AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1070680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1070680 MtrunA17_Chr7g0253151 82.822 163 8 1 20 162 5 167 4.63e-92 265
Msa1070680 MtrunA17_Chr4g0003161 61.078 167 35 3 1 142 164 325 3.99e-58 188
Msa1070680 MtrunA17_Chr2g0333241 62.500 152 33 2 1 133 164 310 1.15e-52 173
Msa1070680 MtrunA17_Chr7g0253251 54.286 175 27 2 7 164 158 296 1.83e-51 166
Msa1070680 MtrunA17_Chr7g0266491 29.655 145 78 2 8 133 236 375 4.98e-15 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1070680 AT1G48900.2 60.843 166 35 3 2 142 165 325 4.63e-57 184
Msa1070680 AT1G48900.1 60.843 166 35 3 2 142 165 325 1.26e-56 185
Msa1070680 AT1G15310.1 60.927 151 35 2 2 133 165 310 1.40e-53 176
Msa1070680 AT5G49500.2 60.667 150 35 2 3 133 46 190 3.75e-53 173
Msa1070680 AT5G49500.1 59.119 159 35 3 3 136 168 321 6.28e-53 175
Msa1070680 AT5G03940.1 28.966 145 79 2 8 133 246 385 6.33e-15 71.6
Msa1070680 AT2G45770.1 30.986 142 65 3 2 115 226 362 9.07e-12 62.4

Find 40 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAACCAGATCTTGTTATAT+TGG 0.248024 7_2:-67008437 Msa1070680:CDS
CCGTTTGTTAGTCGTCTATT+AGG 0.257109 7_2:-67008023 Msa1070680:CDS
AGCTGTAATTGTTTCTAAAA+TGG 0.274828 7_2:-67008329 Msa1070680:CDS
GGCAGGTTTAGAGGCAATTC+AGG 0.299728 7_2:+67007957 None:intergenic
TTTCTTTCTGGCAGGTTTAG+AGG 0.311232 7_2:+67007948 None:intergenic
CCCTCCATCGTTGCACCACT+TGG 0.347749 7_2:-67007898 Msa1070680:CDS
TTGGTTATCGATGGCAATAT+TGG 0.409844 7_2:-67008418 Msa1070680:CDS
CTTCTTGTTTGTGACCCCAC+TGG 0.426708 7_2:+67008588 None:intergenic
GTCTATTAGGCATGGATGAC+TGG 0.428294 7_2:-67008010 Msa1070680:CDS
AAGAGTCCGGTCATATTCAT+AGG 0.428991 7_2:-67008089 Msa1070680:CDS
CATAGGAACTGGTGAACATA+TGG 0.442484 7_2:-67008072 Msa1070680:CDS
GATGGCTATGCCATGGGTGG+TGG 0.461610 7_2:-67008307 Msa1070680:CDS
CCGGTCATATTCATAGGAAC+TGG 0.464779 7_2:-67008083 Msa1070680:CDS
ATAACCAATATAACAAGATC+TGG 0.467853 7_2:+67008433 None:intergenic
TGATCATTGTAGTCGTAAGC+AGG 0.494522 7_2:-67008383 Msa1070680:CDS
CTTGTTATATTGGTTATCGA+TGG 0.521115 7_2:-67008427 Msa1070680:CDS
GTAATTGTTTCTAAAATGGA+TGG 0.523200 7_2:-67008325 Msa1070680:CDS
TGTTAGTCGTCTATTAGGCA+TGG 0.525929 7_2:-67008018 Msa1070680:CDS
TCATAATTGTTGATGCCAGT+GGG 0.539872 7_2:-67008603 Msa1070680:CDS
TTTACACATAGTGTTGACAT+TGG 0.544116 7_2:-67008352 Msa1070680:CDS
TGTTGCAGCAACAAAGAGTC+CGG 0.545682 7_2:-67008102 Msa1070680:CDS
CCTAATAGACGACTAACAAA+CGG 0.558547 7_2:+67008023 None:intergenic
ACCAAGTGGTGCAACGATGG+AGG 0.564330 7_2:+67007897 None:intergenic
CCAAGTGGTGCAACGATGGA+GGG 0.569337 7_2:+67007898 None:intergenic
CAAAATTGCCACGGAAGGTG+TGG 0.575652 7_2:-67008653 Msa1070680:CDS
