AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354750


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1354750 MtrunA17_CPg0492421 87.179 156 10 1 1 146 1 156 9.14e-94 270
Msa1354750 MtrunA17_Chr4g0016101 87.179 156 10 1 1 146 1 156 9.14e-94 270
Msa1354750 MtrunA17_Chr3g0090841 87.179 156 10 1 1 146 1 156 9.14e-94 270
Msa1354750 MtrunA17_CPg0492431 96.875 64 2 0 148 211 4 67 1.74e-36 129
Msa1354750 MtrunA17_Chr3g0090851 96.875 64 2 0 148 211 4 67 1.74e-36 129
Msa1354750 MtrunA17_Chr4g0016091 96.875 64 2 0 148 211 4 67 1.74e-36 129
Msa1354750 MtrunA17_Chr4g0002541 73.333 60 8 1 25 76 1 60 8.48e-22 84.7
Msa1354750 MtrunA17_Chr4g0057401 87.179 39 5 0 108 146 1 39 4.82e-16 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1354750 ATCG00900.1 89.610 154 8 1 1 146 1 154 3.01e-97 280
Msa1354750 ATCG01240.1 89.610 154 8 1 1 146 1 154 3.01e-97 280
Msa1354750 ATMG01270.1 31.655 139 77 4 22 146 11 145 2.19e-13 65.5
Msa1354750 AT2G07696.1 31.655 139 77 4 22 146 11 145 2.19e-13 65.5

Find 32 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAATCGATTACGATAAAT+TGG 0.238141 tig0014543:+498428 None:intergenic
CTTGCCATTCGTTGGTTATT+AGG 0.268444 tig0014543:-498179 Msa1354750:CDS
CATCAAGTTCCCGTTGAAAT+AGG 0.307921 tig0014543:-498221 Msa1354750:CDS
AAAACGTCCAGGTCGAAATA+TGG 0.317789 tig0014543:-498147 Msa1354750:CDS
CAAATTAAGTTCCGAATTAG+TGG 0.342047 tig0014543:-498120 Msa1354750:CDS
TGGCGATGCCATACGCAAAA+AGG 0.366109 tig0014543:-498081 Msa1354750:CDS
TTTGGCAGCATCCACTAATT+CGG 0.404543 tig0014543:+498109 None:intergenic
ACGTATTGCTTGACGTAAAA+CGG 0.405511 tig0014543:+498295 None:intergenic
GCTTGACGTAAAACGGATAG+TGG 0.418362 tig0014543:+498302 None:intergenic
GTAAAAGCAAGACGCGTAAA+CGG 0.427761 tig0014543:-498251 Msa1354750:CDS
TATGGCATCGCCATTCCCTT+TGG 0.436234 tig0014543:+498091 None:intergenic
TGTGTGGATCCTATTTCAAC+GGG 0.470768 tig0014543:+498212 None:intergenic
TTATCTATCGAGCTATGAAA+AGG 0.512086 tig0014543:-498349 Msa1354750:CDS
GAAAAGCACTTGCCATTCGT+TGG 0.526859 tig0014543:-498187 Msa1354750:CDS
GTGGATGCTGCCAAAGGGAA+TGG 0.532446 tig0014543:-498101 Msa1354750:CDS
TAATCGATTAGTTAACATGT+TGG 0.538486 tig0014543:-498417 Msa1354750:CDS
GGCGCATCCCGAAAACGTCC+AGG 0.540732 tig0014543:-498158 Msa1354750:CDS
AAAGGAAGAGACTCATAGAA+TGG 0.548096 tig0014543:-498063 Msa1354750:CDS
TTGTGTGGATCCTATTTCAA+CGG 0.548545 tig0014543:+498211 None:intergenic
ATCGAAAAGAAGCAAATGAA+AGG 0.561694 tig0014543:+497718 None:intergenic
