AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043593


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043593.t1 MTR_3g053540 100.000 101 0 0 1 101 1 101 1.20e-72 211
MS.gene043593.t1 MTR_3g053520 98.020 101 2 0 1 101 1 101 2.23e-71 207
MS.gene043593.t1 MTR_8g010480 59.459 74 30 0 21 94 165 238 2.35e-27 102
MS.gene043593.t1 MTR_8g010480 61.972 71 27 0 23 93 244 314 1.33e-22 89.4
MS.gene043593.t1 MTR_8g010480 55.128 78 31 1 20 93 83 160 9.56e-22 87.0
MS.gene043593.t1 MTR_8g010480 43.678 87 46 2 15 100 2 86 5.60e-16 71.6
MS.gene043593.t1 MTR_8g010490 46.237 93 49 1 3 95 10 101 1.60e-26 97.1
MS.gene043593.t1 MTR_8g010490 52.632 76 36 0 23 98 108 183 7.15e-22 85.1
MS.gene043593.t1 MTR_8g085340 38.710 93 56 1 10 101 14 106 2.91e-18 74.3
MS.gene043593.t1 MTR_8g085320 33.333 99 65 1 1 98 1 99 8.80e-18 72.4
MS.gene043593.t1 MTR_3g053640 50.000 70 35 0 20 89 82 151 1.19e-15 70.9
MS.gene043593.t1 MTR_3g053640 51.562 64 31 0 29 92 15 78 1.71e-15 70.5
MS.gene043593.t1 MTR_0007s0030 64.103 39 14 0 48 86 1 39 1.53e-14 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043593.t1 AT4G26840 90.000 90 9 0 7 96 2 91 3.86e-57 171
MS.gene043593.t1 AT5G55160 90.426 94 6 2 5 98 2 92 4.53e-57 171
MS.gene043593.t1 AT5G55160 79.439 107 6 3 5 98 2 105 1.64e-53 163
MS.gene043593.t1 AT5G55856 49.438 89 45 0 10 98 2 90 1.38e-26 94.4
MS.gene043593.t1 AT5G55170 51.685 89 41 1 12 98 5 93 1.03e-25 92.8
MS.gene043593.t1 AT5G55855 47.674 86 45 0 13 98 5 90 2.13e-24 89.0
MS.gene043593.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene043593.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene043593.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene043593.t1 AT5G55170 48.315 89 40 2 12 98 5 89 2.83e-21 81.3
MS.gene043593.t1 AT2G32765 37.778 90 55 1 10 98 14 103 1.98e-20 79.0
MS.gene043593.t1 AT5G55170 49.296 71 34 1 12 80 5 75 7.39e-18 72.4
MS.gene043593.t1 AT5G48700 42.222 90 50 2 11 98 19 108 9.23e-18 72.4
MS.gene043593.t1 AT5G48710 39.437 71 42 1 12 81 17 87 5.73e-14 62.4

Find 30 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGTGAGCACCACCTGCTT+CGG 0.338312 3.2:+45596403 None:intergenic
TTCTTGTCTTCCTCGGTGTT+GGG 0.340524 3.2:+45596428 None:intergenic
ATGTGAGCACCACCTGCTTC+GGG 0.344186 3.2:+45596404 None:intergenic
CTTCTTGTCTTCCTCGGTGT+TGG 0.351501 3.2:+45596427 None:intergenic
TCGTAAACACAAACCTCATC+TGG 0.362733 3.2:+45594934 None:intergenic