GAATCTCTCCACACCTTCCG+TGG 0.577689 7_2:+67008645 None:intergenic
CCAGTTCCTATGAATATGAC+CGG 0.578609 7_2:+67008083 None:intergenic
TCAACCAAGTGGTGCAACGA+TGG 0.584956 7_2:+67007894 None:intergenic
CTCATAATTGTTGATGCCAG+TGG 0.592193 7_2:-67008604 Msa1070680:CDS
GGAAGGTGTGGAGAGATTCA+CGG 0.595583 7_2:-67008641 Msa1070680:CDS
CGTGTCAAAATTGCCACGGA+AGG 0.613659 7_2:-67008658 Msa1070680:CDS
GCTAAGAGAACCACCACCCA+TGG 0.613918 7_2:+67008297 None:intergenic
CTTACGACTACAATGATCAA+AGG 0.629516 7_2:+67008387 None:intergenic
AAAATGGATGGCTATGCCAT+GGG 0.631223 7_2:-67008313 Msa1070680:CDS
TAAAATGGATGGCTATGCCA+TGG 0.631944 7_2:-67008314 Msa1070680:CDS
CGATCGTGTCAAAATTGCCA+CGG 0.650216 7_2:-67008662 Msa1070680:CDS
AACACTATGTGTAAATGCTG+TGG 0.655117 7_2:+67008360 None:intergenic
ATGGATGGCTATGCCATGGG+TGG 0.678999 7_2:-67008310 Msa1070680:CDS
CATAATTGTTGATGCCAGTG+GGG 0.681522 7_2:-67008602 Msa1070680:intron
CTCAGTCAGAGTCAACCAAG+TGG 0.715782 7_2:+67007883 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATTTTTTTTATGTGTTT+TGG - chr7_2:67008395-67008414 Msa1070680:CDS 10.0%
!!! ATATTTTTTTTATGTGTTTT+GGG - chr7_2:67008396-67008415 Msa1070680:CDS 10.0%
!!! TATATTTTTTTTATGTGTTT+TGG - chr7_2:67008395-67008414 Msa1070680:CDS 10.0%
!!! ATATTTTTTTTATGTGTTTT+GGG - chr7_2:67008396-67008415 Msa1070680:CDS 10.0%
!!! ATTCGATACATTTGTTATAT+TGG - chr7_2:67008056-67008075 Msa1070680:CDS 20.0%
!!! CTTTAAACTTTAAAGTGAAT+TGG + chr7_2:67008293-67008312 None:intergenic 20.0%
!!! TCAACAATTGAATTTTTTAG+CGG + chr7_2:67008329-67008348 None:intergenic 20.0%
!!! ATTCGATACATTTGTTATAT+TGG - chr7_2:67008056-67008075 Msa1070680:CDS 20.0%
!!! CTTTAAACTTTAAAGTGAAT+TGG + chr7_2:67008293-67008312 None:intergenic 20.0%
!!! TCAACAATTGAATTTTTTAG+CGG + chr7_2:67008329-67008348 None:intergenic 20.0%
! ATAACCAATATAACAAGATC+TGG + chr7_2:67008124-67008143 None:intergenic 25.0%
!!! AGCTGTAATTGTTTCTAAAA+TGG - chr7_2:67008225-67008244 Msa1070680:intron 25.0%
!!! GTAATTGTTTCTAAAATGGA+TGG - chr7_2:67008229-67008248 Msa1070680:intron 25.0%
! ATAACCAATATAACAAGATC+TGG + chr7_2:67008124-67008143 None:intergenic 25.0%
!!! AGCTGTAATTGTTTCTAAAA+TGG - chr7_2:67008225-67008244 Msa1070680:intron 25.0%
!!! GTAATTGTTTCTAAAATGGA+TGG - chr7_2:67008229-67008248 Msa1070680:intron 25.0%
!!! ATACCGTTGCTTTTGAAATT+TGG + chr7_2:67008014-67008033 None:intergenic 30.0%
! TTTGTTATATTGGTCATCGA+TGG - chr7_2:67008066-67008085 Msa1070680:CDS 30.0%
! GAAACCAGATCTTGTTATAT+TGG - chr7_2:67008117-67008136 Msa1070680:intron 30.0%
! CTTGTTATATTGGTTATCGA+TGG - chr7_2:67008127-67008146 Msa1070680:intron 30.0%
!! TTTACACATAGTGTTGACAT+TGG - chr7_2:67008202-67008221 Msa1070680:intron 30.0%
!! TATGTGTTTTGGGTACATAT+TGG - chr7_2:67008406-67008425 Msa1070680:CDS 30.0%
