AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1174980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1174980 MtrunA17_Chr8g0344991 97.521 121 3 0 1 121 1 121 8.44e-83 238
Msa1174980 MtrunA17_Chr3g0124361 42.105 76 44 0 7 82 92 167 8.49e-16 69.7
Msa1174980 MtrunA17_Chr2g0295651 41.892 74 43 0 6 79 31 104 1.09e-14 65.9
Msa1174980 MtrunA17_Chr4g0055191 63.636 44 16 0 39 82 73 116 2.02e-14 65.5
Msa1174980 MtrunA17_Chr4g0067541 40.000 80 37 2 17 89 33 108 4.65e-14 63.5
Msa1174980 MtrunA17_Chr4g0070221 46.377 69 23 2 39 107 178 232 2.20e-13 64.3
Msa1174980 MtrunA17_Chr8g0336591 53.571 56 24 1 39 92 38 93 9.34e-13 60.1
Msa1174980 MtrunA17_Chr3g0115551 54.545 44 20 0 39 82 90 133 1.28e-12 60.8
Msa1174980 MtrunA17_Chr7g0260011 54.348 46 21 0 39 84 215 260 8.45e-12 60.1
Msa1174980 MtrunA17_Chr5g0400051 61.364 44 16 1 39 82 85 127 2.33e-11 57.8
Msa1174980 MtrunA17_Chr2g0301141 59.091 44 17 1 39 82 186 228 5.35e-11 57.8
Msa1174980 MtrunA17_Chr1g0148411 52.941 51 22 1 39 89 275 323 7.61e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1174980 AT1G53885.1 51.261 119 53 4 1 116 4 120 1.57e-33 114
Msa1174980 AT1G53903.1 51.261 119 53 4 1 116 4 120 1.57e-33 114
Msa1174980 AT5G65040.1 65.116 43 15 0 39 81 57 99 5.61e-15 66.2
Msa1174980 AT1G22160.1 59.091 44 18 0 39 82 78 121 2.14e-14 65.5
Msa1174980 AT5G49120.1 54.167 48 22 0 36 83 65 112 3.60e-14 65.1
Msa1174980 AT1G78020.1 59.091 44 18 0 39 82 89 132 5.47e-14 64.7
Msa1174980 AT2G44670.1 59.091 44 18 0 39 82 16 59 2.51e-13 61.2
Msa1174980 AT4G39795.1 55.814 43 19 0 39 81 73 115 9.22e-13 60.8
Msa1174980 AT4G17670.1 55.357 56 21 1 39 90 76 131 1.84e-12 60.8
Msa1174980 AT5G47060.2 61.364 44 17 0 39 82 97 140 6.47e-12 59.7
Msa1174980 AT5G47060.1 61.364 44 17 0 39 82 97 140 6.47e-12 59.7

Find 15 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTCTTTGAGCTGATAATT+TGG 0.208127 8_1:+6215645 None:intergenic
CAGGAACAGACAAATAGTTT+TGG 0.346572 8_1:-6214661 Msa1174980:CDS
TACATGTAAATATCTTTGTC+TGG 0.359115 8_1:+6215518 None:intergenic
TTAAGGAAGCAGAAATCAAT+AGG 0.365984 8_1:+6215572 None:intergenic
AGAAATCAATAGGTATGGTT+TGG 0.393389 8_1:+6215582 None:intergenic
TTATTATGCAGGGGTGATCA+AGG 0.486797 8_1:-6214702 Msa1174980:intron
ACAAAGATATTTACATGTAC+AGG 0.496534 8_1:-6215514 Msa1174980:intron
TATAGTATCACCATGGAAGT+TGG 0.509119 8_1:-6215683 None:intergenic
