AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035826


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035826.t1 MTR_3g053540 100.000 101 0 0 1 101 1 101 1.20e-72 211
MS.gene035826.t1 MTR_3g053520 98.020 101 2 0 1 101 1 101 2.23e-71 207
MS.gene035826.t1 MTR_8g010480 59.459 74 30 0 21 94 165 238 2.35e-27 102
MS.gene035826.t1 MTR_8g010480 61.972 71 27 0 23 93 244 314 1.33e-22 89.4
MS.gene035826.t1 MTR_8g010480 55.128 78 31 1 20 93 83 160 9.56e-22 87.0
MS.gene035826.t1 MTR_8g010480 43.678 87 46 2 15 100 2 86 5.60e-16 71.6
MS.gene035826.t1 MTR_8g010490 46.237 93 49 1 3 95 10 101 1.60e-26 97.1
MS.gene035826.t1 MTR_8g010490 52.632 76 36 0 23 98 108 183 7.15e-22 85.1
MS.gene035826.t1 MTR_8g085340 38.710 93 56 1 10 101 14 106 2.91e-18 74.3
MS.gene035826.t1 MTR_8g085320 33.333 99 65 1 1 98 1 99 8.80e-18 72.4
MS.gene035826.t1 MTR_3g053640 50.000 70 35 0 20 89 82 151 1.19e-15 70.9
MS.gene035826.t1 MTR_3g053640 51.562 64 31 0 29 92 15 78 1.71e-15 70.5
MS.gene035826.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.gene035826.t1 AT4G26840 90.000 90 9 0 7 96 2 91 3.86e-57 171
MS.gene035826.t1 AT5G55160 90.426 94 6 2 5 98 2 92 4.53e-57 171
MS.gene035826.t1 AT5G55160 79.439 107 6 3 5 98 2 105 1.64e-53 163
MS.gene035826.t1 AT5G55856 49.438 89 45 0 10 98 2 90 1.38e-26 94.4
MS.gene035826.t1 AT5G55170 51.685 89 41 1 12 98 5 93 1.03e-25 92.8
MS.gene035826.t1 AT5G55855 47.674 86 45 0 13 98 5 90 2.13e-24 89.0
MS.gene035826.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene035826.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene035826.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene035826.t1 AT5G55170 48.315 89 40 2 12 98 5 89 2.83e-21 81.3
MS.gene035826.t1 AT2G32765 37.778 90 55 1 10 98 14 103 1.98e-20 79.0
MS.gene035826.t1 AT5G55170 49.296 71 34 1 12 80 5 75 7.39e-18 72.4
MS.gene035826.t1 AT5G48700 42.222 90 50 2 11 98 19 108 9.23e-18 72.4
MS.gene035826.t1 AT5G48710 39.437 71 42 1 12 81 17 87 5.73e-14 62.4

Find 28 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGTGAGCACCACCTGCTT+CGG 0.338312 3.4:+50441423 None:intergenic
TTCTTGTCTTCCTCGGTGTT+GGG 0.340524 3.4:+50441448 None:intergenic
ATGTGAGCACCACCTGCTTC+GGG 0.344186 3.4:+50441424 None:intergenic
CTTCTTGTCTTCCTCGGTGT+TGG 0.351501 3.4:+50441447 None:intergenic
TCGTAAACACAAACCTCATC+TGG 0.362733 3.4:+50439951 None:intergenic
ATGGGAATGAAGTGTTCTTC+AGG 0.382849 3.4:-50440091 MS.gene035826:CDS
GAACCTGGCCTTTGACTTTG+AGG 0.404598 3.4:+50441398 None:intergenic
TTCGGGCTTCTTGTCTTCCT+CGG 0.415650 3.4:+50441441 None:intergenic
GAAGACAAGAAGCCCGAAGC+AGG 0.445397 3.4:-50441436 MS.gene035826:CDS
CGGAAACTGAAGATGTCGTC+AGG 0.500483 3.4:-50441481 None:intergenic
TTGCAGCTGGAAATGGAAGA+TGG 0.502872 3.4:-50439847 MS.gene035826:intron
CGTAAACACAAACCTCATCT+GGG 0.526755 3.4:+50439952 None:intergenic
CATCTGGGGTCTGCTCTGCA+CGG 0.560850 3.4:+50439967 None:intergenic