!!! ATACCGTTGCTTTTGAAATT+TGG + chr7_2:67008014-67008033 None:intergenic 30.0%
! TTTGTTATATTGGTCATCGA+TGG - chr7_2:67008066-67008085 Msa1070680:CDS 30.0%
! GAAACCAGATCTTGTTATAT+TGG - chr7_2:67008117-67008136 Msa1070680:intron 30.0%
! CTTGTTATATTGGTTATCGA+TGG - chr7_2:67008127-67008146 Msa1070680:intron 30.0%
!! TTTACACATAGTGTTGACAT+TGG - chr7_2:67008202-67008221 Msa1070680:intron 30.0%
!! TATGTGTTTTGGGTACATAT+TGG - chr7_2:67008406-67008425 Msa1070680:CDS 30.0%
TCATAATTGTTGATGCCAGT+GGG - chr7_2:67007951-67007970 Msa1070680:CDS 35.0%
GCACCAAATTTCAAAAGCAA+CGG - chr7_2:67008008-67008027 Msa1070680:CDS 35.0%
TTGGTTATCGATGGCAATAT+TGG - chr7_2:67008136-67008155 Msa1070680:intron 35.0%
CTTACGACTACAATGATCAA+AGG + chr7_2:67008170-67008189 None:intergenic 35.0%
AACACTATGTGTAAATGCTG+TGG + chr7_2:67008197-67008216 None:intergenic 35.0%
CCTAATAGACGACTAACAAA+CGG + chr7_2:67008534-67008553 None:intergenic 35.0%
TCATAATTGTTGATGCCAGT+GGG - chr7_2:67007951-67007970 Msa1070680:CDS 35.0%
GCACCAAATTTCAAAAGCAA+CGG - chr7_2:67008008-67008027 Msa1070680:CDS 35.0%
TTGGTTATCGATGGCAATAT+TGG - chr7_2:67008136-67008155 Msa1070680:intron 35.0%
CTTACGACTACAATGATCAA+AGG + chr7_2:67008170-67008189 None:intergenic 35.0%
AACACTATGTGTAAATGCTG+TGG + chr7_2:67008197-67008216 None:intergenic 35.0%
CCTAATAGACGACTAACAAA+CGG + chr7_2:67008534-67008553 None:intergenic 35.0%
CTCATAATTGTTGATGCCAG+TGG - chr7_2:67007950-67007969 Msa1070680:CDS 40.0%
CATAATTGTTGATGCCAGTG+GGG - chr7_2:67007952-67007971 Msa1070680:CDS 40.0%
TGATCATTGTAGTCGTAAGC+AGG - chr7_2:67008171-67008190 Msa1070680:intron 40.0%
TAAAATGGATGGCTATGCCA+TGG - chr7_2:67008240-67008259 Msa1070680:intron 40.0%
AAAATGGATGGCTATGCCAT+GGG - chr7_2:67008241-67008260 Msa1070680:intron 40.0%
AAGAGTCCGGTCATATTCAT+AGG - chr7_2:67008465-67008484 Msa1070680:intron 40.0%
CCAGTTCCTATGAATATGAC+CGG + chr7_2:67008474-67008493 None:intergenic 40.0%
CATAGGAACTGGTGAACATA+TGG - chr7_2:67008482-67008501 Msa1070680:intron 40.0%
! CCGTTTGTTAGTCGTCTATT+AGG - chr7_2:67008531-67008550 Msa1070680:intron 40.0%
TGTTAGTCGTCTATTAGGCA+TGG - chr7_2:67008536-67008555 Msa1070680:intron 40.0%
! TTTCTTTCTGGCAGGTTTAG+AGG + chr7_2:67008609-67008628 None:intergenic 40.0%
ACCTGCCAGAAAGAAAAATC+TGG - chr7_2:67008613-67008632 Msa1070680:CDS 40.0%
!! TCCAGATTTTTCTTTCTGGC+AGG + chr7_2:67008617-67008636 None:intergenic 40.0%
! GGCATCCAGATTTTTCTTTC+TGG + chr7_2:67008621-67008640 None:intergenic 40.0%
CTCATAATTGTTGATGCCAG+TGG - chr7_2:67007950-67007969 Msa1070680:CDS 40.0%
CATAATTGTTGATGCCAGTG+GGG - chr7_2:67007952-67007971 Msa1070680:CDS 40.0%
TGATCATTGTAGTCGTAAGC+AGG - chr7_2:67008171-67008190 Msa1070680:intron 40.0%
