AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0991190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0991190 MtrunA17_Chr6g0484731 88.732 71 8 0 1 71 499 569 4.72e-39 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0991190 AT1G49050.1 63.793 58 21 0 1 58 517 574 1.03e-22 89.7
Msa0991190 AT1G49050.2 63.793 58 21 0 1 58 344 401 1.47e-21 86.3

Find 27 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTCCAAATTCCTACATTA+TGG 0.236616 6_4:-54930494 None:intergenic
CATTTCACTGCGAGGACATT+TGG 0.309662 6_4:+54930304 Msa0991190:CDS
ACAGCCATAATGTAGGAATT+TGG 0.323570 6_4:+54930490 Msa0991190:three_prime_UTR
CTGACTGACATCTAAGATTC+TGG 0.356340 6_4:-54930443 None:intergenic
GTTTGCTTAGCTATCCTTGA+TGG 0.362073 6_4:+54929648 Msa0991190:CDS
CAGCATAGAAGTTTATTAGA+AGG 0.387910 6_4:-54929610 None:intergenic
GACAATGTGAACAAGAAAAT+TGG 0.390168 6_4:+54930335 Msa0991190:CDS
AATGAAAATAAAGCTCATAA+TGG 0.401448 6_4:-54930707 None:intergenic
GTCTTCTTCAACATTCTGCT+TGG 0.430467 6_4:-54930383 None:intergenic
GAAAGTACCTCCAAGTATAA+TGG 0.441127 6_4:-54929694 None:intergenic
CATTTACATTGCTACCATCA+AGG 0.483225 6_4:-54929662 None:intergenic
CACAACTTTAACCAACTGAC+AGG 0.485605 6_4:+54930611 Msa0991190:three_prime_UTR
GATGGATCCTCCATTATACT+TGG 0.487511 6_4:+54929684 Msa0991190:CDS
GTGTAAAATAGTATGTGTAT+AGG 0.508629 6_4:+54930466 Msa0991190:three_prime_UTR
CAGAATCTTAGATGTCAGTC+AGG 0.510750 6_4:+54930444 Msa0991190:three_prime_UTR
TGTGAACAAGAAAATTGGTT+GGG 0.514352 6_4:+54930340 Msa0991190:CDS
GGATCCTCCATTATACTTGG+AGG 0.553808 6_4:+54929687 Msa0991190:CDS
ATACATTGAGTTTCACCGCT+AGG 0.569090 6_4:-54930553 None:intergenic
GATGGTAGCAATGTAAATGA+TGG 0.578345 6_4:+54929666 Msa0991190:CDS
GCCATAATGTAGGAATTTGG+AGG 0.580014 6_4:+54930493 Msa0991190:three_prime_UTR
ACTTCTATGCTGCAGAACAA+AGG 0.581078 6_4:+54929621 Msa0991190:exon
ATGTGAACAAGAAAATTGGT+TGG 0.596695 6_4:+54930339 Msa0991190:CDS
TATAGGTACAGCCATAATGT+AGG 0.599924 6_4:+54930483 Msa0991190:three_prime_UTR
AGTACCTCCAAGTATAATGG+AGG 0.647121 6_4:-54929691 None:intergenic
GGTTGGGAGAGAACAAAATG+TGG 0.665136 6_4:+54930356 Msa0991190:CDS
TTTGCAGACATTTCACTGCG+AGG 0.715890 6_4:+54930296 Msa0991190:intron
ATGTTATCTTAAGAGCCTAG+CGG 0.723387 6_4:+54930538 Msa0991190:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATGAATCAAGAGTT+AGG - chr6_4:54930016-54930035 None:intergenic 20.0%
!! TGTTCACAAATTAGAAAATA+AGG - chr6_4:54930240-54930259 None:intergenic 20.0%
!!! ATTTTAAGTAAGCAAAACTA+AGG + chr6_4:54930647-54930666 Msa0991190:three_prime_UTR 20.0%
!! AATGAAAATAAAGCTCATAA+TGG - chr6_4:54930710-54930729 None:intergenic 20.0%
!! ATATATATGAATCAAGAGTT+AGG - chr6_4:54930016-54930035 None:intergenic 20.0%
!! TGTTCACAAATTAGAAAATA+AGG - chr6_4:54930240-54930259 None:intergenic 20.0%
!!! ATTTTAAGTAAGCAAAACTA+AGG + chr6_4:54930647-54930666 Msa0991190:three_prime_UTR 20.0%