TGCAGCTGGAAATGGAAGAT+GGG 0.572615 3.4:-50439846 MS.gene035826:intron
GATGCCATGCTTCATCAGAC+AGG 0.575586 3.4:-50439814 MS.gene035826:CDS
CACATCAACCTCAAAGTCAA+AGG 0.580464 3.4:-50441406 MS.gene035826:CDS
ACCTCCTGTCTGATGAAGCA+TGG 0.580486 3.4:+50439810 None:intergenic
CCCATCAAATAGAAAAGCAA+TGG 0.583133 3.4:+50439998 None:intergenic
CAACCTCAAAGTCAAAGGCC+AGG 0.584554 3.4:-50441401 MS.gene035826:intron
AAGTGTTCTTCAGGATCAAG+AGG 0.592447 3.4:-50440082 MS.gene035826:CDS
GCCATGCTTCATCAGACAGG+AGG 0.614785 3.4:-50439811 MS.gene035826:CDS
GACAAGAAGCCCGAAGCAGG+TGG 0.627526 3.4:-50441433 MS.gene035826:CDS
TGCAGAGCAGACCCCAGATG+AGG 0.644394 3.4:-50439964 MS.gene035826:intron
TTACTGTGATCGTCAGTCTG+TGG 0.670146 3.4:-50440030 MS.gene035826:CDS
CTGGGGTCTGCTCTGCACGG+AGG 0.678982 3.4:+50439970 None:intergenic
GCAGCTGGAAATGGAAGATG+GGG 0.689173 3.4:-50439845 MS.gene035826:intron
GTAAACACAAACCTCATCTG+GGG 0.707969 3.4:+50439953 None:intergenic
TGCAGCTGCTCCCAACACCG+AGG 0.715016 3.4:-50441458 MS.gene035826:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATACAATAAAAATGTT+TGG + chr3.4:50440751-50440770 None:intergenic 10.0%
!!! ATTTTATATGTTTAGATTAA+CGG - chr3.4:50440096-50440115 MS.gene035826:intron 10.0%
!! ATTTGATAAAAAATACACTT+TGG + chr3.4:50440690-50440709 None:intergenic 15.0%
!! TGAATTATATACAATTTGTA+AGG - chr3.4:50440262-50440281 MS.gene035826:intron 15.0%
!!! TTTTATATGTTTAGATTAAC+GGG - chr3.4:50440097-50440116 MS.gene035826:intron 15.0%
!! AATAAAAATGTTTGGATTGA+CGG + chr3.4:50440743-50440762 None:intergenic 20.0%
!! ACAAGATAACAATATCATAT+AGG + chr3.4:50440942-50440961 None:intergenic 20.0%
!! TTTATATGTTTAGATTAACG+GGG - chr3.4:50440098-50440117 MS.gene035826:intron 20.0%
!!! ATTTCTGTTATTAGTTTCAT+TGG - chr3.4:50440823-50440842 MS.gene035826:intron 20.0%
!!! ATTTTAATATGTTCTAGGAT+GGG - chr3.4:50441158-50441177 MS.gene035826:intron 20.0%
!!! GTATTTTTTATCAAATCACT+TGG - chr3.4:50440694-50440713 MS.gene035826:intron 20.0%
!!! TATTCGATCGTTAATTTTTA+GGG - chr3.4:50439951-50439970 MS.gene035826:intron 20.0%
!!! TTTGTAAGGAATTTTTGTTT+TGG - chr3.4:50440276-50440295 MS.gene035826:intron 20.0%
!!! TTTTTATTGAATTTGTGTGT+TGG - chr3.4:50440767-50440786 MS.gene035826:intron 20.0%
! TGCATTCATGTAAAACATAT+TGG - chr3.4:50440983-50441002 MS.gene035826:intron 25.0%
! TTTCTGTTATCAGTTTCATT+AGG - chr3.4:50440450-50440469 MS.gene035826:intron 25.0%
!! GAGTTATGTATGCTAATTTT+TGG - chr3.4:50441134-50441153 MS.gene035826:intron 25.0%
!! GTATTCGATCGTTAATTTTT+AGG - chr3.4:50439950-50439969 MS.gene035826:intron 25.0%
!! TATATTTGAAACTCTTGACA+TGG - chr3.4:50441042-50441061 MS.gene035826:intron 25.0%
!! TTTGTTTAAAACGTTGGTTA+GGG - chr3.4:50440414-50440433 MS.gene035826:intron 25.0%
!!! CATTTTAATATGTTCTAGGA+TGG - chr3.4:50441157-50441176 MS.gene035826:intron 25.0%
!!! GTATATGATTTGGTGAAAAT+AGG - chr3.4:50440579-50440598 MS.gene035826:intron 25.0%
!!! TTGGCATTTTAATATGTTCT+AGG - chr3.4:50441153-50441172 MS.gene035826:intron 25.0%