TTGAGCTGATAATTTGGAGA+AGG 0.510013 8_1:+6215651 None:intergenic
GAAGCAGAAATCAATAGGTA+TGG 0.532981 8_1:+6215577 None:intergenic
GAGACTTAGACCAACTTCCA+TGG 0.574855 8_1:+6215673 None:intergenic
ACATGTAAATATCTTTGTCT+GGG 0.575313 8_1:+6215519 None:intergenic
GTTTCTGCAGTATAGAGTGC+AGG 0.581254 8_1:-6214680 Msa1174980:CDS
TTATAGACAATGTAGTAATG+AGG 0.609088 8_1:-6214592 Msa1174980:CDS
AGAGACACGTCTTATACTTG+AGG 0.618514 8_1:-6214562 Msa1174980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGAGCAAATATATTATTTTT+TGG - chr8_1:6214769-6214788 Msa1174980:intron 15.0%
!!! GAGCAAATATATTATTTTTT+GGG - chr8_1:6214770-6214789 Msa1174980:intron 15.0%
!!! ATATCATCTTATTTTTAGTA+TGG + chr8_1:6215374-6215393 None:intergenic 15.0%
!!! AGAGCAAATATATTATTTTT+TGG - chr8_1:6214769-6214788 Msa1174980:intron 15.0%
!!! GAGCAAATATATTATTTTTT+GGG - chr8_1:6214770-6214789 Msa1174980:intron 15.0%
!!! ATATCATCTTATTTTTAGTA+TGG + chr8_1:6215374-6215393 None:intergenic 15.0%
!!! AAAATAGTATCGATCAAAAT+CGG + chr8_1:6215131-6215150 None:intergenic 20.0%
!!! ATAACATTGTACCATTTTTT+TGG + chr8_1:6215590-6215609 None:intergenic 20.0%
!!! AAAATAGTATCGATCAAAAT+CGG + chr8_1:6215131-6215150 None:intergenic 20.0%
!!! ATAACATTGTACCATTTTTT+TGG + chr8_1:6215590-6215609 None:intergenic 20.0%
! ACATGTAAATATCTTTGTCT+GGG + chr8_1:6214682-6214701 None:intergenic 25.0%
! TACATGTAAATATCTTTGTC+TGG + chr8_1:6214683-6214702 None:intergenic 25.0%
! ACAAAGATATTTACATGTAC+AGG - chr8_1:6214684-6214703 Msa1174980:CDS 25.0%
! TGGAATAAAAAAAGAGAGTA+TGG + chr8_1:6214728-6214747 None:intergenic 25.0%
! CTAAAGCAATTTCAATTTAC+TGG - chr8_1:6215052-6215071 Msa1174980:intron 25.0%
! TTTACAATACAACCTCAATT+GGG + chr8_1:6215263-6215282 None:intergenic 25.0%
! ATTAAGAAAGGTTAGATCAT+GGG + chr8_1:6215341-6215360 None:intergenic 25.0%
! AATTAAGAAAGGTTAGATCA+TGG + chr8_1:6215342-6215361 None:intergenic 25.0%
! GGATTTGATAGAATTAAGAA+AGG + chr8_1:6215353-6215372 None:intergenic 25.0%
!!! TATGTTGGTAATTATTATGC+AGG - chr8_1:6215485-6215504 Msa1174980:intron 25.0%
!!! ATGTTGGTAATTATTATGCA+GGG - chr8_1:6215486-6215505 Msa1174980:intron 25.0%
! TTATAGACAATGTAGTAATG+AGG - chr8_1:6215606-6215625 Msa1174980:CDS 25.0%
! ACATGTAAATATCTTTGTCT+GGG + chr8_1:6214682-6214701 None:intergenic 25.0%
! TACATGTAAATATCTTTGTC+TGG + chr8_1:6214683-6214702 None:intergenic 25.0%
! ACAAAGATATTTACATGTAC+AGG - chr8_1:6214684-6214703 Msa1174980:CDS 25.0%