!! AATGAAAATAAAGCTCATAA+TGG - chr6_4:54930710-54930729 None:intergenic 20.0%
!! CATAATAAAGTTTTCCTTGA+GGG - chr6_4:54929723-54929742 None:intergenic 25.0%
!! TCATAATAAAGTTTTCCTTG+AGG - chr6_4:54929724-54929743 None:intergenic 25.0%
! AACCTTGTATAAAAACTAGA+AGG - chr6_4:54929754-54929773 None:intergenic 25.0%
!!! GGTTTTTTTATGTTGATGAA+TGG + chr6_4:54929770-54929789 Msa0991190:intron 25.0%
!!! ATGCTTTATACACTCTTTTT+TGG + chr6_4:54929809-54929828 Msa0991190:intron 25.0%
!!! TGCTATTTTACATTAAGCTT+TGG + chr6_4:54929929-54929948 Msa0991190:intron 25.0%
! GTGTAAAATAGTATGTGTAT+AGG + chr6_4:54930466-54930485 Msa0991190:three_prime_UTR 25.0%
!! CATAATAAAGTTTTCCTTGA+GGG - chr6_4:54929723-54929742 None:intergenic 25.0%
!! TCATAATAAAGTTTTCCTTG+AGG - chr6_4:54929724-54929743 None:intergenic 25.0%
! AACCTTGTATAAAAACTAGA+AGG - chr6_4:54929754-54929773 None:intergenic 25.0%
!!! GGTTTTTTTATGTTGATGAA+TGG + chr6_4:54929770-54929789 Msa0991190:intron 25.0%
!!! ATGCTTTATACACTCTTTTT+TGG + chr6_4:54929809-54929828 Msa0991190:intron 25.0%
!!! TGCTATTTTACATTAAGCTT+TGG + chr6_4:54929929-54929948 Msa0991190:intron 25.0%
! GTGTAAAATAGTATGTGTAT+AGG + chr6_4:54930466-54930485 Msa0991190:three_prime_UTR 25.0%
CAGCATAGAAGTTTATTAGA+AGG - chr6_4:54929613-54929632 None:intergenic 30.0%
!!! TGCCTTCTAGTTTTTATACA+AGG + chr6_4:54929749-54929768 Msa0991190:intron 30.0%
! TGTTGATAAATAACTCAGCT+AGG + chr6_4:54929837-54929856 Msa0991190:intron 30.0%
CCTCAATAACACTTAATGAA+TGG - chr6_4:54929869-54929888 None:intergenic 30.0%
! CCATTCATTAAGTGTTATTG+AGG + chr6_4:54929866-54929885 Msa0991190:intron 30.0%
GACAATGTGAACAAGAAAAT+TGG + chr6_4:54930335-54930354 Msa0991190:CDS 30.0%
ATGTGAACAAGAAAATTGGT+TGG + chr6_4:54930339-54930358 Msa0991190:CDS 30.0%
TGTGAACAAGAAAATTGGTT+GGG + chr6_4:54930340-54930359 Msa0991190:CDS 30.0%
CAGCATAGAAGTTTATTAGA+AGG - chr6_4:54929613-54929632 None:intergenic 30.0%
!!! TGCCTTCTAGTTTTTATACA+AGG + chr6_4:54929749-54929768 Msa0991190:intron 30.0%
! TGTTGATAAATAACTCAGCT+AGG + chr6_4:54929837-54929856 Msa0991190:intron 30.0%
CCTCAATAACACTTAATGAA+TGG - chr6_4:54929869-54929888 None:intergenic 30.0%
! CCATTCATTAAGTGTTATTG+AGG + chr6_4:54929866-54929885 Msa0991190:intron 30.0%
GACAATGTGAACAAGAAAAT+TGG + chr6_4:54930335-54930354 Msa0991190:CDS 30.0%
ATGTGAACAAGAAAATTGGT+TGG + chr6_4:54930339-54930358 Msa0991190:CDS 30.0%
TGTGAACAAGAAAATTGGTT+GGG + chr6_4:54930340-54930359 Msa0991190:CDS 30.0%
CATTTACATTGCTACCATCA+AGG - chr6_4:54929665-54929684 None:intergenic 35.0%
GATGGTAGCAATGTAAATGA+TGG + chr6_4:54929666-54929685 Msa0991190:CDS 35.0%
!! GAAAGTACCTCCAAGTATAA+TGG - chr6_4:54929697-54929716 None:intergenic 35.0%
CATTCGAAGGTAGCAAAAAT+TGG - chr6_4:54930046-54930065 None:intergenic 35.0%
TTGTTTCAGTCAACATTCGA+AGG - chr6_4:54930059-54930078 None:intergenic 35.0%
