AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0097630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097630 MtrunA17_Chr1g0152281 96.429 84 2 1 1 84 1 83 7.46e-54 161
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097630 AT3G49780.1 45.783 83 40 4 1 82 1 79 8.91e-14 60.8

Find 33 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGATTTGAATGAAGAATT+TGG 0.192068 1_3:-3457559 Msa0097630:three_prime_UTR
ACACCTGTAAATACAAAATT+AGG 0.274179 1_3:+3458202 None:intergenic
TGAAAGCTTTCTTCACCCTT+AGG 0.365213 1_3:+3457602 None:intergenic
TAGTTTAATGTTTCAACCTA+AGG 0.402258 1_3:-3457618 Msa0097630:three_prime_UTR
TGAACTCACTATGTCAAAAC+TGG 0.413207 1_3:-3458281 Msa0097630:exon
AGGTTGAAACATTAAACTAT+AGG 0.419413 1_3:+3457622 None:intergenic
CTTTGTTCGAGTTCTGTTGT+TGG 0.438286 1_3:-3457328 Msa0097630:three_prime_UTR
TAGAAGAGCTAAGGTGAAGA+GGG 0.441297 1_3:+3458255 None:intergenic
AACAAGAATGTTTGACAAGA+AGG 0.470793 1_3:-3457860 Msa0097630:CDS
AGTTTAATGTTTCAACCTAA+GGG 0.517045 1_3:-3457617 Msa0097630:three_prime_UTR
TTAGGATATTGTTTCTAGCA+AGG 0.518999 1_3:-3457934 Msa0097630:intron
TAAAGAATTAAGAATTACAA+TGG 0.519029 1_3:-3457375 Msa0097630:three_prime_UTR
TAATCAGAAATTGTGGAAGA+TGG 0.524624 1_3:-3457527 Msa0097630:three_prime_UTR
GAGAATTGTGAAGGAGTGGA+AGG 0.529911 1_3:-3457885 Msa0097630:CDS
AAAATTAGGACGGGAGGCAG+AGG 0.534908 1_3:+3458216 None:intergenic
ATAGAAGAGCTAAGGTGAAG+AGG 0.536160 1_3:+3458254 None:intergenic
AAATGAGAATTGTGAAGGAG+TGG 0.536266 1_3:-3457889 Msa0097630:CDS
TGTAAATACAAAATTAGGAC+GGG 0.537151 1_3:+3458207 None:intergenic
TGTTCGAGTTCTGTTGTTGG+TGG 0.538277 1_3:-3457325 Msa0097630:three_prime_UTR
TTAGAAAATGAGAATTGTGA+AGG 0.542330 1_3:-3457894 Msa0097630:CDS
TTCAAATCAGAGAAGCGTAT+GGG 0.547158 1_3:+3457571 None:intergenic
TTCAGCATAATCAGAAATTG+TGG 0.547601 1_3:-3457534 Msa0097630:three_prime_UTR
TATTTGAATATATACATGTA+CGG 0.549368 1_3:-3457662 Msa0097630:three_prime_UTR
CAAGCTTAATAGAAGAGCTA+AGG 0.557176 1_3:+3458246 None:intergenic
ATTCAAATCAGAGAAGCGTA+TGG 0.573306 1_3:+3457570 None:intergenic
TGTTGGTGGAAAGACCTTGT+CGG 0.582430 1_3:-3457311 Msa0097630:three_prime_UTR
CTGTAAATACAAAATTAGGA+CGG 0.605617 1_3:+3458206 None:intergenic
CATACTATTATTTACCGACA+AGG 0.613201 1_3:+3457297 None:intergenic
AGGTGTCTCTTCACTACATG+AGG 0.640533 1_3:-3458185 Msa0097630:intron
AAATACAAAATTAGGACGGG+AGG 0.641028 1_3:+3458210 None:intergenic
TCAAATCAGAGAAGCGTATG+GGG 0.646004 1_3:+3457572 None:intergenic
AATCAGAGAAGCGTATGGGG+TGG 0.699372 1_3:+3457575 None:intergenic
TGGCTTTAATCTCAAGTACG+AGG 0.711072 1_3:-3457507 Msa0097630:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTAAAGACATTAATTTTT+GGG + chr1_3:3457785-3457804 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG + chr1_3:3457786-3457805 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG - chr1_3:3457785-3457804 Msa0097630:three_prime_UTR 15.0%