TCATGGGTTCTTCTCTCCAT+CGG 0.567612 tig0014543:+497549 None:intergenic
TAACGGCGCTGTTGTTCCGA+TGG 0.571426 tig0014543:-497565 Msa1354750:CDS
AATTAGTGGATGCTGCCAAA+GGG 0.575951 tig0014543:-498106 Msa1354750:CDS
GAATTAGTGGATGCTGCCAA+AGG 0.584526 tig0014543:-498107 Msa1354750:CDS
AGAGACTCATAGAATGGCAG+AGG 0.593635 tig0014543:-498057 Msa1354750:CDS
TTGAAAGCCATATTTCGACC+TGG 0.605724 tig0014543:+498140 None:intergenic
TGCGCCTAATAACCAACGAA+TGG 0.620213 tig0014543:+498175 None:intergenic
TCGATTACGATAAATTGGAT+CGG 0.627987 tig0014543:+498433 None:intergenic
AAGTTTAGTAATGAGCATAA+CGG 0.644237 tig0014543:-497582 Msa1354750:CDS
GTTAACCGTATTATGAAACA+CGG 0.650772 tig0014543:-498395 Msa1354750:CDS
TTTACGCTCATGTCACGGCG+AGG 0.672550 tig0014543:-498482 None:intergenic
GTTGAAATAGGATCCACACA+AGG 0.731975 tig0014543:-498209 Msa1354750:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAATAAAGAGGAATATT+TGG - tig0014543:498184-498203 Msa1354750:CDS 15.0%
!! AATAAATAAAGAGGAATATT+TGG - tig0014543:498184-498203 Msa1354750:CDS 15.0%
!! AGAATCAATAGAAAAAGAAT+CGG - tig0014543:498081-498100 Msa1354750:CDS 20.0%
!! TTGCTTAAGAATAAATAAAG+AGG - tig0014543:498175-498194 Msa1354750:CDS 20.0%
!!! AGGAATATTTGGTATTTTTT+TGG - tig0014543:498195-498214 Msa1354750:CDS 20.0%
!! AGAATCAATAGAAAAAGAAT+CGG - tig0014543:498081-498100 Msa1354750:CDS 20.0%
!! TTGCTTAAGAATAAATAAAG+AGG - tig0014543:498175-498194 Msa1354750:CDS 20.0%
!!! AGGAATATTTGGTATTTTTT+TGG - tig0014543:498195-498214 Msa1354750:CDS 20.0%
! ACTAATCGATTACGATAAAT+TGG + tig0014543:497595-497614 None:intergenic 25.0%
!! TAATCGATTAGTTAACATGT+TGG - tig0014543:497603-497622 Msa1354750:CDS 25.0%
!! TTTTTCCGTGTTTCATAATA+CGG + tig0014543:497633-497652 None:intergenic 25.0%
!! GATTCTTTTCCAATTATGTA+TGG + tig0014543:498067-498086 None:intergenic 25.0%
! GAAGAATTAGACCAAAAATT+AGG + tig0014543:498354-498373 None:intergenic 25.0%
! AAGTTTAGTAATGAGCATAA+CGG - tig0014543:498438-498457 Msa1354750:CDS 25.0%
! ACTAATCGATTACGATAAAT+TGG + tig0014543:497595-497614 None:intergenic 25.0%
!! TAATCGATTAGTTAACATGT+TGG - tig0014543:497603-497622 Msa1354750:CDS 25.0%
!! TTTTTCCGTGTTTCATAATA+CGG + tig0014543:497633-497652 None:intergenic 25.0%
!! GATTCTTTTCCAATTATGTA+TGG + tig0014543:498067-498086 None:intergenic 25.0%
! GAAGAATTAGACCAAAAATT+AGG + tig0014543:498354-498373 None:intergenic 25.0%
! AAGTTTAGTAATGAGCATAA+CGG - tig0014543:498438-498457 Msa1354750:CDS 25.0%
! ATAAATTGGATCGGATTTTG+CGG + tig0014543:497581-497600 None:intergenic 30.0%
