AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0097540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097540 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
Msa0097540 AT3G49780.1 45.783 83 40 4 1 82 1 79 8.91e-14 60.8

Find 34 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACCTGTAAATACAAAATT+AGG 0.274179 1_3:-3352180 None:intergenic
TCACCTGCATGGCTAGAAAA+AGG 0.336857 1_3:-3353160 None:intergenic
TGAAAGCTTTCTTCACCCTT+AGG 0.365213 1_3:-3352778 None:intergenic
TAGTTTCATGTTTCAACCTA+AGG 0.406321 1_3:+3352762 Msa0097540:three_prime_UTR
TGAACTCACTATGTCAAAAC+TGG 0.413207 1_3:+3352101 Msa0097540:exon
CTTTGTTCGAGTTCTGTTGT+TGG 0.438286 1_3:+3353052 Msa0097540:three_prime_UTR
TAGAAGAGCTAAGGTGAAGA+GGG 0.441297 1_3:-3352127 None:intergenic
AACAAGAATGTTTGACAAGA+AGG 0.470793 1_3:+3352522 Msa0097540:CDS
AGTTTCATGTTTCAACCTAA+GGG 0.514155 1_3:+3352763 Msa0097540:three_prime_UTR
TTAGGATATTGTTTCTAGCA+AGG 0.518999 1_3:+3352448 Msa0097540:intron
TAAAGAATTAAGAATTACAA+TGG 0.519029 1_3:+3353005 Msa0097540:three_prime_UTR
TAATCAGAAATTGTGGAAGA+TGG 0.524624 1_3:+3352853 Msa0097540:three_prime_UTR
GAGAATTGTGAAGGAGTGGA+AGG 0.529911 1_3:+3352497 Msa0097540:CDS
AAAATTAGGACGGGAGGCAG+AGG 0.534908 1_3:-3352166 None:intergenic
ATAGAAGAGCTAAGGTGAAG+AGG 0.536160 1_3:-3352128 None:intergenic
AAATGAGAATTGTGAAGGAG+TGG 0.536266 1_3:+3352493 Msa0097540:CDS
TGTAAATACAAAATTAGGAC+GGG 0.537151 1_3:-3352175 None:intergenic
TGTTCGAGTTCTGTTGTTGG+TGG 0.538277 1_3:+3353055 Msa0097540:three_prime_UTR
TTAGAAAATGAGAATTGTGA+AGG 0.542330 1_3:+3352488 Msa0097540:CDS
TATTTGAATATATACGTGTA+CGG 0.546262 1_3:+3352718 Msa0097540:three_prime_UTR
TTCAAATCAGAGAAGCGTAT+GGG 0.547158 1_3:-3352809 None:intergenic
TTCAGCATAATCAGAAATTG+TGG 0.547601 1_3:+3352846 Msa0097540:three_prime_UTR
AGGTTGAAACATGAAACTAT+AGG 0.552775 1_3:-3352758 None:intergenic
CAAGCTTAATAGAAGAGCTA+AGG 0.557176 1_3:-3352136 None:intergenic
ATTCAAATCAGAGAAGCGTA+TGG 0.573306 1_3:-3352810 None:intergenic
TATATATATCCTCACCTGCA+TGG 0.595996 1_3:-3353171 None:intergenic
CTGTAAATACAAAATTAGGA+CGG 0.605617 1_3:-3352176 None:intergenic
AGGTGTCTCTTCACTACATG+AGG 0.640533 1_3:+3352197 Msa0097540:CDS
AAATACAAAATTAGGACGGG+AGG 0.641028 1_3:-3352172 None:intergenic
TCAAATCAGAGAAGCGTATG+GGG 0.646004 1_3:-3352808 None:intergenic
CATACTATTATTTACCGACG+AGG 0.673704 1_3:-3353083 None:intergenic
TGTTGGTGGAAAGACCTCGT+CGG 0.695170 1_3:+3353069 Msa0097540:three_prime_UTR
AATCAGAGAAGCGTATGGGG+TGG 0.699372 1_3:-3352805 None:intergenic
TGGCTTTAATCTCAAGTACG+AGG 0.711072 1_3:+3352873 Msa0097540:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTAAAGACATTAATTTTT+GGG - chr1_3:3352590-3352609 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG - chr1_3:3352591-3352610 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG + chr1_3:3352590-3352609 Msa0097540:exon 15.0%