!!! TTTTTTTGAACAAGCCATAT+AGG + chr3.4:50440911-50440930 None:intergenic 25.0%
AACAATCACAAACACAACAA+AGG + chr3.4:50439987-50440006 None:intergenic 30.0%
AATCCAAACATAATTGAGAC+TGG - chr3.4:50440218-50440237 MS.gene035826:intron 30.0%
AATTATGTTTGGATTGACGA+TGG + chr3.4:50440213-50440232 None:intergenic 30.0%
ATCCAAAAAGTCCTAACATA+TGG + chr3.4:50440805-50440824 None:intergenic 30.0%
ATTCCAGTCTCAATTATGTT+TGG + chr3.4:50440224-50440243 None:intergenic 30.0%
CAAATATTGATGTTGCGTTA+TGG + chr3.4:50440370-50440389 None:intergenic 30.0%
GATAACAGAAACCCAAAAAA+AGG + chr3.4:50440441-50440460 None:intergenic 30.0%
TACGATATTGTTGAAGAACT+GGG - chr3.4:50440538-50440557 MS.gene035826:intron 30.0%
TAGTTCTTATCAGAATCACT+TGG - chr3.4:50440167-50440186 MS.gene035826:intron 30.0%
TGATTCTGATAAGAACTACA+CGG + chr3.4:50440165-50440184 None:intergenic 30.0%
! CTTTGTTTAAAACGTTGGTT+AGG - chr3.4:50440413-50440432 MS.gene035826:intron 30.0%
! GATTGTTTGTTGAAGAACTA+GGG - chr3.4:50440000-50440019 MS.gene035826:CDS 30.0%
! TACCATATGTTAGGACTTTT+TGG - chr3.4:50440800-50440819 MS.gene035826:intron 30.0%
! TGATTGTTTGTTGAAGAACT+AGG - chr3.4:50439999-50440018 MS.gene035826:CDS 30.0%
!! AAAATATGTTTTGTTGCAGC+TGG - chr3.4:50441407-50441426 MS.gene035826:CDS 30.0%
!! ACCAACGTTTTAAACAAAGT+TGG + chr3.4:50440412-50440431 None:intergenic 30.0%
!! CAACGTTTTAAACAAAGTTG+GGG + chr3.4:50440410-50440429 None:intergenic 30.0%
!! CCAACGTTTTAAACAAAGTT+GGG + chr3.4:50440411-50440430 None:intergenic 30.0%
!! CCATTGCTTTTCTATTTGAT+GGG - chr3.4:50441269-50441288 MS.gene035826:intron 30.0%
!! TGGAAATGATGCATTGATTT+CGG - chr3.4:50440296-50440315 MS.gene035826:intron 30.0%
AAAAATGTTTGGATTGACGG+TGG + chr3.4:50440740-50440759 None:intergenic 35.0%
AACAAAAACCCTAGAATCGA+AGG + chr3.4:50439906-50439925 None:intergenic 35.0%
ACGATATTGTTGAAGAACTG+GGG - chr3.4:50440539-50440558 MS.gene035826:intron 35.0%
ATATAGGAGACAAGTTAGAG+TGG + chr3.4:50440895-50440914 None:intergenic 35.0%
CCCATCAAATAGAAAAGCAA+TGG + chr3.4:50441272-50441291 None:intergenic 35.0%
CTGTTTGCATACCATATGTT+AGG - chr3.4:50440791-50440810 MS.gene035826:intron 35.0%
GTACGATATTGTTGAAGAAC+TGG - chr3.4:50440537-50440556 MS.gene035826:intron 35.0%
GTTCTTCAACAATATCGTAC+AGG + chr3.4:50440537-50440556 None:intergenic 35.0%
! ACTCTAACTTGTCTCCTATA+TGG - chr3.4:50440894-50440913 MS.gene035826:intron 35.0%
! CACACTAGGAGTATATGATT+TGG - chr3.4:50440569-50440588 MS.gene035826:intron 35.0%
! CCCAACTTTGTTTAAAACGT+TGG - chr3.4:50440408-50440427 MS.gene035826:intron 35.0%
!! GCCATTGCTTTTCTATTTGA+TGG - chr3.4:50441268-50441287 MS.gene035826:intron 35.0%
!!! TTGGTTAGGGTCCTTTTTTT+GGG - chr3.4:50440427-50440446 MS.gene035826:intron 35.0%
AAGTGTTCTTCAGGATCAAG+AGG - chr3.4:50441185-50441204 MS.gene035826:intron 40.0%
CACATCAACCTCAAAGTCAA+AGG - chr3.4:50439861-50439880 MS.gene035826:intron 40.0%
CGTAAACACAAACCTCATCT+GGG + chr3.4:50441318-50441337 None:intergenic 40.0%
