AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0885380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0885380 MtrunA17_Chr2g0313001 84.337 83 9 1 92 174 53 131 1.96e-41 135
Msa0885380 MtrunA17_Chr8g0345501 43.429 175 43 4 4 138 556 714 5.32e-33 123
Msa0885380 MtrunA17_Chr8g0345511 53.704 54 21 1 39 92 57 106 5.98e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 133 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGTCATTATGAAACATT+TGG 0.297182 6_1:-41421847 Msa0885380:CDS
TGCTCATTTGATTCACTGTT+GGG 0.303948 6_1:+41421792 None:intergenic
CTTCCGTACACATCGCAAAA+AGG 0.331253 6_1:-41422430 Msa0885380:CDS
ATGAAACATTTGGGATTTGT+TGG 0.353696 6_1:-41421837 Msa0885380:CDS
CACTGTTGGGGTTTGAAACA+TGG 0.393708 6_1:+41421805 None:intergenic
GCTGTCATTATGAAACATTT+GGG 0.422376 6_1:-41421846 Msa0885380:CDS
TTGATTTGAAGATGGAATCA+AGG 0.453518 6_1:+41422028 None:intergenic
ATGCTCATTTGATTCACTGT+TGG 0.464568 6_1:+41421791 None:intergenic
AAAGGGAGGATATTTGGCCT+TGG 0.468123 6_1:-41422065 Msa0885380:CDS
TTTGTTTGTTGATTTGAAGA+TGG 0.472897 6_1:+41422020 None:intergenic
AACAAGAAAAGTTGCAGATG+AGG 0.532029 6_1:-41421920 Msa0885380:CDS
GCTCATTTGATTCACTGTTG+GGG 0.539156 6_1:+41421793 None:intergenic
ACTGTTGGGGTTTGAAACAT+GGG 0.581536 6_1:+41421806 None:intergenic
AAACACACATGCTAATTCAG+AGG 0.635059 6_1:-41422000 Msa0885380:CDS
CACACATGCTAATTCAGAGG+AGG 0.683200 6_1:-41421997 Msa0885380:CDS
AAGTAAAACTCAGTCAGCGA+CGG 0.698708 6_1:+41422450 None:intergenic
TTCTGTTGAAGATGTCGATG+AGG 0.709983 6_1:-41421745 Msa0885380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTCTGTAAATTATAAAC+AGG + chr6_1:41423562-41423581 None:intergenic 15.0%
!! TGTTTATAATTTACAGAAAA+AGG - chr6_1:41423561-41423580 Msa0885380:intron 15.0%
!!! CTATTTTGTTGACATTTAAT+GGG + chr6_1:41421726-41421745 None:intergenic 20.0%
!!! ACTATTTTGTTGACATTTAA+TGG + chr6_1:41421727-41421746 None:intergenic 20.0%
!!! AACAAAATAGTATTTTGTGT+TGG - chr6_1:41421736-41421755 Msa0885380:CDS 20.0%
!!! ACAAAATAGTATTTTGTGTT+GGG - chr6_1:41421737-41421756 Msa0885380:CDS 20.0%
!!! AAATGGACTTAAAGATAAAT+GGG + chr6_1:41421822-41421841 None:intergenic 20.0%
!!! TAAATGGACTTAAAGATAAA+TGG + chr6_1:41421823-41421842 None:intergenic 20.0%
!! AATTGAATATAGAATCCTTA+GGG + chr6_1:41422104-41422123 None:intergenic 20.0%
!! ACTTATTTGAACTTATTTAG+TGG - chr6_1:41422270-41422289 Msa0885380:intron 20.0%
!! TTATCAACAAAAAAATTTCG+AGG + chr6_1:41422744-41422763 None:intergenic 20.0%
!! ACTTATTTGAACTTATTTAC+TGG - chr6_1:41422857-41422876 Msa0885380:intron 20.0%
!!! TTTTAGAGAACTTATGAAAA+CGG - chr6_1:41422971-41422990 Msa0885380:intron 20.0%
!!! AAATGAACATTTTTAAAGCA+AGG + chr6_1:41423109-41423128 None:intergenic 20.0%