! ATGTTGACTGAAACAATCGT+TGG + chr6_4:54930063-54930082 Msa0991190:intron 35.0%
TATAGGTACAGCCATAATGT+AGG + chr6_4:54930483-54930502 Msa0991190:three_prime_UTR 35.0%
ACAGCCATAATGTAGGAATT+TGG + chr6_4:54930490-54930509 Msa0991190:three_prime_UTR 35.0%
TCCTCCAAATTCCTACATTA+TGG - chr6_4:54930497-54930516 None:intergenic 35.0%
ATGTTATCTTAAGAGCCTAG+CGG + chr6_4:54930538-54930557 Msa0991190:three_prime_UTR 35.0%
!! CAATTTGTTTTCCTGTCAGT+TGG - chr6_4:54930625-54930644 None:intergenic 35.0%
CATTTACATTGCTACCATCA+AGG - chr6_4:54929665-54929684 None:intergenic 35.0%
GATGGTAGCAATGTAAATGA+TGG + chr6_4:54929666-54929685 Msa0991190:CDS 35.0%
!! GAAAGTACCTCCAAGTATAA+TGG - chr6_4:54929697-54929716 None:intergenic 35.0%
CATTCGAAGGTAGCAAAAAT+TGG - chr6_4:54930046-54930065 None:intergenic 35.0%
TTGTTTCAGTCAACATTCGA+AGG - chr6_4:54930059-54930078 None:intergenic 35.0%
! ATGTTGACTGAAACAATCGT+TGG + chr6_4:54930063-54930082 Msa0991190:intron 35.0%
TATAGGTACAGCCATAATGT+AGG + chr6_4:54930483-54930502 Msa0991190:three_prime_UTR 35.0%
ACAGCCATAATGTAGGAATT+TGG + chr6_4:54930490-54930509 Msa0991190:three_prime_UTR 35.0%
TCCTCCAAATTCCTACATTA+TGG - chr6_4:54930497-54930516 None:intergenic 35.0%
ATGTTATCTTAAGAGCCTAG+CGG + chr6_4:54930538-54930557 Msa0991190:three_prime_UTR 35.0%
!! CAATTTGTTTTCCTGTCAGT+TGG - chr6_4:54930625-54930644 None:intergenic 35.0%
ACTTCTATGCTGCAGAACAA+AGG + chr6_4:54929621-54929640 Msa0991190:exon 40.0%
GTTTGCTTAGCTATCCTTGA+TGG + chr6_4:54929648-54929667 Msa0991190:CDS 40.0%
GATGGATCCTCCATTATACT+TGG + chr6_4:54929684-54929703 Msa0991190:CDS 40.0%
AGTACCTCCAAGTATAATGG+AGG - chr6_4:54929694-54929713 None:intergenic 40.0%
GTCTTCTTCAACATTCTGCT+TGG - chr6_4:54930386-54930405 None:intergenic 40.0%
! CTGACTGACATCTAAGATTC+TGG - chr6_4:54930446-54930465 None:intergenic 40.0%
CAGAATCTTAGATGTCAGTC+AGG + chr6_4:54930444-54930463 Msa0991190:three_prime_UTR 40.0%
GCCATAATGTAGGAATTTGG+AGG + chr6_4:54930493-54930512 Msa0991190:three_prime_UTR 40.0%
ATACATTGAGTTTCACCGCT+AGG - chr6_4:54930556-54930575 None:intergenic 40.0%
CACAACTTTAACCAACTGAC+AGG + chr6_4:54930611-54930630 Msa0991190:three_prime_UTR 40.0%
ACTTCTATGCTGCAGAACAA+AGG + chr6_4:54929621-54929640 Msa0991190:exon 40.0%
GTTTGCTTAGCTATCCTTGA+TGG + chr6_4:54929648-54929667 Msa0991190:CDS 40.0%
GATGGATCCTCCATTATACT+TGG + chr6_4:54929684-54929703 Msa0991190:CDS 40.0%
AGTACCTCCAAGTATAATGG+AGG - chr6_4:54929694-54929713 None:intergenic 40.0%
GTCTTCTTCAACATTCTGCT+TGG - chr6_4:54930386-54930405 None:intergenic 40.0%
! CTGACTGACATCTAAGATTC+TGG - chr6_4:54930446-54930465 None:intergenic 40.0%
CAGAATCTTAGATGTCAGTC+AGG + chr6_4:54930444-54930463 Msa0991190:three_prime_UTR 40.0%
GCCATAATGTAGGAATTTGG+AGG + chr6_4:54930493-54930512 Msa0991190:three_prime_UTR 40.0%
ATACATTGAGTTTCACCGCT+AGG - chr6_4:54930556-54930575 None:intergenic 40.0%
