AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0072180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0072180 MtrunA17_Chr1g0178931 90.805 87 7 1 1 87 1 86 3.49e-41 137
Msa0072180 MtrunA17_Chr1g0178951 70.769 65 18 1 23 87 3 66 1.11e-27 96.7
Msa0072180 MtrunA17_Chr1g0178941 72.308 65 17 1 23 87 26 89 3.78e-27 101
Msa0072180 MtrunA17_Chr7g0266061 60.870 69 23 1 23 87 23 91 1.11e-23 92.0
Msa0072180 MtrunA17_Chr1g0198411 76.471 51 10 1 38 88 32 80 2.15e-21 80.1
Msa0072180 MtrunA17_Chr1g0198391 74.510 51 11 1 38 88 33 81 5.04e-19 79.3
Msa0072180 MtrunA17_Chr1g0198381 72.549 51 12 1 38 88 2 50 2.15e-18 77.0
Msa0072180 MtrunA17_Chr1g0198351 48.684 76 35 2 15 88 18 91 5.95e-18 76.3
Msa0072180 MtrunA17_Chr8g0344941 38.554 83 45 2 9 87 14 94 9.79e-12 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0072180 AT5G03610.1 60.241 83 30 2 7 87 11 92 3.14e-25 96.3
Msa0072180 AT3G09930.2 62.500 64 21 1 24 87 28 88 1.41e-19 81.3
Msa0072180 AT3G09930.1 62.500 64 21 1 24 87 28 88 1.41e-19 81.3
Msa0072180 AT2G36325.1 50.000 88 35 2 8 87 10 96 3.01e-17 74.7
Msa0072180 AT5G03590.2 49.367 79 38 2 9 87 7 83 3.58e-17 72.4
Msa0072180 AT5G03600.2 48.649 74 36 2 13 86 25 96 6.81e-17 73.9
Msa0072180 AT5G03600.1 53.333 60 27 1 27 86 3 61 4.27e-16 71.2
Msa0072180 AT1G53920.1 38.095 84 48 1 8 87 18 101 1.53e-11 58.9
Msa0072180 AT3G48460.1 31.522 92 58 2 1 87 1 92 6.94e-11 57.0

Find 24 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGTTGAGAGAAGGAAAATA+AGG 0.314493 1_2:+44851957 None:intergenic
CATCTTCTCATGTCTTTCGC+TGG 0.362737 1_2:-44851785 Msa0072180:CDS
CCTTATGGCATAACCTTTCC+CGG 0.367441 1_2:-44851172 Msa0072180:CDS
CTGGTTCTTGTACTTCTCTC+AGG 0.405056 1_2:-44851766 Msa0072180:intron
CCGGGAAAGGTTATGCCATA+AGG 0.417887 1_2:+44851172 None:intergenic
TCTACCGTCGGAGAATCTTC+CGG 0.453026 1_2:+44851141 None:intergenic
GGTTCATGGAAAGAACCTTA+TGG 0.453293 1_2:-44851187 Msa0072180:CDS
AGAGAAACGTGGCCAAGACT+TGG 0.477614 1_2:+44852042 None:intergenic
GGAGACTCTTATGTTGATAC+CGG 0.484084 1_2:-44851232 Msa0072180:CDS
AATTCTCACATTCCAAGTCT+TGG 0.491733 1_2:-44852054 None:intergenic
ACCTTTCCCGGAAAACCTGC+CGG 0.522743 1_2:-44851160 Msa0072180:CDS
TGTTGAGAGAAGGAAAATAA+GGG 0.530179 1_2:+44851958 None:intergenic
GAACTCTGAAGAAAATATGT+AGG 0.533255 1_2:+44851993 None:intergenic
TAAGGTTCTTTCCATGAACC+AGG 0.564705 1_2:+44851190 None:intergenic
CCGTCGGAGAATCTTCCGGC+AGG 0.570452 1_2:+44851145 None:intergenic
TCCTTCAAAACTAGGCACCT+TGG 0.574769 1_2:-44851852 Msa0072180:five_prime_UTR
ATAACTATGATGTTGAGAGA+AGG 0.589710 1_2:+44851948 None:intergenic