TAAAATGGATGGCTATGCCA+TGG - chr7_2:67008240-67008259 Msa1070680:intron 40.0%
AAAATGGATGGCTATGCCAT+GGG - chr7_2:67008241-67008260 Msa1070680:intron 40.0%
AAGAGTCCGGTCATATTCAT+AGG - chr7_2:67008465-67008484 Msa1070680:intron 40.0%
CCAGTTCCTATGAATATGAC+CGG + chr7_2:67008474-67008493 None:intergenic 40.0%
CATAGGAACTGGTGAACATA+TGG - chr7_2:67008482-67008501 Msa1070680:intron 40.0%
! CCGTTTGTTAGTCGTCTATT+AGG - chr7_2:67008531-67008550 Msa1070680:intron 40.0%
TGTTAGTCGTCTATTAGGCA+TGG - chr7_2:67008536-67008555 Msa1070680:intron 40.0%
! TTTCTTTCTGGCAGGTTTAG+AGG + chr7_2:67008609-67008628 None:intergenic 40.0%
ACCTGCCAGAAAGAAAAATC+TGG - chr7_2:67008613-67008632 Msa1070680:CDS 40.0%
!! TCCAGATTTTTCTTTCTGGC+AGG + chr7_2:67008617-67008636 None:intergenic 40.0%
! GGCATCCAGATTTTTCTTTC+TGG + chr7_2:67008621-67008640 None:intergenic 40.0%
!! CGTGGCAATTTTGACACGAT+CGG + chr7_2:67007894-67007913 None:intergenic 45.0%
CGATCGTGTCAAAATTGCCA+CGG - chr7_2:67007892-67007911 Msa1070680:CDS 45.0%
TGTTGCAGCAACAAAGAGTC+CGG - chr7_2:67008452-67008471 Msa1070680:intron 45.0%
CCGGTCATATTCATAGGAAC+TGG - chr7_2:67008471-67008490 Msa1070680:intron 45.0%
GTCTATTAGGCATGGATGAC+TGG - chr7_2:67008544-67008563 Msa1070680:intron 45.0%
!! CGTGGCAATTTTGACACGAT+CGG + chr7_2:67007894-67007913 None:intergenic 45.0%
CGATCGTGTCAAAATTGCCA+CGG - chr7_2:67007892-67007911 Msa1070680:CDS 45.0%
TGTTGCAGCAACAAAGAGTC+CGG - chr7_2:67008452-67008471 Msa1070680:intron 45.0%
CCGGTCATATTCATAGGAAC+TGG - chr7_2:67008471-67008490 Msa1070680:intron 45.0%
GTCTATTAGGCATGGATGAC+TGG - chr7_2:67008544-67008563 Msa1070680:intron 45.0%
CGTGTCAAAATTGCCACGGA+AGG - chr7_2:67007896-67007915 Msa1070680:CDS 50.0%
CAAAATTGCCACGGAAGGTG+TGG - chr7_2:67007901-67007920 Msa1070680:CDS 50.0%
! GGAAGGTGTGGAGAGATTCA+CGG - chr7_2:67007913-67007932 Msa1070680:CDS 50.0%
! CTTCTTGTTTGTGACCCCAC+TGG + chr7_2:67007969-67007988 None:intergenic 50.0%
GGCAGGTTTAGAGGCAATTC+AGG + chr7_2:67008600-67008619 None:intergenic 50.0%
GATGGAGGGAAAAACGCACA+AGG + chr7_2:67008645-67008664 None:intergenic 50.0%
TCAACCAAGTGGTGCAACGA+TGG + chr7_2:67008663-67008682 None:intergenic 50.0%
CGTGTCAAAATTGCCACGGA+AGG - chr7_2:67007896-67007915 Msa1070680:CDS 50.0%
CAAAATTGCCACGGAAGGTG+TGG - chr7_2:67007901-67007920 Msa1070680:CDS 50.0%
! GGAAGGTGTGGAGAGATTCA+CGG - chr7_2:67007913-67007932 Msa1070680:CDS 50.0%
! CTTCTTGTTTGTGACCCCAC+TGG + chr7_2:67007969-67007988 None:intergenic 50.0%
GGCAGGTTTAGAGGCAATTC+AGG + chr7_2:67008600-67008619 None:intergenic 50.0%
GATGGAGGGAAAAACGCACA+AGG + chr7_2:67008645-67008664 None:intergenic 50.0%
TCAACCAAGTGGTGCAACGA+TGG + chr7_2:67008663-67008682 None:intergenic 50.0%
GAATCTCTCCACACCTTCCG+TGG + chr7_2:67007912-67007931 None:intergenic 55.0%