TCGATTACGATAAATTGGAT+CGG + tig0014543:497590-497609 None:intergenic 30.0%
GTTAACCGTATTATGAAACA+CGG - tig0014543:497625-497644 Msa1354750:CDS 30.0%
GAAACACGGAAAAAAATCAT+TGG - tig0014543:497639-497658 Msa1354750:CDS 30.0%
TTATCTATCGAGCTATGAAA+AGG - tig0014543:497671-497690 Msa1354750:CDS 30.0%
!! TCTTGCTTTTACTGCTATAT+CGG + tig0014543:497761-497780 None:intergenic 30.0%
CAAATTAAGTTCCGAATTAG+TGG - tig0014543:497900-497919 Msa1354750:intron 30.0%
ACATAGACCTATGTTATGTA+TGG - tig0014543:498039-498058 Msa1354750:CDS 30.0%
TATGGATCCATACATAACAT+AGG + tig0014543:498049-498068 None:intergenic 30.0%
TGTATGGATCCATACATAAT+TGG - tig0014543:498055-498074 Msa1354750:CDS 30.0%
GAAAGACGAAATAGAAATGA+TGG - tig0014543:498129-498148 Msa1354750:CDS 30.0%
ATCGAAAAGAAGCAAATGAA+AGG + tig0014543:498305-498324 None:intergenic 30.0%
! TTTCATTTGCTTCTTTTCGA+TGG - tig0014543:498304-498323 Msa1354750:CDS 30.0%
!!! CGATGGAAGTTTTATTTTTC+CGG - tig0014543:498321-498340 Msa1354750:CDS 30.0%
CCAAAAATTAGGATCAATTC+CGG + tig0014543:498343-498362 None:intergenic 30.0%
! AGATAGATCTTTTTGATCAG+AGG + tig0014543:498395-498414 None:intergenic 30.0%
CTGATCAAAAAGATCTATCT+TGG - tig0014543:498395-498414 Msa1354750:CDS 30.0%
! ATAAATTGGATCGGATTTTG+CGG + tig0014543:497581-497600 None:intergenic 30.0%
TCGATTACGATAAATTGGAT+CGG + tig0014543:497590-497609 None:intergenic 30.0%
GTTAACCGTATTATGAAACA+CGG - tig0014543:497625-497644 Msa1354750:CDS 30.0%
GAAACACGGAAAAAAATCAT+TGG - tig0014543:497639-497658 Msa1354750:CDS 30.0%
TTATCTATCGAGCTATGAAA+AGG - tig0014543:497671-497690 Msa1354750:CDS 30.0%
!! TCTTGCTTTTACTGCTATAT+CGG + tig0014543:497761-497780 None:intergenic 30.0%
CAAATTAAGTTCCGAATTAG+TGG - tig0014543:497900-497919 Msa1354750:intron 30.0%
ACATAGACCTATGTTATGTA+TGG - tig0014543:498039-498058 Msa1354750:CDS 30.0%
TATGGATCCATACATAACAT+AGG + tig0014543:498049-498068 None:intergenic 30.0%
TGTATGGATCCATACATAAT+TGG - tig0014543:498055-498074 Msa1354750:CDS 30.0%
GAAAGACGAAATAGAAATGA+TGG - tig0014543:498129-498148 Msa1354750:CDS 30.0%
ATCGAAAAGAAGCAAATGAA+AGG + tig0014543:498305-498324 None:intergenic 30.0%
! TTTCATTTGCTTCTTTTCGA+TGG - tig0014543:498304-498323 Msa1354750:CDS 30.0%
!!! CGATGGAAGTTTTATTTTTC+CGG - tig0014543:498321-498340 Msa1354750:CDS 30.0%
CCAAAAATTAGGATCAATTC+CGG + tig0014543:498343-498362 None:intergenic 30.0%
! AGATAGATCTTTTTGATCAG+AGG + tig0014543:498395-498414 None:intergenic 30.0%
CTGATCAAAAAGATCTATCT+TGG - tig0014543:498395-498414 Msa1354750:CDS 30.0%