! TGGAATAAAAAAAGAGAGTA+TGG + chr8_1:6214728-6214747 None:intergenic 25.0%
! CTAAAGCAATTTCAATTTAC+TGG - chr8_1:6215052-6215071 Msa1174980:intron 25.0%
! TTTACAATACAACCTCAATT+GGG + chr8_1:6215263-6215282 None:intergenic 25.0%
! ATTAAGAAAGGTTAGATCAT+GGG + chr8_1:6215341-6215360 None:intergenic 25.0%
! AATTAAGAAAGGTTAGATCA+TGG + chr8_1:6215342-6215361 None:intergenic 25.0%
! GGATTTGATAGAATTAAGAA+AGG + chr8_1:6215353-6215372 None:intergenic 25.0%
!!! TATGTTGGTAATTATTATGC+AGG - chr8_1:6215485-6215504 Msa1174980:intron 25.0%
!!! ATGTTGGTAATTATTATGCA+GGG - chr8_1:6215486-6215505 Msa1174980:intron 25.0%
! TTATAGACAATGTAGTAATG+AGG - chr8_1:6215606-6215625 Msa1174980:CDS 25.0%
TACTCTTTGAGCTGATAATT+TGG + chr8_1:6214556-6214575 None:intergenic 30.0%
AGAAATCAATAGGTATGGTT+TGG + chr8_1:6214619-6214638 None:intergenic 30.0%
TTAAGGAAGCAGAAATCAAT+AGG + chr8_1:6214629-6214648 None:intergenic 30.0%
! TACACAGATTGCAAGTTTTA+AGG + chr8_1:6214646-6214665 None:intergenic 30.0%
TTGCTCTATACTTAAGAAGT+TGG + chr8_1:6214756-6214775 None:intergenic 30.0%
!!! ATTTTTTGGGTGAGCTAATT+AGG - chr8_1:6214783-6214802 Msa1174980:intron 30.0%
!! CTTCATTAGTCTTGATGATT+TGG - chr8_1:6214837-6214856 Msa1174980:intron 30.0%
TTATAGTTTCAAATTAGCCG+CGG - chr8_1:6214976-6214995 Msa1174980:intron 30.0%
! CACATTTTATTGCAGTATCA+TGG + chr8_1:6215031-6215050 None:intergenic 30.0%
GTTTACAATACAACCTCAAT+TGG + chr8_1:6215264-6215283 None:intergenic 30.0%
TTAAGAAAGGTTAGATCATG+GGG + chr8_1:6215340-6215359 None:intergenic 30.0%
CATAATGTTTCATCAGATCA+AGG + chr8_1:6215469-6215488 None:intergenic 30.0%
GATCTGATGAAACATTATGT+TGG - chr8_1:6215470-6215489 Msa1174980:intron 30.0%
!! TGTTGGTAATTATTATGCAG+GGG - chr8_1:6215487-6215506 Msa1174980:intron 30.0%
AGAGACATCTACCAAAAAAA+TGG - chr8_1:6215576-6215595 Msa1174980:CDS 30.0%
TACTCTTTGAGCTGATAATT+TGG + chr8_1:6214556-6214575 None:intergenic 30.0%
AGAAATCAATAGGTATGGTT+TGG + chr8_1:6214619-6214638 None:intergenic 30.0%
TTAAGGAAGCAGAAATCAAT+AGG + chr8_1:6214629-6214648 None:intergenic 30.0%
! TACACAGATTGCAAGTTTTA+AGG + chr8_1:6214646-6214665 None:intergenic 30.0%
TTGCTCTATACTTAAGAAGT+TGG + chr8_1:6214756-6214775 None:intergenic 30.0%
!!! ATTTTTTGGGTGAGCTAATT+AGG - chr8_1:6214783-6214802 Msa1174980:intron 30.0%
!! CTTCATTAGTCTTGATGATT+TGG - chr8_1:6214837-6214856 Msa1174980:intron 30.0%