ATGGATGGCTATGCCATGGG+TGG - chr7_2:67008244-67008263 Msa1070680:intron 55.0%
GCTAAGAGAACCACCACCCA+TGG + chr7_2:67008260-67008279 None:intergenic 55.0%
GGAGGGAAAAACGCACAAGG+AGG + chr7_2:67008642-67008661 None:intergenic 55.0%
CCAAGTGGTGCAACGATGGA+GGG + chr7_2:67008659-67008678 None:intergenic 55.0%
ACCAAGTGGTGCAACGATGG+AGG + chr7_2:67008660-67008679 None:intergenic 55.0%
GAATCTCTCCACACCTTCCG+TGG + chr7_2:67007912-67007931 None:intergenic 55.0%
ATGGATGGCTATGCCATGGG+TGG - chr7_2:67008244-67008263 Msa1070680:intron 55.0%
GCTAAGAGAACCACCACCCA+TGG + chr7_2:67008260-67008279 None:intergenic 55.0%
GGAGGGAAAAACGCACAAGG+AGG + chr7_2:67008642-67008661 None:intergenic 55.0%
CCAAGTGGTGCAACGATGGA+GGG + chr7_2:67008659-67008678 None:intergenic 55.0%
ACCAAGTGGTGCAACGATGG+AGG + chr7_2:67008660-67008679 None:intergenic 55.0%
GATGGCTATGCCATGGGTGG+TGG - chr7_2:67008247-67008266 Msa1070680:intron 60.0%
CCCTCCATCGTTGCACCACT+TGG - chr7_2:67008656-67008675 Msa1070680:CDS 60.0%
GATGGCTATGCCATGGGTGG+TGG - chr7_2:67008247-67008266 Msa1070680:intron 60.0%
CCCTCCATCGTTGCACCACT+TGG - chr7_2:67008656-67008675 Msa1070680:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 67007884 67008692 67007884 ID=Msa1070680;Name=Msa1070680
chr7_2 mRNA 67007884 67008692 67007884 ID=Msa1070680-mRNA-1;Parent=Msa1070680;Name=Msa1070680-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|1|1|3|0|164
chr7_2 exon 67008603 67008692 67008603 ID=Msa1070680-mRNA-1:exon:14487;Parent=Msa1070680-mRNA-1
chr7_2 exon 67008295 67008458 67008295 ID=Msa1070680-mRNA-1:exon:14486;Parent=Msa1070680-mRNA-1
chr7_2 exon 67007884 67008124 67007884 ID=Msa1070680-mRNA-1:exon:14485;Parent=Msa1070680-mRNA-1
chr7_2 CDS 67008603 67008692 67008603 ID=Msa1070680-mRNA-1:cds;Parent=Msa1070680-mRNA-1
chr7_2 CDS 67008295 67008458 67008295 ID=Msa1070680-mRNA-1:cds;Parent=Msa1070680-mRNA-1
chr7_2 CDS 67007884 67008124 67007884 ID=Msa1070680-mRNA-1:cds;Parent=Msa1070680-mRNA-1
Gene Sequence

>Msa1070680

ATGGAGTCCGATCGTGTCAAAATTGCCACGGAAGGTGTGGAGAGATTCACGGAAGAAAACTGTGATCTCATAATTGTTGATGCCAGTGGGAAACCAGATCTTGTTATATTGGTTATCGATGGCAATATTGGTCAGCATGCCTTTGATCATTGTAGTCGTAAGCAGGCCACAGCATTTACACATAGTGTTGACATTGGAGCTGTAATTGTTTCTAAAATGGATGGCTATGCCATGGGTGGTGGTTCTCTTAGCGCTGTTGCAGCAACAAAGAGTCCGGTCATATTCATAGGAACTGGTGAACATATGGATGAGTTTGAAGTTTTTGAAGTTAAGCCGTTTGTTAGTCGTCTATTAGGCATGGATGACTGGTATGAGTTTATTGACAGAGTTTATGAAGTGCCTGAATTGCCTCTAAACCTGCCAGAAAGAAAAATCTGGATGCCTCCTTGTGCGTTTTTCCCTCCATCGTTGCACCACTTGGTTGACTCTGACTGA

Protein sequence

>Msa1070680

MESDRVKIATEGVERFTEENCDLIIVDASGKPDLVILVIDGNIGQHAFDHCSRKQATAFTHSVDIGAVIVSKMDGYAMGGGSLSAVAATKSPVIFIGTGEHMDEFEVFEVKPFVSRLLGMDDWYEFIDRVYEVPELPLNLPERKIWMPPCAFFPPSLHHLVDSD*