ATTGTTAGGGCTGCAAGCTG+AGG 0.595633 1_2:-44851302 Msa0072180:intron
AAATACAATTGAATGAACAA+TGG 0.603442 1_2:+44851923 None:intergenic
GAGAGAAGGAAAATAAGGGT+TGG 0.615653 1_2:+44851962 None:intergenic
GTCAGTTAAAACTCTACCGT+CGG 0.618067 1_2:+44851129 None:intergenic
AATAGCTATGAAAATGACCA+AGG 0.674457 1_2:+44851835 None:intergenic
CCTGCCGGAAGATTCTCCGA+CGG 0.737578 1_2:-44851145 Msa0072180:CDS
ATAGTGAAAGGAGAGAAACG+TGG 0.805186 1_2:+44852031 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAATTAAGAAAAATCAAT+GGG + chr1_2:44851797-44851816 None:intergenic 10.0%
!! TATTAATTAAGAAAAATCAA+TGG + chr1_2:44851798-44851817 None:intergenic 10.0%
!! ATTAATTAAGAAAAATCAAT+GGG + chr1_2:44851797-44851816 None:intergenic 10.0%
!! TATTAATTAAGAAAAATCAA+TGG + chr1_2:44851798-44851817 None:intergenic 10.0%
!! TTCAATATACTTTAATAGAA+TGG - chr1_2:44851580-44851599 Msa0072180:intron 15.0%
!! TTCAATATACTTTAATAGAA+TGG - chr1_2:44851580-44851599 Msa0072180:intron 15.0%
!!! ATGAGATTTTATATAGTGAA+AGG + chr1_2:44851147-44851166 None:intergenic 20.0%
!! AAATACAATTGAATGAACAA+TGG + chr1_2:44851243-44851262 None:intergenic 20.0%
!!! CACAATACAATATAGTATTT+TGG - chr1_2:44851675-44851694 Msa0072180:intron 20.0%
!!! ATGAGATTTTATATAGTGAA+AGG + chr1_2:44851147-44851166 None:intergenic 20.0%
!! AAATACAATTGAATGAACAA+TGG + chr1_2:44851243-44851262 None:intergenic 20.0%
!!! CACAATACAATATAGTATTT+TGG - chr1_2:44851675-44851694 Msa0072180:intron 20.0%
!!! TAGTTTTGAAGGAAGTTAAA+AGG + chr1_2:44851304-44851323 None:intergenic 25.0%
!!! TTTTAACTTCCTTCAAAACT+AGG - chr1_2:44851303-44851322 Msa0072180:intron 25.0%
!! ATTTTCATAGCTATTCATCA+TGG - chr1_2:44851336-44851355 Msa0072180:intron 25.0%
!!! CATGTTTGTTTTTGAGATAT+AGG + chr1_2:44851497-44851516 None:intergenic 25.0%
! GGAACAAGTTAAAATAAAAG+GGG + chr1_2:44851776-44851795 None:intergenic 25.0%
! GGGAACAAGTTAAAATAAAA+GGG + chr1_2:44851777-44851796 None:intergenic 25.0%
! TGGGAACAAGTTAAAATAAA+AGG + chr1_2:44851778-44851797 None:intergenic 25.0%
!! AAAACGAACAATTCTTTTGT+AGG + chr1_2:44851910-44851929 None:intergenic 25.0%
!! ACAAAAGAATTGTTCGTTTT+TGG - chr1_2:44851910-44851929 Msa0072180:five_prime_UTR 25.0%
!!! TAGTTTTGAAGGAAGTTAAA+AGG + chr1_2:44851304-44851323 None:intergenic 25.0%
!!! TTTTAACTTCCTTCAAAACT+AGG - chr1_2:44851303-44851322 Msa0072180:intron 25.0%
!! ATTTTCATAGCTATTCATCA+TGG - chr1_2:44851336-44851355 Msa0072180:intron 25.0%
!!! CATGTTTGTTTTTGAGATAT+AGG + chr1_2:44851497-44851516 None:intergenic 25.0%
! GGAACAAGTTAAAATAAAAG+GGG + chr1_2:44851776-44851795 None:intergenic 25.0%
