTGAATGTGATCACATATGT+CGG - chr8_3:4665613-4665632 None:intergenic 30.0%
! CCTGTTTGAATTGGTTTATT+TGG + chr8_3:4665780-4665799 Msa1271210:three_prime_UTR 30.0%
! GAAAAGCAAAACATTTTCTC+GGG + chr8_3:4665086-4665105 Msa1271210:five_prime_UTR 30.0%
! GAAAATCACTCTGATTTGTA+TGG + chr8_3:4665138-4665157 Msa1271210:exon 30.0%
GTGTTCAATTCTTGTAATGA+TGG - chr8_3:4665203-4665222 None:intergenic 30.0%
AAAAATAGTAAAAGGGGCTA+AGG - chr8_3:4665440-4665459 None:intergenic 30.0%
TTGAATGTGATCACATATGT+CGG - chr8_3:4665613-4665632 None:intergenic 30.0%
TGTTACATACTGTTTGAGCA+AGG - chr8_3:4665245-4665264 None:intergenic 35.0%
!! TCCTTCAAGTGCAGTTTTAA+GGG - chr8_3:4665377-4665396 None:intergenic 35.0%
! TTCCTTCAAGTGCAGTTTTA+AGG - chr8_3:4665378-4665397 None:intergenic 35.0%
! CACGTCTTCATTAGAAGTAT+TGG - chr8_3:4665562-4665581 None:intergenic 35.0%
TGTTACATACTGTTTGAGCA+AGG - chr8_3:4665245-4665264 None:intergenic 35.0%
!! TCCTTCAAGTGCAGTTTTAA+GGG - chr8_3:4665377-4665396 None:intergenic 35.0%
! TTCCTTCAAGTGCAGTTTTA+AGG - chr8_3:4665378-4665397 None:intergenic 35.0%
! CACGTCTTCATTAGAAGTAT+TGG - chr8_3:4665562-4665581 None:intergenic 35.0%
TTCGGGAAAATTGAAGCTGA+AGG + chr8_3:4665059-4665078 Msa1271210:five_prime_UTR 40.0%
! ATCACTCTGATTTGTATGGC+AGG + chr8_3:4665142-4665161 Msa1271210:exon 40.0%
ATTTGTATGGCAGGATCAGA+AGG + chr8_3:4665151-4665170 Msa1271210:exon 40.0%
TTCATCACTAGTCATGGCAT+AGG - chr8_3:4665401-4665420 None:intergenic 40.0%
ACTTCTAATGAAGACGTGCT+TGG + chr8_3:4665564-4665583 Msa1271210:three_prime_UTR 40.0%
ACAGACACAAACACGAACAT+TGG - chr8_3:4665696-4665715 None:intergenic 40.0%
AACTTAGGGCCTGTTTGAAT+TGG + chr8_3:4665771-4665790 Msa1271210:three_prime_UTR 40.0%
TTCGGGAAAATTGAAGCTGA+AGG + chr8_3:4665059-4665078 Msa1271210:five_prime_UTR 40.0%
! ATCACTCTGATTTGTATGGC+AGG + chr8_3:4665142-4665161 Msa1271210:exon 40.0%
ATTTGTATGGCAGGATCAGA+AGG + chr8_3:4665151-4665170 Msa1271210:exon 40.0%
TTCATCACTAGTCATGGCAT+AGG - chr8_3:4665401-4665420 None:intergenic 40.0%
ACTTCTAATGAAGACGTGCT+TGG + chr8_3:4665564-4665583 Msa1271210:three_prime_UTR 40.0%
ACAGACACAAACACGAACAT+TGG - chr8_3:4665696-4665715 None:intergenic 40.0%
AACTTAGGGCCTGTTTGAAT+TGG + chr8_3:4665771-4665790 Msa1271210:three_prime_UTR 40.0%
GCCCTTAAAACTGCACTTGA+AGG + chr8_3:4665373-4665392 Msa1271210:CDS 45.0%
GCAACGTTCATCACTAGTCA+TGG - chr8_3:4665407-4665426 None:intergenic 45.0%
GACTAGTGATGAACGTTGCA+AGG + chr8_3:4665408-4665427 Msa1271210:CDS 45.0%
GCCCTTAAAACTGCACTTGA+AGG + chr8_3:4665373-4665392 Msa1271210:CDS 45.0%
GCAACGTTCATCACTAGTCA+TGG - chr8_3:4665407-4665426 None:intergenic 45.0%
GACTAGTGATGAACGTTGCA+AGG + chr8_3:4665408-4665427 Msa1271210:CDS 45.0%
!!! TAATAAAGTTTAAATTTTTA+TGG - chr8_3:4665473-4665492 None:intergenic 5.0%
!!! TAATAAAGTTTAAATTTTTA+TGG - chr8_3:4665473-4665492 None:intergenic 5.0%
!!! GCAGTTTTAAGGGCTTCCAC+TGG - chr8_3:4665367-4665386 None:intergenic 50.0%
GGTGTCAGACACCTGAAATG+TGG - chr8_3:4665592-4665611 None:intergenic 50.0%
!!! GCAGTTTTAAGGGCTTCCAC+TGG - chr8_3:4665367-4665386 None:intergenic 50.0%
GGTGTCAGACACCTGAAATG+TGG - chr8_3:4665592-4665611 None:intergenic 50.0%
CGTGCTTGGCGCCACATTTC+AGG + chr8_3:4665578-4665597 Msa1271210:three_prime_UTR 60.0%
CGTGCTTGGCGCCACATTTC+AGG + chr8_3:4665578-4665597 Msa1271210:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 4665046 4665801 4665046 ID=Msa1271210;Name=Msa1271210
chr8_3 mRNA 4665046 4665801 4665046 ID=Msa1271210-mRNA-1;Parent=Msa1271210;Name=Msa1271210-mRNA-1;_AED=0.00;_eAED=0.00;_QI=111|1|1|1|1|1|2|318|74
chr8_3 exon 4665046 4665254 4665046 ID=Msa1271210-mRNA-1:exon:1597;Parent=Msa1271210-mRNA-1
chr8_3 exon 4665357 4665801 4665357 ID=Msa1271210-mRNA-1:exon:1598;Parent=Msa1271210-mRNA-1
chr8_3 five_prime_UTR 4665046 4665156 4665046 ID=Msa1271210-mRNA-1:five_prime_utr;Parent=Msa1271210-mRNA-1
chr8_3 CDS 4665157 4665254 4665157 ID=Msa1271210-mRNA-1:cds;Parent=Msa1271210-mRNA-1
chr8_3 CDS 4665357 4665483 4665357 ID=Msa1271210-mRNA-1:cds;Parent=Msa1271210-mRNA-1
chr8_3 three_prime_UTR 4665484 4665801 4665484 ID=Msa1271210-mRNA-1:three_prime_utr;Parent=Msa1271210-mRNA-1
Gene Sequence

>Msa1271210

ATGGCAGGATCAGAAGGATTCGTTGAAGCTGATAACGCAGAAGCCATCATTACAAGAATTGAACACAAAACACGCAAGATCGAAACCTTGCTCAAACAATATAAACCAGTGGAAGCCCTTAAAACTGCACTTGAAGGAACCTATGCCATGACTAGTGATGAACGTTGCAAGGTTTTTTCCTTAGCCCCTTTTACTATTTTTATGCATTTTTCCATAAAAATTTAA

Protein sequence

>Msa1271210

MAGSEGFVEADNAEAIITRIEHKTRKIETLLKQYKPVEALKTALEGTYAMTSDERCKVFSLAPFTIFMHFSIKI*