!! AACAAAAACTCAATAAAATT+AGG + chr1_3:3457889-3457908 None:intergenic 15.0%
!! TATTTGAATATATACATGTA+CGG - chr1_3:3457915-3457934 Msa0097630:CDS 15.0%
!! TAAAGAATTAAGAATTACAA+TGG - chr1_3:3458202-3458221 Msa0097630:CDS 15.0%
!!! TTCTAAAGACATTAATTTTT+GGG + chr1_3:3457785-3457804 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG + chr1_3:3457786-3457805 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG - chr1_3:3457785-3457804 Msa0097630:three_prime_UTR 15.0%
!! AACAAAAACTCAATAAAATT+AGG + chr1_3:3457889-3457908 None:intergenic 15.0%
!! TATTTGAATATATACATGTA+CGG - chr1_3:3457915-3457934 Msa0097630:CDS 15.0%
!! TAAAGAATTAAGAATTACAA+TGG - chr1_3:3458202-3458221 Msa0097630:CDS 15.0%
!! CACTAATTACTTAATTAAGA+AGG + chr1_3:3457427-3457446 None:intergenic 20.0%
!! TACCATATTTCATTTGAATT+AGG - chr1_3:3457625-3457644 Msa0097630:three_prime_UTR 20.0%
!! ATCCTAATTCAAATGAAATA+TGG + chr1_3:3457630-3457649 None:intergenic 20.0%
!! CACTAATTACTTAATTAAGA+AGG + chr1_3:3457427-3457446 None:intergenic 20.0%
!! TACCATATTTCATTTGAATT+AGG - chr1_3:3457625-3457644 Msa0097630:three_prime_UTR 20.0%
!! ATCCTAATTCAAATGAAATA+TGG + chr1_3:3457630-3457649 None:intergenic 20.0%
! TGTAAATACAAAATTAGGAC+GGG + chr1_3:3457373-3457392 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG + chr1_3:3457374-3457393 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG + chr1_3:3457378-3457397 None:intergenic 25.0%
! TTAGAAAATGAGAATTGTGA+AGG - chr1_3:3457683-3457702 Msa0097630:three_prime_UTR 25.0%
! AGGTTGAAACATTAAACTAT+AGG + chr1_3:3457958-3457977 None:intergenic 25.0%
! TAGTTTAATGTTTCAACCTA+AGG - chr1_3:3457959-3457978 Msa0097630:intron 25.0%
! AGTTTAATGTTTCAACCTAA+GGG - chr1_3:3457960-3457979 Msa0097630:intron 25.0%
!! TCTGATTTGAATGAAGAATT+TGG - chr1_3:3458018-3458037 Msa0097630:intron 25.0%
! TGTAAATACAAAATTAGGAC+GGG + chr1_3:3457373-3457392 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG + chr1_3:3457374-3457393 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG + chr1_3:3457378-3457397 None:intergenic 25.0%
! TTAGAAAATGAGAATTGTGA+AGG - chr1_3:3457683-3457702 Msa0097630:three_prime_UTR 25.0%
! AGGTTGAAACATTAAACTAT+AGG + chr1_3:3457958-3457977 None:intergenic 25.0%
! TAGTTTAATGTTTCAACCTA+AGG - chr1_3:3457959-3457978 Msa0097630:intron 25.0%
! AGTTTAATGTTTCAACCTAA+GGG - chr1_3:3457960-3457979 Msa0097630:intron 25.0%
!! TCTGATTTGAATGAAGAATT+TGG - chr1_3:3458018-3458037 Msa0097630:intron 25.0%
! CGTCCTAATTTTGTATTTAC+AGG - chr1_3:3457372-3457391 Msa0097630:three_prime_UTR 30.0%