! GGGAACAAGTTAAAATAAAA+GGG + chr1_2:44851777-44851796 None:intergenic 25.0%
! TGGGAACAAGTTAAAATAAA+AGG + chr1_2:44851778-44851797 None:intergenic 25.0%
!! AAAACGAACAATTCTTTTGT+AGG + chr1_2:44851910-44851929 None:intergenic 25.0%
!! ACAAAAGAATTGTTCGTTTT+TGG - chr1_2:44851910-44851929 Msa0072180:five_prime_UTR 25.0%
! GAACTCTGAAGAAAATATGT+AGG + chr1_2:44851173-44851192 None:intergenic 30.0%
! ACATATTTTCTTCAGAGTTC+TGG - chr1_2:44851173-44851192 Msa0072180:CDS 30.0%
TGTTGAGAGAAGGAAAATAA+GGG + chr1_2:44851208-44851227 None:intergenic 30.0%
ATGTTGAGAGAAGGAAAATA+AGG + chr1_2:44851209-44851228 None:intergenic 30.0%
ATAACTATGATGTTGAGAGA+AGG + chr1_2:44851218-44851237 None:intergenic 30.0%
AATAGCTATGAAAATGACCA+AGG + chr1_2:44851331-44851350 None:intergenic 30.0%
GAAAATCATACACATACACA+TGG + chr1_2:44851554-44851573 None:intergenic 30.0%
!!! ATAGTATTTTGGTGTGAATC+AGG - chr1_2:44851686-44851705 Msa0072180:intron 30.0%
!! ACATCTTGTTGTTCATTGTT+AGG - chr1_2:44851847-44851866 Msa0072180:five_prime_UTR 30.0%
!! CATCTTGTTGTTCATTGTTA+GGG - chr1_2:44851848-44851867 Msa0072180:five_prime_UTR 30.0%
! CTTTTGTAGGATGATATTTG+AGG + chr1_2:44851897-44851916 None:intergenic 30.0%
!!! TGAACCAGGTTTACTTTTTT+GGG + chr1_2:44851962-44851981 None:intergenic 30.0%
!!! ATGAACCAGGTTTACTTTTT+TGG + chr1_2:44851963-44851982 None:intergenic 30.0%
AAAAAAGTAAACCTGGTTCA+TGG - chr1_2:44851962-44851981 Msa0072180:five_prime_UTR 30.0%
!!! AGAGTTTTAACTGACTTCAT+TGG - chr1_2:44852042-44852061 Msa0072180:five_prime_UTR 30.0%
! GAACTCTGAAGAAAATATGT+AGG + chr1_2:44851173-44851192 None:intergenic 30.0%
! ACATATTTTCTTCAGAGTTC+TGG - chr1_2:44851173-44851192 Msa0072180:CDS 30.0%
TGTTGAGAGAAGGAAAATAA+GGG + chr1_2:44851208-44851227 None:intergenic 30.0%
ATGTTGAGAGAAGGAAAATA+AGG + chr1_2:44851209-44851228 None:intergenic 30.0%
ATAACTATGATGTTGAGAGA+AGG + chr1_2:44851218-44851237 None:intergenic 30.0%
AATAGCTATGAAAATGACCA+AGG + chr1_2:44851331-44851350 None:intergenic 30.0%
GAAAATCATACACATACACA+TGG + chr1_2:44851554-44851573 None:intergenic 30.0%
!!! ATAGTATTTTGGTGTGAATC+AGG - chr1_2:44851686-44851705 Msa0072180:intron 30.0%
!! ACATCTTGTTGTTCATTGTT+AGG - chr1_2:44851847-44851866 Msa0072180:five_prime_UTR 30.0%
!! CATCTTGTTGTTCATTGTTA+GGG - chr1_2:44851848-44851867 Msa0072180:five_prime_UTR 30.0%
! CTTTTGTAGGATGATATTTG+AGG + chr1_2:44851897-44851916 None:intergenic 30.0%
!!! TGAACCAGGTTTACTTTTTT+GGG + chr1_2:44851962-44851981 None:intergenic 30.0%
!!! ATGAACCAGGTTTACTTTTT+TGG + chr1_2:44851963-44851982 None:intergenic 30.0%