ACGTATTGCTTGACGTAAAA+CGG + tig0014543:497728-497747 None:intergenic 35.0%
! TTTTACGTCAAGCAATACGT+GGG - tig0014543:497728-497747 Msa1354750:intron 35.0%
!! CTTGCTTTTACTGCTATATC+GGG + tig0014543:497760-497779 None:intergenic 35.0%
TTGTGTGGATCCTATTTCAA+CGG + tig0014543:497812-497831 None:intergenic 35.0%
AAAGGAAGAGACTCATAGAA+TGG - tig0014543:497957-497976 Msa1354750:intron 35.0%
! ATTTTCGTTAATCCATGAGC+AGG - tig0014543:498004-498023 Msa1354750:intron 35.0%
! CCGGAATTGATCCTAATTTT+TGG - tig0014543:498340-498359 Msa1354750:CDS 35.0%
ACGTATTGCTTGACGTAAAA+CGG + tig0014543:497728-497747 None:intergenic 35.0%
! TTTTACGTCAAGCAATACGT+GGG - tig0014543:497728-497747 Msa1354750:intron 35.0%
!! CTTGCTTTTACTGCTATATC+GGG + tig0014543:497760-497779 None:intergenic 35.0%
TTGTGTGGATCCTATTTCAA+CGG + tig0014543:497812-497831 None:intergenic 35.0%
AAAGGAAGAGACTCATAGAA+TGG - tig0014543:497957-497976 Msa1354750:intron 35.0%
! ATTTTCGTTAATCCATGAGC+AGG - tig0014543:498004-498023 Msa1354750:intron 35.0%
! CCGGAATTGATCCTAATTTT+TGG - tig0014543:498340-498359 Msa1354750:CDS 35.0%
! GTTTTACGTCAAGCAATACG+TGG - tig0014543:497727-497746 Msa1354750:intron 40.0%
TTTACGTCAAGCAATACGTG+GGG - tig0014543:497729-497748 Msa1354750:intron 40.0%
GTAAAAGCAAGACGCGTAAA+CGG - tig0014543:497769-497788 Msa1354750:intron 40.0%
CATCAAGTTCCCGTTGAAAT+AGG - tig0014543:497799-497818 Msa1354750:intron 40.0%
TGTGTGGATCCTATTTCAAC+GGG + tig0014543:497811-497830 None:intergenic 40.0%
GTTGAAATAGGATCCACACA+AGG - tig0014543:497811-497830 Msa1354750:intron 40.0%
! CTTGCCATTCGTTGGTTATT+AGG - tig0014543:497841-497860 Msa1354750:intron 40.0%
! TATTTCGACCTGGACGTTTT+CGG + tig0014543:497873-497892 None:intergenic 40.0%
AAAACGTCCAGGTCGAAATA+TGG - tig0014543:497873-497892 Msa1354750:intron 40.0%
TTGAAAGCCATATTTCGACC+TGG + tig0014543:497883-497902 None:intergenic 40.0%
TTTGGCAGCATCCACTAATT+CGG + tig0014543:497914-497933 None:intergenic 40.0%
! AATTAGTGGATGCTGCCAAA+GGG - tig0014543:497914-497933 Msa1354750:intron 40.0%
! AGTCTCTTCCTTTTTGCGTA+TGG + tig0014543:497950-497969 None:intergenic 40.0%
GTGTATATAGATCCTGCTCA+TGG + tig0014543:498019-498038 None:intergenic 40.0%
! ATGGCTCAACTAAGCACTTT+TGG - tig0014543:498148-498167 Msa1354750:CDS 40.0%
! TGGCTCAACTAAGCACTTTT+GGG - tig0014543:498149-498168 Msa1354750:CDS 40.0%
! GTTTTACGTCAAGCAATACG+TGG - tig0014543:497727-497746 Msa1354750:intron 40.0%
TTTACGTCAAGCAATACGTG+GGG - tig0014543:497729-497748 Msa1354750:intron 40.0%