TTATCTTATTCTTGTGATGC+TGG - chr1_3:3457567-3457586 Msa0097630:three_prime_UTR 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG - chr1_3:3457643-3457662 Msa0097630:three_prime_UTR 30.0%
AACAAGAATGTTTGACAAGA+AGG - chr1_3:3457717-3457736 Msa0097630:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG - chr1_3:3458043-3458062 Msa0097630:intron 30.0%
TAATCAGAAATTGTGGAAGA+TGG - chr1_3:3458050-3458069 Msa0097630:intron 30.0%
CATACTATTATTTACCGACA+AGG + chr1_3:3458283-3458302 None:intergenic 30.0%
! CGTCCTAATTTTGTATTTAC+AGG - chr1_3:3457372-3457391 Msa0097630:three_prime_UTR 30.0%
TTATCTTATTCTTGTGATGC+TGG - chr1_3:3457567-3457586 Msa0097630:three_prime_UTR 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG - chr1_3:3457643-3457662 Msa0097630:three_prime_UTR 30.0%
AACAAGAATGTTTGACAAGA+AGG - chr1_3:3457717-3457736 Msa0097630:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG - chr1_3:3458043-3458062 Msa0097630:intron 30.0%
TAATCAGAAATTGTGGAAGA+TGG - chr1_3:3458050-3458069 Msa0097630:intron 30.0%
CATACTATTATTTACCGACA+AGG + chr1_3:3458283-3458302 None:intergenic 30.0%
TGAACTCACTATGTCAAAAC+TGG - chr1_3:3457296-3457315 Msa0097630:three_prime_UTR 35.0%
CAAGCTTAATAGAAGAGCTA+AGG + chr1_3:3457334-3457353 None:intergenic 35.0%
AAATACAAAATTAGGACGGG+AGG + chr1_3:3457370-3457389 None:intergenic 35.0%
AAATGAGAATTGTGAAGGAG+TGG - chr1_3:3457688-3457707 Msa0097630:three_prime_UTR 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG + chr1_3:3458009-3458028 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG + chr1_3:3458010-3458029 None:intergenic 35.0%
TGAACTCACTATGTCAAAAC+TGG - chr1_3:3457296-3457315 Msa0097630:three_prime_UTR 35.0%
CAAGCTTAATAGAAGAGCTA+AGG + chr1_3:3457334-3457353 None:intergenic 35.0%
AAATACAAAATTAGGACGGG+AGG + chr1_3:3457370-3457389 None:intergenic 35.0%
AAATGAGAATTGTGAAGGAG+TGG - chr1_3:3457688-3457707 Msa0097630:three_prime_UTR 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG + chr1_3:3458009-3458028 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG + chr1_3:3458010-3458029 None:intergenic 35.0%
TAGAAGAGCTAAGGTGAAGA+GGG + chr1_3:3457325-3457344 None:intergenic 40.0%
ATAGAAGAGCTAAGGTGAAG+AGG + chr1_3:3457326-3457345 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG + chr1_3:3457978-3457997 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG + chr1_3:3458008-3458027 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG - chr1_3:3458070-3458089 Msa0097630:intron 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG - chr1_3:3458249-3458268 Msa0097630:CDS 40.0%
TAGAAGAGCTAAGGTGAAGA+GGG + chr1_3:3457325-3457344 None:intergenic 40.0%