TTATAGTTTCAAATTAGCCG+CGG - chr8_1:6214976-6214995 Msa1174980:intron 30.0%
! CACATTTTATTGCAGTATCA+TGG + chr8_1:6215031-6215050 None:intergenic 30.0%
GTTTACAATACAACCTCAAT+TGG + chr8_1:6215264-6215283 None:intergenic 30.0%
TTAAGAAAGGTTAGATCATG+GGG + chr8_1:6215340-6215359 None:intergenic 30.0%
CATAATGTTTCATCAGATCA+AGG + chr8_1:6215469-6215488 None:intergenic 30.0%
GATCTGATGAAACATTATGT+TGG - chr8_1:6215470-6215489 Msa1174980:intron 30.0%
!! TGTTGGTAATTATTATGCAG+GGG - chr8_1:6215487-6215506 Msa1174980:intron 30.0%
AGAGACATCTACCAAAAAAA+TGG - chr8_1:6215576-6215595 Msa1174980:CDS 30.0%
TTGAGCTGATAATTTGGAGA+AGG + chr8_1:6214550-6214569 None:intergenic 35.0%
! TTTTCACTGCAGATTTGACA+AGG + chr8_1:6214589-6214608 None:intergenic 35.0%
GAAGCAGAAATCAATAGGTA+TGG + chr8_1:6214624-6214643 None:intergenic 35.0%
TACTTAAGAAGTTGGCAAGT+TGG + chr8_1:6214748-6214767 None:intergenic 35.0%
GTATCATGGATCATTTCATG+AGG + chr8_1:6215017-6215036 None:intergenic 35.0%
!! TAGTATCGATCAAAATCGGA+TGG + chr8_1:6215127-6215146 None:intergenic 35.0%
! TGCGTGACTTCATCATTTTA+TGG - chr8_1:6215220-6215239 Msa1174980:intron 35.0%
! TGACTTCATCATTTTATGGC+AGG - chr8_1:6215224-6215243 Msa1174980:intron 35.0%
GTAAATCCAAATCCCAATTG+AGG - chr8_1:6215248-6215267 Msa1174980:intron 35.0%
ATACAACCTCAATTGGGATT+TGG + chr8_1:6215257-6215276 None:intergenic 35.0%
! CAGGAACAGACAAATAGTTT+TGG - chr8_1:6215537-6215556 Msa1174980:CDS 35.0%
TTGAGCTGATAATTTGGAGA+AGG + chr8_1:6214550-6214569 None:intergenic 35.0%
! TTTTCACTGCAGATTTGACA+AGG + chr8_1:6214589-6214608 None:intergenic 35.0%
GAAGCAGAAATCAATAGGTA+TGG + chr8_1:6214624-6214643 None:intergenic 35.0%
TACTTAAGAAGTTGGCAAGT+TGG + chr8_1:6214748-6214767 None:intergenic 35.0%
GTATCATGGATCATTTCATG+AGG + chr8_1:6215017-6215036 None:intergenic 35.0%
!! TAGTATCGATCAAAATCGGA+TGG + chr8_1:6215127-6215146 None:intergenic 35.0%
! TGCGTGACTTCATCATTTTA+TGG - chr8_1:6215220-6215239 Msa1174980:intron 35.0%
! TGACTTCATCATTTTATGGC+AGG - chr8_1:6215224-6215243 Msa1174980:intron 35.0%
GTAAATCCAAATCCCAATTG+AGG - chr8_1:6215248-6215267 Msa1174980:intron 35.0%
ATACAACCTCAATTGGGATT+TGG + chr8_1:6215257-6215276 None:intergenic 35.0%
! CAGGAACAGACAAATAGTTT+TGG - chr8_1:6215537-6215556 Msa1174980:CDS 35.0%
! TATGTCTAGGACTGCATTCT+TGG + chr8_1:6215316-6215335 None:intergenic 40.0%
TAGATCATGGGGTTATGTCT+AGG + chr8_1:6215329-6215348 None:intergenic 40.0%