GTAAAAGCAAGACGCGTAAA+CGG - tig0014543:497769-497788 Msa1354750:intron 40.0%
CATCAAGTTCCCGTTGAAAT+AGG - tig0014543:497799-497818 Msa1354750:intron 40.0%
TGTGTGGATCCTATTTCAAC+GGG + tig0014543:497811-497830 None:intergenic 40.0%
GTTGAAATAGGATCCACACA+AGG - tig0014543:497811-497830 Msa1354750:intron 40.0%
! CTTGCCATTCGTTGGTTATT+AGG - tig0014543:497841-497860 Msa1354750:intron 40.0%
! TATTTCGACCTGGACGTTTT+CGG + tig0014543:497873-497892 None:intergenic 40.0%
AAAACGTCCAGGTCGAAATA+TGG - tig0014543:497873-497892 Msa1354750:intron 40.0%
TTGAAAGCCATATTTCGACC+TGG + tig0014543:497883-497902 None:intergenic 40.0%
TTTGGCAGCATCCACTAATT+CGG + tig0014543:497914-497933 None:intergenic 40.0%
! AATTAGTGGATGCTGCCAAA+GGG - tig0014543:497914-497933 Msa1354750:intron 40.0%
! AGTCTCTTCCTTTTTGCGTA+TGG + tig0014543:497950-497969 None:intergenic 40.0%
GTGTATATAGATCCTGCTCA+TGG + tig0014543:498019-498038 None:intergenic 40.0%
! ATGGCTCAACTAAGCACTTT+TGG - tig0014543:498148-498167 Msa1354750:CDS 40.0%
! TGGCTCAACTAAGCACTTTT+GGG - tig0014543:498149-498168 Msa1354750:CDS 40.0%
GCTTGACGTAAAACGGATAG+TGG + tig0014543:497721-497740 None:intergenic 45.0%
!! GAAAAGCACTTGCCATTCGT+TGG - tig0014543:497833-497852 Msa1354750:intron 45.0%
TGCGCCTAATAACCAACGAA+TGG + tig0014543:497848-497867 None:intergenic 45.0%
! ATTTCGACCTGGACGTTTTC+GGG + tig0014543:497872-497891 None:intergenic 45.0%
! GAATTAGTGGATGCTGCCAA+AGG - tig0014543:497913-497932 Msa1354750:intron 45.0%
AGAGACTCATAGAATGGCAG+AGG - tig0014543:497963-497982 Msa1354750:intron 45.0%
! GGCTCAACTAAGCACTTTTG+GGG - tig0014543:498150-498169 Msa1354750:CDS 45.0%
TCATGGGTTCTTCTCTCCAT+CGG + tig0014543:498474-498493 None:intergenic 45.0%
GCTTGACGTAAAACGGATAG+TGG + tig0014543:497721-497740 None:intergenic 45.0%
!! GAAAAGCACTTGCCATTCGT+TGG - tig0014543:497833-497852 Msa1354750:intron 45.0%
TGCGCCTAATAACCAACGAA+TGG + tig0014543:497848-497867 None:intergenic 45.0%
! ATTTCGACCTGGACGTTTTC+GGG + tig0014543:497872-497891 None:intergenic 45.0%
! GAATTAGTGGATGCTGCCAA+AGG - tig0014543:497913-497932 Msa1354750:intron 45.0%
AGAGACTCATAGAATGGCAG+AGG - tig0014543:497963-497982 Msa1354750:intron 45.0%
! GGCTCAACTAAGCACTTTTG+GGG - tig0014543:498150-498169 Msa1354750:CDS 45.0%
TCATGGGTTCTTCTCTCCAT+CGG + tig0014543:498474-498493 None:intergenic 45.0%
! GGCAAGTGCTTTTCCTTGTG+TGG + tig0014543:497827-497846 None:intergenic 50.0%
TATGGCATCGCCATTCCCTT+TGG + tig0014543:497932-497951 None:intergenic 50.0%