ATGGGAATGAAGTGTTCTTC+AGG 0.382849 3.2:-45595074 MS.gene043593:CDS
GAACCTGGCCCTTGACTTTG+AGG 0.387240 3.2:+45596378 None:intergenic
TTCGGGCTTCTTGTCTTCCT+CGG 0.415650 3.2:+45596421 None:intergenic
GAAGACAAGAAGCCCGAAGC+AGG 0.445397 3.2:-45596416 MS.gene043593:CDS
CGGAAACTGAAGATGTCGTC+AGG 0.500483 3.2:-45596461 None:intergenic
GTCTTCCTCGGTGTTGGGAG+CGG 0.500639 3.2:+45596433 None:intergenic
TTGCAGCTGGAAATGGAAGA+TGG 0.502872 3.2:-45594830 MS.gene043593:intron
CGTAAACACAAACCTCATCT+GGG 0.526755 3.2:+45594935 None:intergenic
CATCTGGGGTCTGCTCTGCA+CGG 0.560850 3.2:+45594950 None:intergenic
TGCAGCTGGAAATGGAAGAT+GGG 0.572615 3.2:-45594829 MS.gene043593:intron
GATGCCATGCTTCATCAGAC+AGG 0.575586 3.2:-45594797 MS.gene043593:CDS
CAACCTCAAAGTCAAGGGCC+AGG 0.579447 3.2:-45596381 MS.gene043593:intron
ACCTCCTGTCTGATGAAGCA+TGG 0.580486 3.2:+45594793 None:intergenic
CCCATCAAATAGAAAAGCAA+TGG 0.583133 3.2:+45594981 None:intergenic
AAGTGTTCTTCAGGATCAAG+AGG 0.592447 3.2:-45595065 MS.gene043593:CDS
TCACATCAACCTCAAAGTCA+AGG 0.600994 3.2:-45596387 MS.gene043593:CDS
CACATCAACCTCAAAGTCAA+GGG 0.612548 3.2:-45596386 MS.gene043593:CDS
GCCATGCTTCATCAGACAGG+AGG 0.614785 3.2:-45594794 MS.gene043593:CDS
GACAAGAAGCCCGAAGCAGG+TGG 0.627526 3.2:-45596413 MS.gene043593:CDS
TGCAGAGCAGACCCCAGATG+AGG 0.644394 3.2:-45594947 MS.gene043593:intron
TTACTGTGATCGTCAGTCTG+TGG 0.670146 3.2:-45595013 MS.gene043593:CDS
CTGGGGTCTGCTCTGCACGG+AGG 0.678982 3.2:+45594953 None:intergenic
GCAGCTGGAAATGGAAGATG+GGG 0.689173 3.2:-45594828 MS.gene043593:intron
GTAAACACAAACCTCATCTG+GGG 0.707969 3.2:+45594936 None:intergenic
TGCAGCCGCTCCCAACACCG+AGG 0.722402 3.2:-45596438 MS.gene043593:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATTTTTTAGGTTTTTTTT+TGG - chr3.2:45594945-45594964 MS.gene043593:intron 10.0%
!! ATAAGTACAATAAAAATGTT+TGG + chr3.2:45595734-45595753 None:intergenic 15.0%
!! TGAATTATATACAATTTGTA+AGG - chr3.2:45595245-45595264 MS.gene043593:intron 15.0%
!!! TTTTTACATGTTTAGATTAA+CGG - chr3.2:45595079-45595098 MS.gene043593:intron 15.0%
!! AATAAAAATGTTTGGATTGA+CGG + chr3.2:45595726-45595745 None:intergenic 20.0%
!! ACAAGATAACAATATCATAT+AGG + chr3.2:45595923-45595942 None:intergenic 20.0%
!! ATTTGATAAAAACTACACTT+TGG + chr3.2:45595673-45595692 None:intergenic 20.0%
!!! AAGTTATAACTTTTCAGAAA+TGG - chr3.2:45595996-45596015 MS.gene043593:intron 20.0%
!!! ATTTTAATATGTTCTAGGAT+GGG - chr3.2:45596138-45596157 MS.gene043593:intron 20.0%