TTATTATGCAGGGGTGATCA+AGG - chr8_1:6215496-6215515 Msa1174980:intron 40.0%
AGAGACACGTCTTATACTTG+AGG - chr8_1:6215636-6215655 Msa1174980:CDS 40.0%
! TATGTCTAGGACTGCATTCT+TGG + chr8_1:6215316-6215335 None:intergenic 40.0%
TAGATCATGGGGTTATGTCT+AGG + chr8_1:6215329-6215348 None:intergenic 40.0%
TTATTATGCAGGGGTGATCA+AGG - chr8_1:6215496-6215515 Msa1174980:intron 40.0%
AGAGACACGTCTTATACTTG+AGG - chr8_1:6215636-6215655 Msa1174980:CDS 40.0%
GTTTCTGCAGTATAGAGTGC+AGG - chr8_1:6215518-6215537 Msa1174980:CDS 45.0%
GTTTCTGCAGTATAGAGTGC+AGG - chr8_1:6215518-6215537 Msa1174980:CDS 45.0%
!! AAAAATTAAAAGATATAAAT+AGG + chr8_1:6215421-6215440 None:intergenic 5.0%
!! AAAAATTAAAAGATATAAAT+AGG + chr8_1:6215421-6215440 None:intergenic 5.0%
GGCATGTGTGATAGTTACCG+CGG + chr8_1:6214996-6215015 None:intergenic 50.0%
TCGATCAAAATCGGATGGCC+AGG + chr8_1:6215122-6215141 None:intergenic 50.0%
GGCATGTGTGATAGTTACCG+CGG + chr8_1:6214996-6215015 None:intergenic 50.0%
TCGATCAAAATCGGATGGCC+AGG + chr8_1:6215122-6215141 None:intergenic 50.0%
CACACTGCTCGTGAATCTCC+TGG - chr8_1:6215101-6215120 Msa1174980:intron 55.0%
CACACTGCTCGTGAATCTCC+TGG - chr8_1:6215101-6215120 Msa1174980:intron 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 6214527 6215693 6214527 ID=Msa1174980;Name=Msa1174980
chr8_1 mRNA 6214527 6215693 6214527 ID=Msa1174980-mRNA-1;Parent=Msa1174980;Name=Msa1174980-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0|1|1|1|2|0|121
chr8_1 exon 6215515 6215693 6215515 ID=Msa1174980-mRNA-1:exon:2184;Parent=Msa1174980-mRNA-1
chr8_1 exon 6214527 6214713 6214527 ID=Msa1174980-mRNA-1:exon:2183;Parent=Msa1174980-mRNA-1
chr8_1 CDS 6215515 6215693 6215515 ID=Msa1174980-mRNA-1:cds;Parent=Msa1174980-mRNA-1
chr8_1 CDS 6214527 6214713 6214527 ID=Msa1174980-mRNA-1:cds;Parent=Msa1174980-mRNA-1
Gene Sequence

>Msa1174980

ATGGAAGTTGGTCTAAGTCTCCTTCTCCAAATTATCAGCTCAAAGAGTAACTCAAATATCCTTGTCAAATCTGCAGTGAAAAAGTCAAACCAAACCATACCTATTGATTTCTGCTTCCTTAAAACTTGCAATCTGTGTAATAAACAGCTCAGCCCAGACAAAGATATTTACATGTACAGGGGTGATCAAGGTTTCTGCAGTATAGAGTGCAGGAACAGACAAATAGTTTTGGATGAGATGAAAGAATTAGAGACATCTACCAAAAAAATGGTACAATGTTATAGACAATGTAGTAATGAGGCACGCAGAGAGACACGTCTTATACTTGAGGACATTCGAATGCAAAGACTTAAAAATAAAGTATAA

Protein sequence

>Msa1174980

MEVGLSLLLQIISSKSNSNILVKSAVKKSNQTIPIDFCFLKTCNLCNKQLSPDKDIYMYRGDQGFCSIECRNRQIVLDEMKELETSTKKMVQCYRQCSNEARRETRLILEDIRMQRLKNKV*