AAAAAAGTAAACCTGGTTCA+TGG - chr1_2:44851962-44851981 Msa0072180:five_prime_UTR 30.0%
!!! AGAGTTTTAACTGACTTCAT+TGG - chr1_2:44852042-44852061 Msa0072180:five_prime_UTR 30.0%
ATAAAAGGGGAATGTATTGC+AGG + chr1_2:44851763-44851782 None:intergenic 35.0%
!!! TTTACTTTTTTGGGTGTTGC+CGG + chr1_2:44851953-44851972 None:intergenic 35.0%
AACACCCAAAAAAGTAAACC+TGG - chr1_2:44851955-44851974 Msa0072180:five_prime_UTR 35.0%
ATAAAAGGGGAATGTATTGC+AGG + chr1_2:44851763-44851782 None:intergenic 35.0%
!!! TTTACTTTTTTGGGTGTTGC+CGG + chr1_2:44851953-44851972 None:intergenic 35.0%
AACACCCAAAAAAGTAAACC+TGG - chr1_2:44851955-44851974 Msa0072180:five_prime_UTR 35.0%
ATAGTGAAAGGAGAGAAACG+TGG + chr1_2:44851135-44851154 None:intergenic 40.0%
GAGAGAAGGAAAATAAGGGT+TGG + chr1_2:44851204-44851223 None:intergenic 40.0%
GGAGACTCTTATGTTGATAC+CGG - chr1_2:44851931-44851950 Msa0072180:five_prime_UTR 40.0%
TAAGGTTCTTTCCATGAACC+AGG + chr1_2:44851976-44851995 None:intergenic 40.0%
GGTTCATGGAAAGAACCTTA+TGG - chr1_2:44851976-44851995 Msa0072180:five_prime_UTR 40.0%
GTCAGTTAAAACTCTACCGT+CGG + chr1_2:44852037-44852056 None:intergenic 40.0%
ATAGTGAAAGGAGAGAAACG+TGG + chr1_2:44851135-44851154 None:intergenic 40.0%
GAGAGAAGGAAAATAAGGGT+TGG + chr1_2:44851204-44851223 None:intergenic 40.0%
GGAGACTCTTATGTTGATAC+CGG - chr1_2:44851931-44851950 Msa0072180:five_prime_UTR 40.0%
TAAGGTTCTTTCCATGAACC+AGG + chr1_2:44851976-44851995 None:intergenic 40.0%
GGTTCATGGAAAGAACCTTA+TGG - chr1_2:44851976-44851995 Msa0072180:five_prime_UTR 40.0%
GTCAGTTAAAACTCTACCGT+CGG + chr1_2:44852037-44852056 None:intergenic 40.0%
TCCTTCAAAACTAGGCACCT+TGG - chr1_2:44851311-44851330 Msa0072180:intron 45.0%
!!! ACCAAGGTGCCTAGTTTTGA+AGG + chr1_2:44851315-44851334 None:intergenic 45.0%
CATCTTCTCATGTCTTTCGC+TGG - chr1_2:44851378-44851397 Msa0072180:intron 45.0%
! CTGGTTCTTGTACTTCTCTC+AGG - chr1_2:44851397-44851416 Msa0072180:intron 45.0%
CCTTATGGCATAACCTTTCC+CGG - chr1_2:44851991-44852010 Msa0072180:five_prime_UTR 45.0%
TCCTTCAAAACTAGGCACCT+TGG - chr1_2:44851311-44851330 Msa0072180:intron 45.0%
!!! ACCAAGGTGCCTAGTTTTGA+AGG + chr1_2:44851315-44851334 None:intergenic 45.0%
CATCTTCTCATGTCTTTCGC+TGG - chr1_2:44851378-44851397 Msa0072180:intron 45.0%
! CTGGTTCTTGTACTTCTCTC+AGG - chr1_2:44851397-44851416 Msa0072180:intron 45.0%
CCTTATGGCATAACCTTTCC+CGG - chr1_2:44851991-44852010 Msa0072180:five_prime_UTR 45.0%
AGAGAAACGTGGCCAAGACT+TGG + chr1_2:44851124-44851143 None:intergenic 50.0%
ATTGTTAGGGCTGCAAGCTG+AGG - chr1_2:44851861-44851880 Msa0072180:five_prime_UTR 50.0%