!!! GTATATGATTTGTTGAAAAT+AGG - chr3.2:45595562-45595581 MS.gene043593:intron 20.0%
!!! TTTGTAAGGAATTTTTGTTT+TGG - chr3.2:45595259-45595278 MS.gene043593:intron 20.0%
! TAAGAATGAACACTAATACA+TGG + chr3.2:45595472-45595491 None:intergenic 25.0%
! TACTTATTGAATTTGTGTGT+TGG - chr3.2:45595747-45595766 MS.gene043593:intron 25.0%
!! GAGTTATGTATGCTAATTTT+TGG - chr3.2:45596114-45596133 MS.gene043593:intron 25.0%
!! GTAGTTTTTATCAAATCACT+TGG - chr3.2:45595677-45595696 MS.gene043593:intron 25.0%
!! GTTTCTGTTATTAGTTTCAT+TGG - chr3.2:45595805-45595824 MS.gene043593:intron 25.0%
!! TATATTTGAAACTCTTGACA+TGG - chr3.2:45596023-45596042 MS.gene043593:intron 25.0%
!! TTTGTTTAAAACGTTGGTTA+GGG - chr3.2:45595397-45595416 MS.gene043593:intron 25.0%
!!! CATTTTAATATGTTCTAGGA+TGG - chr3.2:45596137-45596156 MS.gene043593:intron 25.0%
!!! TTGGCATTTTAATATGTTCT+AGG - chr3.2:45596133-45596152 MS.gene043593:intron 25.0%
!!! TTTTTTTGAACAAGCCATAT+AGG + chr3.2:45595893-45595912 None:intergenic 25.0%
AAAGCAGAAACCCAAAAAAA+AGG + chr3.2:45595424-45595443 None:intergenic 30.0%
CAAATATTGATGTTGCGTTA+TGG + chr3.2:45595353-45595372 None:intergenic 30.0%
CCTAAAAAATTAACGATCGA+AGG + chr3.2:45594937-45594956 None:intergenic 30.0%
TAGTTCTTATCAGAATCACT+TGG - chr3.2:45595150-45595169 MS.gene043593:intron 30.0%
TGATTCTGATAAGAACTACA+CGG + chr3.2:45595148-45595167 None:intergenic 30.0%
TGCGTTCATGTAAAACATAT+TGG - chr3.2:45595964-45595983 MS.gene043593:intron 30.0%
TGGAAACGATGCATTAATTT+CGG - chr3.2:45595279-45595298 MS.gene043593:intron 30.0%
! ACCATATGTTAGGACTTTTT+GGG - chr3.2:45595783-45595802 MS.gene043593:intron 30.0%
! CTTTGTTTAAAACGTTGGTT+AGG - chr3.2:45595396-45595415 MS.gene043593:intron 30.0%
! GATTGTTTGTTGAAGAACTA+GGG - chr3.2:45594983-45595002 MS.gene043593:CDS 30.0%
! TACCATATGTTAGGACTTTT+TGG - chr3.2:45595782-45595801 MS.gene043593:intron 30.0%
! TGATTGTTTGTTGAAGAACT+AGG - chr3.2:45594982-45595001 MS.gene043593:CDS 30.0%
! TTGTCTCTTCTTCGATTTTA+GGG - chr3.2:45594877-45594896 MS.gene043593:intron 30.0%
! TTTGTCTCTTCTTCGATTTT+AGG - chr3.2:45594876-45594895 MS.gene043593:intron 30.0%
!! AAAATATGTTTTGTTGCAGC+TGG - chr3.2:45596387-45596406 MS.gene043593:CDS 30.0%
!! ACCAACGTTTTAAACAAAGT+CGG + chr3.2:45595395-45595414 None:intergenic 30.0%
!! CCATTGCTTTTCTATTTGAT+GGG - chr3.2:45596249-45596268 MS.gene043593:intron 30.0%