!! ATGAAAAGTAATCACAAAAA+AGG + chr6_1:41423459-41423478 None:intergenic 20.0%
!! AATTTACAGAAAAAGGAAAA+AGG - chr6_1:41423568-41423587 Msa0885380:intron 20.0%
!! CAAATTTGAACAAAAAAAGA+TGG - chr6_1:41423854-41423873 Msa0885380:intron 20.0%
! GTTATGTCTGAAAGATTAAA+TGG + chr6_1:41421839-41421858 None:intergenic 25.0%
! CAATTGAATATAGAATCCTT+AGG + chr6_1:41422105-41422124 None:intergenic 25.0%
! GTCATTAATCATAAGTTGTT+TGG - chr6_1:41422393-41422412 Msa0885380:CDS 25.0%
! AAACCATGTAAAGTTTCATT+AGG - chr6_1:41422426-41422445 Msa0885380:CDS 25.0%
!! TCTAAAGGCTCTTAAATTTT+GGG + chr6_1:41422457-41422476 None:intergenic 25.0%
!!! TTCTAAAGGCTCTTAAATTT+TGG + chr6_1:41422458-41422477 None:intergenic 25.0%
!!! AATTGATTTGAAGCTGTATA+AGG - chr6_1:41422702-41422721 Msa0885380:intron 25.0%
!! TAGTGTTTTATCTATGAGTT+TGG - chr6_1:41422802-41422821 Msa0885380:intron 25.0%
!! ACTTATTTGACTTTATGTAG+TGG - chr6_1:41422888-41422907 Msa0885380:intron 25.0%
!! TTTATGTAGTGGAATAAGTT+TGG - chr6_1:41422303-41422322 Msa0885380:intron 25.0%
!!! GACTTATTTTACTTATCTCA+AGG - chr6_1:41422935-41422954 Msa0885380:intron 25.0%
! GTCATTAATCATAAGTTGTT+TGG - chr6_1:41422393-41422412 Msa0885380:CDS 25.0%
! TACATTTCAATTTGATTGCA+AGG - chr6_1:41423177-41423196 Msa0885380:intron 25.0%
! TGAAAAAACTTAGTTGTTAC+AGG + chr6_1:41423423-41423442 None:intergenic 25.0%
!! ATTTGAATTTGAAGCATACA+AGG + chr6_1:41423485-41423504 None:intergenic 25.0%
! TGAACAAATTTATGCATATG+TGG - chr6_1:41423756-41423775 Msa0885380:intron 25.0%
!!! GACTTCTTTTATTTTCGTTT+AGG - chr6_1:41423830-41423849 Msa0885380:intron 25.0%
! TATGGGTAGATTAGAAAAAA+AGG - chr6_1:41423965-41423984 Msa0885380:intron 25.0%
! ATGGGTAGATTAGAAAAAAA+GGG - chr6_1:41423966-41423985 Msa0885380:intron 25.0%
!!! TTTGTTTGTTGATTTGAAGA+TGG + chr6_1:41424031-41424050 None:intergenic 25.0%
! TTTTATCTCTCATAACCCTA+AGG - chr6_1:41422086-41422105 Msa0885380:intron 30.0%
CATGATACGAAAACAGAATT+TGG + chr6_1:41422160-41422179 None:intergenic 30.0%
TATCTGATATTGCTATCTCA+AGG - chr6_1:41422223-41422242 Msa0885380:intron 30.0%
GAATACTTGACTTTATGTAG+TGG - chr6_1:41422292-41422311 Msa0885380:intron 30.0%
!! GACTTATTTGACTTTTCTCA+AGG - chr6_1:41422339-41422358 Msa0885380:intron 30.0%
TGACCTAATGAAACTTTACA+TGG + chr6_1:41422432-41422451 None:intergenic 30.0%
!! TTTAAGAGCCTTTAGAATTC+AGG - chr6_1:41422461-41422480 Msa0885380:CDS 30.0%
AATCAACACCTGAATTCTAA+AGG + chr6_1:41422472-41422491 None:intergenic 30.0%
TATCTGTGAACGAAAATTTC+AGG - chr6_1:41422672-41422691 Msa0885380:intron 30.0%
TGTATAAGGAAACAAATCTC+AGG - chr6_1:41422716-41422735 Msa0885380:intron 30.0%
CACAACAATAGAATAAAGCA+AGG + chr6_1:41423061-41423080 None:intergenic 30.0%