TGGCGATGCCATACGCAAAA+AGG - tig0014543:497939-497958 Msa1354750:intron 50.0%
! GGCAAGTGCTTTTCCTTGTG+TGG + tig0014543:497827-497846 None:intergenic 50.0%
TATGGCATCGCCATTCCCTT+TGG + tig0014543:497932-497951 None:intergenic 50.0%
TGGCGATGCCATACGCAAAA+AGG - tig0014543:497939-497958 Msa1354750:intron 50.0%
GTGGATGCTGCCAAAGGGAA+TGG - tig0014543:497919-497938 Msa1354750:intron 55.0%
TAACGGCGCTGTTGTTCCGA+TGG - tig0014543:498455-498474 Msa1354750:CDS 55.0%
GTGGATGCTGCCAAAGGGAA+TGG - tig0014543:497919-497938 Msa1354750:intron 55.0%
TAACGGCGCTGTTGTTCCGA+TGG - tig0014543:498455-498474 Msa1354750:CDS 55.0%
GGCGCATCCCGAAAACGTCC+AGG - tig0014543:497862-497881 Msa1354750:intron 65.0%
GGCGCATCCCGAAAACGTCC+AGG - tig0014543:497862-497881 Msa1354750:intron 65.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 497547 498495 497547 ID=Msa1354750;Name=Msa1354750
tig0014543 mRNA 497547 498495 497547 ID=Msa1354750-mRNA-1;Parent=Msa1354750;Name=Msa1354750-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|0|0|1|0|0|3|0|211
tig0014543 exon 498297 498495 498297 ID=Msa1354750-mRNA-1:exon:9242;Parent=Msa1354750-mRNA-1
tig0014543 exon 498033 498272 498033 ID=Msa1354750-mRNA-1:exon:9241;Parent=Msa1354750-mRNA-1
tig0014543 exon 497547 497740 497547 ID=Msa1354750-mRNA-1:exon:9240;Parent=Msa1354750-mRNA-1
tig0014543 CDS 498297 498495 498297 ID=Msa1354750-mRNA-1:cds;Parent=Msa1354750-mRNA-1
tig0014543 CDS 498033 498272 498033 ID=Msa1354750-mRNA-1:cds;Parent=Msa1354750-mRNA-1
tig0014543 CDS 497547 497740 497547 ID=Msa1354750-mRNA-1:cds;Parent=Msa1354750-mRNA-1
Gene Sequence

>Msa1354750

ATGTCACGGCGAGGTACTGCAGAAAAAAAAACCGCAAAATCCGATCCAATTTATCGTAATCGATTAGTTAACATGTTGGTTAACCGTATTATGAAACACGGAAAAAAATCATTGGCTTATCAAATTATCTATCGAGCTATGAAAAGGATTCAACAAAAGACAGAAACAAATCCACTATCCGTTTTACGTCAAGCAATACTAAAAGCAAGACGCGTAAACGGATCGACTCATCAAGTTCCCGTTGAAATAGGATCCACACAAGGAAAAGCACTTGCCATTCGTTGGTTATTAGGCGCATCCCGAAAACGTCCAGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTGGATGCTGCCAAAGGGAATGGCGATGCCATACGCAAAAAGGAAGAGACTCATAGAATGGCAGAGGCAAATAGAGCTTTTGCACATTTTCCCTTTCATTTGCTTCTTTTCGATGGAAGTTTTATTTTTCCGGAATTGATCCTAATTTTTGGTCTAATTCTTCTTCTGATGATTGATTTAACCTCTGATCAAAAAGATCTATCTTGGTTCTATTTTATCTCTTCAACAAGTTTAGTAATGAGCATAACGGCGCTGTTGTTCCGATGGAGAGAAGAACCCATGATT

Protein sequence

>Msa1354750

MSRRGTAEKKTAKSDPIYRNRLVNMLVNRIMKHGKKSLAYQIIYRAMKRIQQKTETNPLSVLRQAILKARRVNGSTHQVPVEIGSTQGKALAIRWLLGASRKRPGRNMAFKLSSELVDAAKGNGDAIRKKEETHRMAEANRAFAHFPFHLLLFDGSFIFPELILIFGLILLLMIDLTSDQKDLSWFYFISSTSLVMSITALLFRWREEPMI