!!! CCTTCGATCGTTAATTTTTT+AGG - chr3.2:45594934-45594953 MS.gene043593:intron 30.0%
AAAAATGTTTGGATTGACGG+TGG + chr3.2:45595723-45595742 None:intergenic 35.0%
AATCCAAACATAACTGAGAC+TGG - chr3.2:45595201-45595220 MS.gene043593:intron 35.0%
ACCCAAAAAGTCCTAACATA+TGG + chr3.2:45595787-45595806 None:intergenic 35.0%
AGTTATGTTTGGATTGACGA+TGG + chr3.2:45595196-45595215 None:intergenic 35.0%
ATATAGGAGACAAGTTAGAG+TGG + chr3.2:45595877-45595896 None:intergenic 35.0%
ATGGAATTGGCAAAATCACA+GGG + chr3.2:45595177-45595196 None:intergenic 35.0%
ATTCCAGTCTCAGTTATGTT+TGG + chr3.2:45595207-45595226 None:intergenic 35.0%
CCCATCAAATAGAAAAGCAA+TGG + chr3.2:45596252-45596271 None:intergenic 35.0%
CTGTTTGCATACCATATGTT+AGG - chr3.2:45595773-45595792 MS.gene043593:intron 35.0%
GTACGATATTGTTGAAGAAC+TGG - chr3.2:45595520-45595539 MS.gene043593:intron 35.0%
GTTCTTCAACAATATCGTAC+AGG + chr3.2:45595520-45595539 None:intergenic 35.0%
TGAGTTTCACAAAATCACTG+CGG - chr3.2:45595102-45595121 MS.gene043593:intron 35.0%
! ACTCTAACTTGTCTCCTATA+TGG - chr3.2:45595876-45595895 MS.gene043593:intron 35.0%
!! CAACGTTTTAAACAAAGTCG+GGG + chr3.2:45595393-45595412 None:intergenic 35.0%
!! CCAACGTTTTAAACAAAGTC+GGG + chr3.2:45595394-45595413 None:intergenic 35.0%
!! GCCATTGCTTTTCTATTTGA+TGG - chr3.2:45596248-45596267 MS.gene043593:intron 35.0%
!!! TGGTTAGGGTCCTTTTTTTT+GGG - chr3.2:45595411-45595430 MS.gene043593:intron 35.0%
!!! TTGGTTAGGGTCCTTTTTTT+TGG - chr3.2:45595410-45595429 MS.gene043593:intron 35.0%
AAGTGTTCTTCAGGATCAAG+AGG - chr3.2:45596165-45596184 MS.gene043593:intron 40.0%
CACATCAACCTCAAAGTCAA+GGG - chr3.2:45594844-45594863 MS.gene043593:intron 40.0%
CGTAAACACAAACCTCATCT+GGG + chr3.2:45596298-45596317 None:intergenic 40.0%
GATGGAATTGGCAAAATCAC+AGG + chr3.2:45595178-45595197 None:intergenic 40.0%
GTAAACACAAACCTCATCTG+GGG + chr3.2:45596297-45596316 None:intergenic 40.0%
GTTTGGATTGACGATGGAAT+TGG + chr3.2:45595190-45595209 None:intergenic 40.0%
TCACATCAACCTCAAAGTCA+AGG - chr3.2:45594843-45594862 MS.gene043593:intron 40.0%
TCGTAAACACAAACCTCATC+TGG + chr3.2:45596299-45596318 None:intergenic 40.0%
TTGAAGAACTAGGGTTTCTC+TGG - chr3.2:45594992-45595011 MS.gene043593:CDS 40.0%
! ACTGGTGTTAATCTCACACT+AGG - chr3.2:45595538-45595557 MS.gene043593:intron 40.0%
! ATGGGAATGAAGTGTTCTTC+AGG - chr3.2:45596156-45596175 MS.gene043593:intron 40.0%
! CCCGACTTTGTTTAAAACGT+TGG - chr3.2:45595391-45595410 MS.gene043593:intron 40.0%