ATTGAAATGTACACATTGCA+AGG + chr6_1:41423168-41423187 None:intergenic 30.0%
AAAAACTTAGTTGTTACAGG+AGG + chr6_1:41423420-41423439 None:intergenic 30.0%
GAAAATAAGAAGACATGCAA+AGG + chr6_1:41423540-41423559 None:intergenic 30.0%
TATATGTGAATCTGCATATG+TGG - chr6_1:41423790-41423809 Msa0885380:intron 30.0%
! TGTGGCTATATTTTATGCAT+TGG - chr6_1:41423808-41423827 Msa0885380:intron 30.0%
ATATGAAATGCCAACTGATT+TGG - chr6_1:41423939-41423958 Msa0885380:intron 30.0%
AGAAAAAAAGGGAGGATATT+TGG - chr6_1:41423977-41423996 Msa0885380:intron 30.0%
! TTGATTTGAAGATGGAATCA+AGG + chr6_1:41424023-41424042 None:intergenic 30.0%
TGCTGTCATTATGAAACATT+TGG - chr6_1:41424201-41424220 Msa0885380:intron 30.0%
GCTGTCATTATGAAACATTT+GGG - chr6_1:41424202-41424221 Msa0885380:intron 30.0%
! ATGAAACATTTGGGATTTGT+TGG - chr6_1:41424211-41424230 Msa0885380:intron 30.0%
GTGTTGGGAATGAGAAAAAA+TGG - chr6_1:41421752-41421771 Msa0885380:CDS 35.0%
! AATGGGCTTATATGTCTGAA+AGG + chr6_1:41421805-41421824 None:intergenic 35.0%
! GATCAGAAAAATCGCGTTTT+AGG + chr6_1:41421875-41421894 None:intergenic 35.0%
!! CTGTTTGGATTGTTTCTGTT+TGG - chr6_1:41422247-41422266 Msa0885380:intron 35.0%
!!! TGCTATGTTGTTTTAGCTTC+TGG - chr6_1:41422512-41422531 Msa0885380:intron 35.0%
ATCAACAAGTAGTTTCCGAT+CGG + chr6_1:41422627-41422646 None:intergenic 35.0%
! CAGTACAAGTTGAAGTTGAA+TGG - chr6_1:41422771-41422790 Msa0885380:intron 35.0%
GTTGAAGTTGAATGGCTTAT+AGG - chr6_1:41422779-41422798 Msa0885380:intron 35.0%
TCTATGAGTTTGGTATCTCA+TGG - chr6_1:41422812-41422831 Msa0885380:intron 35.0%
TAAACTGAAACAGTCCAAAC+AGG + chr6_1:41422838-41422857 None:intergenic 35.0%
! TTCTCTAAAAATAGCCGAAC+AGG + chr6_1:41422961-41422980 None:intergenic 35.0%
! ATTCTACTTTGTGTGCTACT+TGG - chr6_1:41423218-41423237 Msa0885380:intron 35.0%
ATCGCAAAAAGGATCAAACT+TGG - chr6_1:41423629-41423648 Msa0885380:intron 35.0%
TCGCAAAAAGGATCAAACTT+GGG - chr6_1:41423630-41423649 Msa0885380:intron 35.0%
AAAAAGGATCAAACTTGGGT+GGG - chr6_1:41423634-41423653 Msa0885380:intron 35.0%
CACATGAGTGCAAACATATA+TGG + chr6_1:41423709-41423728 None:intergenic 35.0%
TCAACTCAGAATACCACATT+TGG - chr6_1:41423882-41423901 Msa0885380:intron 35.0%
CAGTTGGCATTTCATATGTT+TGG + chr6_1:41423936-41423955 None:intergenic 35.0%
!! TGCCAACTGATTTGGATATA+TGG - chr6_1:41423947-41423966 Msa0885380:intron 35.0%
!! GCCAACTGATTTGGATATAT+GGG - chr6_1:41423948-41423967 Msa0885380:intron 35.0%
ACCCATATATCCAAATCAGT+TGG + chr6_1:41423952-41423971 None:intergenic 35.0%
GGTAGATTAGAAAAAAAGGG+AGG - chr6_1:41423969-41423988 Msa0885380:intron 35.0%
! TGGAATCAAGGTTTTTGATG+TGG + chr6_1:41424011-41424030 None:intergenic 35.0%
AAACACACATGCTAATTCAG+AGG - chr6_1:41424048-41424067 Msa0885380:intron 35.0%