CACAACTTTAACCAACTGAC+AGG + chr6_4:54930611-54930630 Msa0991190:three_prime_UTR 40.0%
GGATCCTCCATTATACTTGG+AGG + chr6_4:54929687-54929706 Msa0991190:CDS 45.0%
!! ACTAGCTTCCTCTTTTCCAG+AGG + chr6_4:54930122-54930141 Msa0991190:intron 45.0%
TTTGCAGACATTTCACTGCG+AGG + chr6_4:54930296-54930315 Msa0991190:intron 45.0%
CATTTCACTGCGAGGACATT+TGG + chr6_4:54930304-54930323 Msa0991190:CDS 45.0%
GGTTGGGAGAGAACAAAATG+TGG + chr6_4:54930356-54930375 Msa0991190:CDS 45.0%
GGATCCTCCATTATACTTGG+AGG + chr6_4:54929687-54929706 Msa0991190:CDS 45.0%
!! ACTAGCTTCCTCTTTTCCAG+AGG + chr6_4:54930122-54930141 Msa0991190:intron 45.0%
TTTGCAGACATTTCACTGCG+AGG + chr6_4:54930296-54930315 Msa0991190:intron 45.0%
CATTTCACTGCGAGGACATT+TGG + chr6_4:54930304-54930323 Msa0991190:CDS 45.0%
GGTTGGGAGAGAACAAAATG+TGG + chr6_4:54930356-54930375 Msa0991190:CDS 45.0%
! GAGGTACTTTCACACCCTCA+AGG + chr6_4:54929706-54929725 Msa0991190:intron 50.0%
! CTTCCTCTTTTCCAGAGGAC+AGG + chr6_4:54930127-54930146 Msa0991190:intron 50.0%
! CATCCTGTCCTCTGGAAAAG+AGG - chr6_4:54930133-54930152 None:intergenic 50.0%
! CTCTTTTCCAGAGGACAGGA+TGG + chr6_4:54930131-54930150 Msa0991190:intron 50.0%
GTCTTAACCATCCTGTCCTC+TGG - chr6_4:54930141-54930160 None:intergenic 50.0%
! GAGGTACTTTCACACCCTCA+AGG + chr6_4:54929706-54929725 Msa0991190:intron 50.0%
! CTTCCTCTTTTCCAGAGGAC+AGG + chr6_4:54930127-54930146 Msa0991190:intron 50.0%
! CATCCTGTCCTCTGGAAAAG+AGG - chr6_4:54930133-54930152 None:intergenic 50.0%
! CTCTTTTCCAGAGGACAGGA+TGG + chr6_4:54930131-54930150 Msa0991190:intron 50.0%
GTCTTAACCATCCTGTCCTC+TGG - chr6_4:54930141-54930160 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 54929594 54930729 54929594 ID=Msa0991190;Name=Msa0991190
chr6_4 mRNA 54929594 54930729 54929594 ID=Msa0991190-mRNA-1;Parent=Msa0991190;Name=Msa0991190-mRNA-1;_AED=0.00;_eAED=0.00;_QI=33|1|1|1|1|1|2|293|71
chr6_4 exon 54929594 54929708 54929594 ID=Msa0991190-mRNA-1:exon:11232;Parent=Msa0991190-mRNA-1
chr6_4 exon 54930303 54930729 54930303 ID=Msa0991190-mRNA-1:exon:11233;Parent=Msa0991190-mRNA-1
chr6_4 five_prime_UTR 54929594 54929626 54929594 ID=Msa0991190-mRNA-1:five_prime_utr;Parent=Msa0991190-mRNA-1
chr6_4 CDS 54929627 54929708 54929627 ID=Msa0991190-mRNA-1:cds;Parent=Msa0991190-mRNA-1
chr6_4 CDS 54930303 54930436 54930303 ID=Msa0991190-mRNA-1:cds;Parent=Msa0991190-mRNA-1
chr6_4 three_prime_UTR 54930437 54930729 54930437 ID=Msa0991190-mRNA-1:three_prime_utr;Parent=Msa0991190-mRNA-1
Gene Sequence

>Msa0991190

ATGCTGCAGAACAAAGGCAATGTTTGCTTAGCTATCCTTGATGGTAGCAATGTAAATGATGGATCCTCCATTATACTTGGAGACATTTCACTGCGAGGACATTTGGTTGTGTATGACAATGTGAACAAGAAAATTGGTTGGGAGAGAACAAAATGTGGCATGCCAAGCAGAATGTTGAAGAAGACTCACAATTTCTTAACTGATAGTATGTTATGA
Protein sequence

>Msa0991190

MLQNKGNVCLAILDGSNVNDGSSIILGDISLRGHLVVYDNVNKKIGWERTKCGMPSRMLKKTHNFLTDSML*