!! AACAAAAACTCAATAAAATT+AGG - chr1_3:3352692-3352711 None:intergenic 15.0%
!! TAAAGAATTAAGAATTACAA+TGG + chr1_3:3353005-3353024 Msa0097540:three_prime_UTR 15.0%
!!! TTCTAAAGACATTAATTTTT+GGG - chr1_3:3352590-3352609 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG - chr1_3:3352591-3352610 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG + chr1_3:3352590-3352609 Msa0097540:exon 15.0%
!! AACAAAAACTCAATAAAATT+AGG - chr1_3:3352692-3352711 None:intergenic 15.0%
!! TAAAGAATTAAGAATTACAA+TGG + chr1_3:3353005-3353024 Msa0097540:three_prime_UTR 15.0%
!! CACTAATTACTTAATTAAGA+AGG - chr1_3:3352232-3352251 None:intergenic 20.0%
!! TCCTAATTCAAATGAAATAT+GGG - chr1_3:3352434-3352453 None:intergenic 20.0%
!! ATCCTAATTCAAATGAAATA+TGG - chr1_3:3352435-3352454 None:intergenic 20.0%
!! TATTTGAATATATACGTGTA+CGG + chr1_3:3352718-3352737 Msa0097540:three_prime_UTR 20.0%
!! CACTAATTACTTAATTAAGA+AGG - chr1_3:3352232-3352251 None:intergenic 20.0%
!! TCCTAATTCAAATGAAATAT+GGG - chr1_3:3352434-3352453 None:intergenic 20.0%
!! ATCCTAATTCAAATGAAATA+TGG - chr1_3:3352435-3352454 None:intergenic 20.0%
!! TATTTGAATATATACGTGTA+CGG + chr1_3:3352718-3352737 Msa0097540:three_prime_UTR 20.0%
! TGTAAATACAAAATTAGGAC+GGG - chr1_3:3352178-3352197 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG - chr1_3:3352179-3352198 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG - chr1_3:3352183-3352202 None:intergenic 25.0%
! TCCCATATTTCATTTGAATT+AGG + chr1_3:3352430-3352449 Msa0097540:intron 25.0%
! TTAGAAAATGAGAATTGTGA+AGG + chr1_3:3352488-3352507 Msa0097540:CDS 25.0%
! TGTAAATACAAAATTAGGAC+GGG - chr1_3:3352178-3352197 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG - chr1_3:3352179-3352198 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG - chr1_3:3352183-3352202 None:intergenic 25.0%
! TCCCATATTTCATTTGAATT+AGG + chr1_3:3352430-3352449 Msa0097540:intron 25.0%
! TTAGAAAATGAGAATTGTGA+AGG + chr1_3:3352488-3352507 Msa0097540:CDS 25.0%
! CGTCCTAATTTTGTATTTAC+AGG + chr1_3:3352177-3352196 Msa0097540:CDS 30.0%
TTATCTTATTCTTGTGATGC+TGG + chr1_3:3352372-3352391 Msa0097540:intron 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG + chr1_3:3352448-3352467 Msa0097540:intron 30.0%
AACAAGAATGTTTGACAAGA+AGG + chr1_3:3352522-3352541 Msa0097540:CDS 30.0%
AGGTTGAAACATGAAACTAT+AGG - chr1_3:3352761-3352780 None:intergenic 30.0%
TAGTTTCATGTTTCAACCTA+AGG + chr1_3:3352762-3352781 Msa0097540:three_prime_UTR 30.0%
AGTTTCATGTTTCAACCTAA+GGG + chr1_3:3352763-3352782 Msa0097540:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG + chr1_3:3352846-3352865 Msa0097540:three_prime_UTR 30.0%
TAATCAGAAATTGTGGAAGA+TGG + chr1_3:3352853-3352872 Msa0097540:three_prime_UTR 30.0%
! CGTCCTAATTTTGTATTTAC+AGG + chr1_3:3352177-3352196 Msa0097540:CDS 30.0%
TTATCTTATTCTTGTGATGC+TGG + chr1_3:3352372-3352391 Msa0097540:intron 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG + chr1_3:3352448-3352467 Msa0097540:intron 30.0%