AACAAGAAAAGTTGCAGATG+AGG - chr6_1:41424128-41424147 Msa0885380:intron 35.0%
TGCTCATTTGATTCACTGTT+GGG + chr6_1:41424259-41424278 None:intergenic 35.0%
ATGCTCATTTGATTCACTGT+TGG + chr6_1:41424260-41424279 None:intergenic 35.0%
! TTTTGTTGAAGATGTTGACG+AGG - chr6_1:41424336-41424355 Msa0885380:intron 35.0%
! ACGCGATTTTTCTGATCTGA+AGG - chr6_1:41421878-41421897 Msa0885380:CDS 40.0%
ATTCCGTTGAAGCTCGAAAA+TGG - chr6_1:41421912-41421931 Msa0885380:CDS 40.0%
!!! TTGCCATTTTCGAGCTTCAA+CGG + chr6_1:41421918-41421937 None:intergenic 40.0%
TTGCTATCTCAAGGACTGTT+TGG - chr6_1:41422232-41422251 Msa0885380:intron 40.0%
! GACTTTTCTCAAGGCATGTT+TGG - chr6_1:41422348-41422367 Msa0885380:intron 40.0%
TACTTATCTCAAGGCCTGTT+CGG - chr6_1:41422944-41422963 Msa0885380:intron 40.0%
TGCACATAGTAGTTCAGTTG+TGG - chr6_1:41423128-41423147 Msa0885380:intron 40.0%
CATAGTAGTTCAGTTGTGGT+TGG - chr6_1:41423132-41423151 Msa0885380:intron 40.0%
GTAGTTGACGTCGATATTGT+TGG + chr6_1:41423372-41423391 None:intergenic 40.0%
AACTTAGTTGTTACAGGAGG+TGG + chr6_1:41423417-41423436 None:intergenic 40.0%
AAGTAAAACTCAGTCAGCGA+CGG + chr6_1:41423601-41423620 None:intergenic 40.0%
! GATCCTTTTTGCGATGTGTA+CGG + chr6_1:41423624-41423643 None:intergenic 40.0%
CAAAAAGGATCAAACTTGGG+TGG - chr6_1:41423633-41423652 Msa0885380:intron 40.0%
! GTGTTGCTCAATGGAAGATT+TGG - chr6_1:41423726-41423745 Msa0885380:intron 40.0%
CAGAATACCACATTTGGTCT+AGG - chr6_1:41423888-41423907 Msa0885380:intron 40.0%
! AGGTTTTTGATGTGGATCCA+AGG + chr6_1:41424003-41424022 None:intergenic 40.0%
! ACTGTTGGGGTTTGAAACAT+GGG + chr6_1:41424245-41424264 None:intergenic 40.0%
GCTCATTTGATTCACTGTTG+GGG + chr6_1:41424258-41424277 None:intergenic 40.0%
TTCTGTTGAAGATGTCGATG+AGG - chr6_1:41424303-41424322 Msa0885380:intron 40.0%
CTGATCTGAAGGAAGAACGA+TGG - chr6_1:41421889-41421908 Msa0885380:CDS 45.0%
AGAGCTTCAACGAGCTTCAA+TGG + chr6_1:41421949-41421968 None:intergenic 45.0%
GCAGAGAAGAGAGCTTCAAT+CGG + chr6_1:41422056-41422075 None:intergenic 45.0%
CTGAGCGAGTAGTTTCAGAT+CGG + chr6_1:41422598-41422617 None:intergenic 45.0%
TTGGTATCTCATGGCCTGTT+TGG - chr6_1:41422821-41422840 Msa0885380:intron 45.0%
GGGATAGGTGGGAACATATA+TGG + chr6_1:41423325-41423344 None:intergenic 45.0%
GTAAAGAGGAAGGGATAGGT+GGG + chr6_1:41423336-41423355 None:intergenic 45.0%
AGTAAAGAGGAAGGGATAGG+TGG + chr6_1:41423337-41423356 None:intergenic 45.0%
CAGAGTAAAGAGGAAGGGAT+AGG + chr6_1:41423340-41423359 None:intergenic 45.0%
! GTCGATATTGTTGGTTGTGG+TGG + chr6_1:41423363-41423382 None:intergenic 45.0%
! GACGTCGATATTGTTGGTTG+TGG + chr6_1:41423366-41423385 None:intergenic 45.0%
TAGTTGTTACAGGAGGTGGA+GGG + chr6_1:41423413-41423432 None:intergenic 45.0%