ATAGAAGAGCTAAGGTGAAG+AGG + chr1_3:3457326-3457345 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG + chr1_3:3457978-3457997 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG + chr1_3:3458008-3458027 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG - chr1_3:3458070-3458089 Msa0097630:intron 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG - chr1_3:3458249-3458268 Msa0097630:CDS 40.0%
AGGTGTCTCTTCACTACATG+AGG - chr1_3:3457392-3457411 Msa0097630:three_prime_UTR 45.0%
GAGAATTGTGAAGGAGTGGA+AGG - chr1_3:3457692-3457711 Msa0097630:three_prime_UTR 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG - chr1_3:3458252-3458271 Msa0097630:CDS 45.0%
! TGTTGGTGGAAAGACCTTGT+CGG - chr1_3:3458266-3458285 Msa0097630:CDS 45.0%
AGGTGTCTCTTCACTACATG+AGG - chr1_3:3457392-3457411 Msa0097630:three_prime_UTR 45.0%
GAGAATTGTGAAGGAGTGGA+AGG - chr1_3:3457692-3457711 Msa0097630:three_prime_UTR 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG - chr1_3:3458252-3458271 Msa0097630:CDS 45.0%
! TGTTGGTGGAAAGACCTTGT+CGG - chr1_3:3458266-3458285 Msa0097630:CDS 45.0%
!! AATAAAATATTTAATTAACA+TGG + chr1_3:3457547-3457566 None:intergenic 5.0%
!! AATAAAATATTTAATTAACA+TGG + chr1_3:3457547-3457566 None:intergenic 5.0%
AAAATTAGGACGGGAGGCAG+AGG + chr1_3:3457364-3457383 None:intergenic 50.0%
! AATCAGAGAAGCGTATGGGG+TGG + chr1_3:3458005-3458024 None:intergenic 50.0%
AAAATTAGGACGGGAGGCAG+AGG + chr1_3:3457364-3457383 None:intergenic 50.0%
! AATCAGAGAAGCGTATGGGG+TGG + chr1_3:3458005-3458024 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 3457263 3458336 3457263 ID=Msa0097630;Name=Msa0097630
chr1_3 mRNA 3457263 3458336 3457263 ID=Msa0097630-mRNA-1;Parent=Msa0097630;Name=Msa0097630-mRNA-1;_AED=0.02;_eAED=0.02;_QI=43|1|1|1|1|1|2|543|84
chr1_3 exon 3457263 3457952 3457263 ID=Msa0097630-mRNA-1:exon:1038;Parent=Msa0097630-mRNA-1
chr1_3 exon 3458186 3458336 3458186 ID=Msa0097630-mRNA-1:exon:1037;Parent=Msa0097630-mRNA-1
chr1_3 five_prime_UTR 3458294 3458336 3458294 ID=Msa0097630-mRNA-1:five_prime_utr;Parent=Msa0097630-mRNA-1
chr1_3 CDS 3458186 3458293 3458186 ID=Msa0097630-mRNA-1:cds;Parent=Msa0097630-mRNA-1
chr1_3 CDS 3457806 3457952 3457806 ID=Msa0097630-mRNA-1:cds;Parent=Msa0097630-mRNA-1
chr1_3 three_prime_UTR 3457263 3457805 3457263 ID=Msa0097630-mRNA-1:three_prime_utr;Parent=Msa0097630-mRNA-1
Gene Sequence

>Msa0097630

ATGTCAAAACTGGTCACCCTCTTCACCTTAGCTCTTCTATTAAGCTTGAGTTTAACCTCTGCCTCCCGTCCTAATTTTGTATTTACAGGTGTCTCTTCACTACATGAGGATATTGTTTCTAGCAAGGCATCAAGTACTGTAGACTTAGAAAATGAGAATTGTGAAGGAGTGGAAGGAGAACAAGAATGTTTGACAAGAAGGACTCTAGCTGCACATCTCGATTATATCTACACTCAGCATAAACCCAAAAATTAA
Protein sequence

>Msa0097630

MSKLVTLFTLALLLSLSLTSASRPNFVFTGVSSLHEDIVSSKASSTVDLENENCEGVEGEQECLTRRTLAAHLDYIYTQHKPKN*