! TGATGTTGCGTTATGGATTG+TGG + chr3.2:45595346-45595365 None:intergenic 40.0%
!! TGTTTTGTTGCAGCTGGAAA+TGG - chr3.2:45596393-45596412 MS.gene043593:CDS 40.0%
CTGTGAGTTCGACAAACTCA+TGG - chr3.2:45595624-45595643 MS.gene043593:intron 45.0%
GAAGAAGAGACAAACGAACC+TGG + chr3.2:45594870-45594889 None:intergenic 45.0%
GTTTGGATTGACGGTGGAAT+TGG + chr3.2:45595717-45595736 None:intergenic 45.0%
TGAGTTCGACAAACTCATGG+TGG - chr3.2:45595627-45595646 MS.gene043593:intron 45.0%
TGCAGCTGGAAATGGAAGAT+GGG - chr3.2:45596401-45596420 MS.gene043593:CDS 45.0%
TTACTGTGATCGTCAGTCTG+TGG - chr3.2:45596217-45596236 MS.gene043593:intron 45.0%
TTGCAGCTGGAAATGGAAGA+TGG - chr3.2:45596400-45596419 MS.gene043593:CDS 45.0%
! GTTGCGTTATGGATTGTGGT+TGG + chr3.2:45595342-45595361 None:intergenic 45.0%
!! TTCTTGTCTTCCTCGGTGTT+GGG + chr3.2:45594805-45594824 None:intergenic 45.0%
ACCTCCTGTCTGATGAAGCA+TGG + chr3.2:45596440-45596459 None:intergenic 50.0%
GATGCCATGCTTCATCAGAC+AGG - chr3.2:45596433-45596452 MS.gene043593:CDS 50.0%
GCAGCTGGAAATGGAAGATG+GGG - chr3.2:45596402-45596421 MS.gene043593:CDS 50.0%
TTCGGGCTTCTTGTCTTCCT+CGG + chr3.2:45594812-45594831 None:intergenic 50.0%
! CTTCTTGTCTTCCTCGGTGT+TGG + chr3.2:45594806-45594825 None:intergenic 50.0%
ACAAAGTCGGGGCTGCGTTA+AGG + chr3.2:45595382-45595401 None:intergenic 55.0%
ATGTGAGCACCACCTGCTTC+GGG + chr3.2:45594829-45594848 None:intergenic 55.0%
CAACCTCAAAGTCAAGGGCC+AGG - chr3.2:45594849-45594868 MS.gene043593:intron 55.0%
GAACCTGGCCCTTGACTTTG+AGG + chr3.2:45594855-45594874 None:intergenic 55.0%
GAAGACAAGAAGCCCGAAGC+AGG - chr3.2:45594814-45594833 MS.gene043593:CDS 55.0%
GATGTGAGCACCACCTGCTT+CGG + chr3.2:45594830-45594849 None:intergenic 55.0%
GCCATGCTTCATCAGACAGG+AGG - chr3.2:45596436-45596455 MS.gene043593:CDS 55.0%
GACAAGAAGCCCGAAGCAGG+TGG - chr3.2:45594817-45594836 MS.gene043593:CDS 60.0%
TGCAGAGCAGACCCCAGATG+AGG - chr3.2:45596283-45596302 MS.gene043593:intron 60.0%
! CATCTGGGGTCTGCTCTGCA+CGG + chr3.2:45596283-45596302 None:intergenic 60.0%
!! GTCTTCCTCGGTGTTGGGAG+CGG + chr3.2:45594800-45594819 None:intergenic 60.0%
CTGGGGTCTGCTCTGCACGG+AGG + chr3.2:45596280-45596299 None:intergenic 70.0%
TGCAGCCGCTCCCAACACCG+AGG - chr3.2:45594792-45594811 MS.gene043593:CDS 70.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 45594781 45596471 45594781 ID=MS.gene043593
chr3.2 mRNA 45594781 45596471 45594781 ID=MS.gene043593.t1;Parent=MS.gene043593