TTAGTTGTTACAGGAGGTGG+AGG + chr6_1:41423414-41423433 None:intergenic 45.0%
CTTCCGTACACATCGCAAAA+AGG - chr6_1:41423618-41423637 Msa0885380:intron 45.0%
! TGCACTCATGTGTTGCTCAA+TGG - chr6_1:41423717-41423736 Msa0885380:intron 45.0%
TACCACATTTGGTCTAGGAG+AGG - chr6_1:41423893-41423912 Msa0885380:intron 45.0%
ATCCTCTCCTAGACCAAATG+TGG + chr6_1:41423898-41423917 None:intergenic 45.0%
AAAGGGAGGATATTTGGCCT+TGG - chr6_1:41423983-41424002 Msa0885380:intron 45.0%
CACACATGCTAATTCAGAGG+AGG - chr6_1:41424051-41424070 Msa0885380:intron 45.0%
! CACTGTTGGGGTTTGAAACA+TGG + chr6_1:41424246-41424265 None:intergenic 45.0%
! CGATCTGAAACTACTCGCTC+AGG - chr6_1:41422596-41422615 Msa0885380:intron 50.0%
CTCGCTCAGGTTATTCCGAT+CGG - chr6_1:41422609-41422628 Msa0885380:intron 50.0%
GGTGGCAGAGTAAAGAGGAA+GGG + chr6_1:41423345-41423364 None:intergenic 50.0%
TGGTGGCAGAGTAAAGAGGA+AGG + chr6_1:41423346-41423365 None:intergenic 50.0%
GTTGTGGTGGCAGAGTAAAG+AGG + chr6_1:41423350-41423369 None:intergenic 50.0%
TACAGGAGGTGGAGGGTGAC+AGG + chr6_1:41423406-41423425 None:intergenic 60.0%
AGGAGGTGGAGGGTGACAGG+AGG + chr6_1:41423403-41423422 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 41421683 41424387 41421683 ID=Msa0885380;Name=Msa0885380
chr6_1 mRNA 41421683 41424387 41421683 ID=Msa0885380-mRNA-1;Parent=Msa0885380;Name=Msa0885380-mRNA-1;_AED=0.30;_eAED=0.41;_QI=0|0|0.33|0.66|1|1|3|0|174
chr6_1 exon 41424379 41424387 41424379 ID=Msa0885380-mRNA-1:exon:9185;Parent=Msa0885380-mRNA-1
chr6_1 exon 41422392 41422493 41422392 ID=Msa0885380-mRNA-1:exon:9184;Parent=Msa0885380-mRNA-1
chr6_1 exon 41421683 41422096 41421683 ID=Msa0885380-mRNA-1:exon:9183;Parent=Msa0885380-mRNA-1
chr6_1 CDS 41424379 41424387 41424379 ID=Msa0885380-mRNA-1:cds;Parent=Msa0885380-mRNA-1
chr6_1 CDS 41422392 41422493 41422392 ID=Msa0885380-mRNA-1:cds;Parent=Msa0885380-mRNA-1
chr6_1 CDS 41421683 41422096 41421683 ID=Msa0885380-mRNA-1:cds;Parent=Msa0885380-mRNA-1
Gene Sequence

>Msa0885380

ATGAGTAGTAAAAAGGAAAAAGGTGCAGAACCGTCGCTGACTGAGTTTTACTTCCGTACACATCGCAAAAAGGATCAAACTTGGGTGGGTGTGCATGCTGAATCTGCATATATTAGAAAAAAAGGGAGGATATTTGGCCTTGGATCCACATCAAAAACCTTGATTCCATCTTCAAATCAACAAACAAACACACATGCTAATTCAGAGGAGGTTGAATTTTTGAGAAGACAAGTGCATGCTTTAAATGCATCATTGCAAAGACAAGAACAAGAAAAGTTGCAGATGAGGCAACAAATGCAACGTCAAGAAAAAGAAATGATTAATACTAATAAAAAACTTGCTGTCATTATGAAACATTTGGGATTTGTTGGATCTTCTTCCCATGTTTCAAACCCCAACAGTGAATCAAATGAGCATATTGATGAAGATGACAACAATGATTCTGTTGAAGATGTCGATGAGGATGACAATGATTTTGTTGAAGATGTTGACGAGGATAACAATAGTTATCATATTGATAACTAG

Protein sequence

>Msa0885380

MSSKKEKGAEPSLTEFYFRTHRKKDQTWVGVHAESAYIRKKGRIFGLGSTSKTLIPSSNQQTNTHANSEEVEFLRRQVHALNASLQRQEQEKLQMRQQMQRQEKEMINTNKKLAVIMKHLGFVGSSSHVSNPNSESNEHIDEDDNNDSVEDVDEDDNDFVEDVDEDNNSYHIDN*