CCGGGAAAGGTTATGCCATA+AGG + chr1_2:44851994-44852013 None:intergenic 50.0%
! AATCTTCCGGCAGGTTTTCC+GGG + chr1_2:44852012-44852031 None:intergenic 50.0%
! GAATCTTCCGGCAGGTTTTC+CGG + chr1_2:44852013-44852032 None:intergenic 50.0%
TCTACCGTCGGAGAATCTTC+CGG + chr1_2:44852025-44852044 None:intergenic 50.0%
AGAGAAACGTGGCCAAGACT+TGG + chr1_2:44851124-44851143 None:intergenic 50.0%
ATTGTTAGGGCTGCAAGCTG+AGG - chr1_2:44851861-44851880 Msa0072180:five_prime_UTR 50.0%
CCGGGAAAGGTTATGCCATA+AGG + chr1_2:44851994-44852013 None:intergenic 50.0%
! AATCTTCCGGCAGGTTTTCC+GGG + chr1_2:44852012-44852031 None:intergenic 50.0%
! GAATCTTCCGGCAGGTTTTC+CGG + chr1_2:44852013-44852032 None:intergenic 50.0%
TCTACCGTCGGAGAATCTTC+CGG + chr1_2:44852025-44852044 None:intergenic 50.0%
ACCTTTCCCGGAAAACCTGC+CGG - chr1_2:44852003-44852022 Msa0072180:five_prime_UTR 55.0%
ACCTTTCCCGGAAAACCTGC+CGG - chr1_2:44852003-44852022 Msa0072180:five_prime_UTR 55.0%
! TCCGGCAGGTTTTCCGGGAA+AGG + chr1_2:44852007-44852026 None:intergenic 60.0%
CCTGCCGGAAGATTCTCCGA+CGG - chr1_2:44852018-44852037 Msa0072180:five_prime_UTR 60.0%
! TCCGGCAGGTTTTCCGGGAA+AGG + chr1_2:44852007-44852026 None:intergenic 60.0%
CCTGCCGGAAGATTCTCCGA+CGG - chr1_2:44852018-44852037 Msa0072180:five_prime_UTR 60.0%
CCGTCGGAGAATCTTCCGGC+AGG + chr1_2:44852021-44852040 None:intergenic 65.0%
CCGTCGGAGAATCTTCCGGC+AGG + chr1_2:44852021-44852040 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 44851114 44852071 44851114 ID=Msa0072180;Name=Msa0072180
chr1_2 mRNA 44851114 44852071 44851114 ID=Msa0072180-mRNA-1;Parent=Msa0072180;Name=Msa0072180-mRNA-1;_AED=0.00;_eAED=0.00;_QI=241|1|0.5|1|1|1|2|0|88
chr1_2 exon 44851114 44851316 44851114 ID=Msa0072180-mRNA-1:exon:13520;Parent=Msa0072180-mRNA-1
chr1_2 exon 44851767 44852071 44851767 ID=Msa0072180-mRNA-1:exon:13519;Parent=Msa0072180-mRNA-1
chr1_2 five_prime_UTR 44851831 44852071 44851831 ID=Msa0072180-mRNA-1:five_prime_utr;Parent=Msa0072180-mRNA-1
chr1_2 CDS 44851767 44851830 44851767 ID=Msa0072180-mRNA-1:cds;Parent=Msa0072180-mRNA-1
chr1_2 CDS 44851114 44851316 44851114 ID=Msa0072180-mRNA-1:cds;Parent=Msa0072180-mRNA-1
Gene Sequence

>Msa0072180

ATGGACTCGTATAAGCAACTTTTCATCTTCTCATGTCTTTCGCTGGTTCTTGTACTTCTCTCAGGGCTGCAAGCTGAGGCAAGTCGTCGCCTCAAATATCATCCTACAAAAGAATTGTTCGTTTTTGGAGACTCTTATGTTGATACCGGCAACACCCAAAAAAGTAAACCTGGTTCATGGAAAGAACCTTATGGCATAACCTTTCCCGGAAAACCTGCCGGAAGATTCTCCGACGGTAGAGTTTTAACTGACTTCATTGGTACGTAA

Protein sequence

>Msa0072180

MDSYKQLFIFSCLSLVLVLLSGLQAEASRRLKYHPTKELFVFGDSYVDTGNTQKSKPGSWKEPYGITFPGKPAGRFSDGRVLTDFIGT*