AACAAGAATGTTTGACAAGA+AGG + chr1_3:3352522-3352541 Msa0097540:CDS 30.0%
AGGTTGAAACATGAAACTAT+AGG - chr1_3:3352761-3352780 None:intergenic 30.0%
TAGTTTCATGTTTCAACCTA+AGG + chr1_3:3352762-3352781 Msa0097540:three_prime_UTR 30.0%
AGTTTCATGTTTCAACCTAA+GGG + chr1_3:3352763-3352782 Msa0097540:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG + chr1_3:3352846-3352865 Msa0097540:three_prime_UTR 30.0%
TAATCAGAAATTGTGGAAGA+TGG + chr1_3:3352853-3352872 Msa0097540:three_prime_UTR 30.0%
TGAACTCACTATGTCAAAAC+TGG + chr1_3:3352101-3352120 Msa0097540:exon 35.0%
CAAGCTTAATAGAAGAGCTA+AGG - chr1_3:3352139-3352158 None:intergenic 35.0%
AAATACAAAATTAGGACGGG+AGG - chr1_3:3352175-3352194 None:intergenic 35.0%
!! TGATGCTGGTGTTGTTTATT+AGG + chr1_3:3352386-3352405 Msa0097540:intron 35.0%
AAATGAGAATTGTGAAGGAG+TGG + chr1_3:3352493-3352512 Msa0097540:CDS 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG - chr1_3:3352812-3352831 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG - chr1_3:3352813-3352832 None:intergenic 35.0%
CATACTATTATTTACCGACG+AGG - chr1_3:3353086-3353105 None:intergenic 35.0%
TATATATATCCTCACCTGCA+TGG - chr1_3:3353174-3353193 None:intergenic 35.0%
TGAACTCACTATGTCAAAAC+TGG + chr1_3:3352101-3352120 Msa0097540:exon 35.0%
CAAGCTTAATAGAAGAGCTA+AGG - chr1_3:3352139-3352158 None:intergenic 35.0%
AAATACAAAATTAGGACGGG+AGG - chr1_3:3352175-3352194 None:intergenic 35.0%
!! TGATGCTGGTGTTGTTTATT+AGG + chr1_3:3352386-3352405 Msa0097540:intron 35.0%
AAATGAGAATTGTGAAGGAG+TGG + chr1_3:3352493-3352512 Msa0097540:CDS 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG - chr1_3:3352812-3352831 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG - chr1_3:3352813-3352832 None:intergenic 35.0%
CATACTATTATTTACCGACG+AGG - chr1_3:3353086-3353105 None:intergenic 35.0%
TATATATATCCTCACCTGCA+TGG - chr1_3:3353174-3353193 None:intergenic 35.0%
TAGAAGAGCTAAGGTGAAGA+GGG - chr1_3:3352130-3352149 None:intergenic 40.0%
ATAGAAGAGCTAAGGTGAAG+AGG - chr1_3:3352131-3352150 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG - chr1_3:3352781-3352800 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG - chr1_3:3352811-3352830 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG + chr1_3:3352873-3352892 Msa0097540:three_prime_UTR 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG + chr1_3:3353052-3353071 Msa0097540:three_prime_UTR 40.0%
TAGAAGAGCTAAGGTGAAGA+GGG - chr1_3:3352130-3352149 None:intergenic 40.0%
ATAGAAGAGCTAAGGTGAAG+AGG - chr1_3:3352131-3352150 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG - chr1_3:3352781-3352800 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG - chr1_3:3352811-3352830 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG + chr1_3:3352873-3352892 Msa0097540:three_prime_UTR 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG + chr1_3:3353052-3353071 Msa0097540:three_prime_UTR 40.0%