chr3.2 exon 45596382 45596471 45596382 ID=MS.gene043593.t1.exon1;Parent=MS.gene043593.t1
chr3.2 CDS 45596382 45596471 45596382 ID=cds.MS.gene043593.t1;Parent=MS.gene043593.t1
chr3.2 exon 45594948 45595097 45594948 ID=MS.gene043593.t1.exon2;Parent=MS.gene043593.t1
chr3.2 CDS 45594948 45595097 45594948 ID=cds.MS.gene043593.t1;Parent=MS.gene043593.t1
chr3.2 exon 45594781 45594846 45594781 ID=MS.gene043593.t1.exon3;Parent=MS.gene043593.t1
chr3.2 CDS 45594781 45594846 45594781 ID=cds.MS.gene043593.t1;Parent=MS.gene043593.t1
Gene Sequence

>MS.gene043593

ATGTCGTCAGGTGCAGCCGCTCCCAACACCGAGGAAGACAAGAAGCCCGAAGCAGGTGGTGCTCACATCAACCTCAAAGTCAAGGGCCAGGTTCGTTTGTCTCTTCTTCGATTTTAGGGTTTTTGTCTTTTTATGAATCGTCTTATTCAAACGCCTTCGATCGTTAATTTTTTAGGTTTTTTTTTGGCTTTGTTGTGTTTATGATTGTTTGTTGAAGAACTAGGGTTTCTCTGGTTTAATTTGATTGTTATTTGTGTTATATAGCATAAGTATGAAAATTTTAAAAATAAAAAGAGAATTTTTACATGTTTAGATTAACGGTGAGTTTCACAAAATCACTGCGGAACTTTGATTTTGTGTAATTCCGTGTAGTTCTTATCAGAATCACTTGGTCCCTGTGATTTTGCCAATTCCATCGTCAATCCAAACATAACTGAGACTGGAATTTATAGTGTTAATTTTATTGAATTATATACAATTTGTAAGGAATTTTTGTTTTGGAAACGATGCATTAATTTCGGTAAGATTTGTGCAATGTTATAATTAAATCACATCGCGCCAACCACAATCCATAACGCAACATCAATATTTGCGAAATCCTTAACGCAGCCCCGACTTTGTTTAAAACGTTGGTTAGGGTCCTTTTTTTTGGGTTTCTGCTTTCAGCTTCATTAGCAAACTTTAGATGCCATGTATTAGTGTTCATTCTTAGTTTATCAATCACTCTAACTTGTTTCCTGTACGATATTGTTGAAGAACTGGTGTTAATCTCACACTAGGAGTATATGATTTGTTGAAAATAGGATAATCACTAATGCTATTTTTTAAACATGTTTAAATTAACTGTGAGTTCGACAAACTCATGGTGGAACTTTGATTTAATGAAGTTCCAAAGTGTAGTTTTTATCAAATCACTTGGTCACTGTGATTTTGCCAATTCCACCGTCAATCCAAACATTTTTATTGTACTTATTGAATTTGTGTGTTGGACTCTGTTTGCATACCATATGTTAGGACTTTTTGGGTTTCTGTTATTAGTTTCATTGGTAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCTACCACTCTAACTTGTCTCCTATATGGCTTGTTCAAAAAAACATGTCTCCTATATGATATTGTTATCTTGTTCTTCGTTCGTTTCTTTATGTTGCGTTCATGTAAAACATATTGGTCTAATCTTAAGTTATAACTTTTCAGAAATGGAAGTTATATTTGAAACTCTTGACATGGTTATAGTTTTTATATTATTAGTCTTCATTACTGTCAAAAGTTTTTAGTCATCATTGAAATTAGCATCAGAGTTATGTATGCTAATTTTTGGCATTTTAATATGTTCTAGGATGGGAATGAAGTGTTCTTCAGGATCAAGAGGAACACTCAACTGAAAAAGCTTATGAATGCTTACTGTGATCGTCAGTCTGTGGATTTCAATGCCATTGCTTTTCTATTTGATGGGCGTCGCCTCCGTGCAGAGCAGACCCCAGATGAGGTTTGTGTTTACGACATTTTTTCATCATTTTCTCTCTATCATAATGTTCAAATAAGTCTAACATTTGTGTTTTTATGACTTGAAAATATGTTTTGTTGCAGCTGGAAATGGAAGATGGGGACGAAATCGATGCCATGCTTCATCAGACAGGAGGTTCTGTTGTCTGA

Protein sequence

>MS.gene043593.t1

MSSGAAAPNTEEDKKPEAGGAHINLKVKGQDGNEVFFRIKRNTQLKKLMNAYCDRQSVDFNAIAFLFDGRRLRAEQTPDELEMEDGDEIDAMLHQTGGSVV