AGGTGTCTCTTCACTACATG+AGG + chr1_3:3352197-3352216 Msa0097540:CDS 45.0%
GAGAATTGTGAAGGAGTGGA+AGG + chr1_3:3352497-3352516 Msa0097540:CDS 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG + chr1_3:3353055-3353074 Msa0097540:three_prime_UTR 45.0%
!! GATCCTTTTTCTAGCCATGC+AGG + chr1_3:3353157-3353176 Msa0097540:three_prime_UTR 45.0%
TCACCTGCATGGCTAGAAAA+AGG - chr1_3:3353163-3353182 None:intergenic 45.0%
!! TTTTTCTAGCCATGCAGGTG+AGG + chr1_3:3353162-3353181 Msa0097540:three_prime_UTR 45.0%
AGGTGTCTCTTCACTACATG+AGG + chr1_3:3352197-3352216 Msa0097540:CDS 45.0%
GAGAATTGTGAAGGAGTGGA+AGG + chr1_3:3352497-3352516 Msa0097540:CDS 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG + chr1_3:3353055-3353074 Msa0097540:three_prime_UTR 45.0%
!! GATCCTTTTTCTAGCCATGC+AGG + chr1_3:3353157-3353176 Msa0097540:three_prime_UTR 45.0%
TCACCTGCATGGCTAGAAAA+AGG - chr1_3:3353163-3353182 None:intergenic 45.0%
!! TTTTTCTAGCCATGCAGGTG+AGG + chr1_3:3353162-3353181 Msa0097540:three_prime_UTR 45.0%
!! AATAAAATATTTAATTAACA+TGG - chr1_3:3352352-3352371 None:intergenic 5.0%
!! AATAAAATATTTAATTAACA+TGG - chr1_3:3352352-3352371 None:intergenic 5.0%
AAAATTAGGACGGGAGGCAG+AGG - chr1_3:3352169-3352188 None:intergenic 50.0%
! AATCAGAGAAGCGTATGGGG+TGG - chr1_3:3352808-3352827 None:intergenic 50.0%
! TGTTGGTGGAAAGACCTCGT+CGG + chr1_3:3353069-3353088 Msa0097540:three_prime_UTR 50.0%
AAAATTAGGACGGGAGGCAG+AGG - chr1_3:3352169-3352188 None:intergenic 50.0%
! AATCAGAGAAGCGTATGGGG+TGG - chr1_3:3352808-3352827 None:intergenic 50.0%
! TGTTGGTGGAAAGACCTCGT+CGG + chr1_3:3353069-3353088 Msa0097540:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 3352067 3353266 3352067 ID=Msa0097540;Name=Msa0097540
chr1_3 mRNA 3352067 3353266 3352067 ID=Msa0097540-mRNA-1;Parent=Msa0097540;Name=Msa0097540-mRNA-1;_AED=0.02;_eAED=0.02;_QI=44|1|1|1|1|1|2|668|84
chr1_3 exon 3352067 3352218 3352067 ID=Msa0097540-mRNA-1:exon:949;Parent=Msa0097540-mRNA-1
chr1_3 exon 3352452 3353266 3352452 ID=Msa0097540-mRNA-1:exon:950;Parent=Msa0097540-mRNA-1
chr1_3 five_prime_UTR 3352067 3352110 3352067 ID=Msa0097540-mRNA-1:five_prime_utr;Parent=Msa0097540-mRNA-1
chr1_3 CDS 3352111 3352218 3352111 ID=Msa0097540-mRNA-1:cds;Parent=Msa0097540-mRNA-1
chr1_3 CDS 3352452 3352598 3352452 ID=Msa0097540-mRNA-1:cds;Parent=Msa0097540-mRNA-1
chr1_3 three_prime_UTR 3352599 3353266 3352599 ID=Msa0097540-mRNA-1:three_prime_utr;Parent=Msa0097540-mRNA-1
Gene Sequence

>Msa0097540

ATGTCAAAACTGGTCACCCTCTTCACCTTAGCTCTTCTATTAAGCTTGAGTTTAACCTCTGCCTCCCGTCCTAATTTTGTATTTACAGGTGTCTCTTCACTACATGAGGATATTGTTTCTAGCAAGGCATCAAGTACTGTAGACTTAGAAAATGAGAATTGTGAAGGAGTGGAAGGAGAACAAGAATGTTTGACAAGAAGGACTCTAGCTGCACATCTCGATTATATCTACACTCAGCATAAACCCAAAAATTAA
Protein sequence

>Msa0097540

MSKLVTLFTLALLLSLSLTSASRPNFVFTGVSSLHEDIVSSKASSTVDLENENCEGVEGEQECLTRRTLAAHLDYIYTQHKPKN*