GTAAACACAAACCTCATCTG+GGG + chr3.4:50441317-50441336 None:intergenic 40.0%
GTTTGGATTGACGATGGAAT+TGG + chr3.4:50440207-50440226 None:intergenic 40.0%
TCGTAAACACAAACCTCATC+TGG + chr3.4:50441319-50441338 None:intergenic 40.0%
TGTCTCTTCCTTCGATTCTA+GGG - chr3.4:50439895-50439914 MS.gene035826:intron 40.0%
TTGAAGAACTAGGGTTTCTC+TGG - chr3.4:50440009-50440028 MS.gene035826:CDS 40.0%
TTGTCTCTTCCTTCGATTCT+AGG - chr3.4:50439894-50439913 MS.gene035826:intron 40.0%
! AAAGTTCCGCAGTGATTTTG+TGG + chr3.4:50440128-50440147 None:intergenic 40.0%
! ATGGGAATGAAGTGTTCTTC+AGG - chr3.4:50441176-50441195 MS.gene035826:intron 40.0%
! TGATGTTGCGTTATGGATTG+CGG + chr3.4:50440363-50440382 None:intergenic 40.0%
!! TGTTTTGTTGCAGCTGGAAA+TGG - chr3.4:50441413-50441432 MS.gene035826:CDS 40.0%
!!! GTTGGTTAGGGTCCTTTTTT+TGG - chr3.4:50440426-50440445 MS.gene035826:intron 40.0%
AAGGAAGAGACAAACGAACC+TGG + chr3.4:50439887-50439906 None:intergenic 45.0%
ACTGGGGTTAATCTCACACT+AGG - chr3.4:50440555-50440574 MS.gene035826:intron 45.0%
CTGTGAGTTCGACAAACTCA+CGG - chr3.4:50440641-50440660 MS.gene035826:intron 45.0%
GGAGTTCCACAAAATCACTG+CGG - chr3.4:50440119-50440138 MS.gene035826:intron 45.0%
GTTTGGATTGACGGTGGAAT+TGG + chr3.4:50440734-50440753 None:intergenic 45.0%
TGCAGCTGGAAATGGAAGAT+GGG - chr3.4:50441421-50441440 MS.gene035826:CDS 45.0%
TTACTGTGATCGTCAGTCTG+TGG - chr3.4:50441237-50441256 MS.gene035826:intron 45.0%
TTGCAGCTGGAAATGGAAGA+TGG - chr3.4:50441420-50441439 MS.gene035826:CDS 45.0%
!! TTCTTGTCTTCCTCGGTGTT+GGG + chr3.4:50439822-50439841 None:intergenic 45.0%
ACAAAGTTGGGGCTGCGTTA+AGG + chr3.4:50440399-50440418 None:intergenic 50.0%
ACCTCCTGTCTGATGAAGCA+TGG + chr3.4:50441460-50441479 None:intergenic 50.0%
CAACCTCAAAGTCAAAGGCC+AGG - chr3.4:50439866-50439885 MS.gene035826:intron 50.0%
GATGCCATGCTTCATCAGAC+AGG - chr3.4:50441453-50441472 MS.gene035826:CDS 50.0%
GCAGCTGGAAATGGAAGATG+GGG - chr3.4:50441422-50441441 MS.gene035826:CDS 50.0%
TGAGTTCGACAAACTCACGG+TGG - chr3.4:50440644-50440663 MS.gene035826:intron 50.0%
TTCGGGCTTCTTGTCTTCCT+CGG + chr3.4:50439829-50439848 None:intergenic 50.0%
! CTTCTTGTCTTCCTCGGTGT+TGG + chr3.4:50439823-50439842 None:intergenic 50.0%
! GAACCTGGCCTTTGACTTTG+AGG + chr3.4:50439872-50439891 None:intergenic 50.0%
! GTTGCGTTATGGATTGCGGT+CGG + chr3.4:50440359-50440378 None:intergenic 50.0%
ATGTGAGCACCACCTGCTTC+GGG + chr3.4:50439846-50439865 None:intergenic 55.0%
GAAGACAAGAAGCCCGAAGC+AGG - chr3.4:50439831-50439850 MS.gene035826:CDS 55.0%
GATGTGAGCACCACCTGCTT+CGG + chr3.4:50439847-50439866 None:intergenic 55.0%
GCCATGCTTCATCAGACAGG+AGG - chr3.4:50441456-50441475 MS.gene035826:CDS 55.0%
GACAAGAAGCCCGAAGCAGG+TGG - chr3.4:50439834-50439853 MS.gene035826:CDS 60.0%
TGCAGAGCAGACCCCAGATG+AGG - chr3.4:50441303-50441322 MS.gene035826:intron 60.0%
! CATCTGGGGTCTGCTCTGCA+CGG + chr3.4:50441303-50441322 None:intergenic 60.0%
TGCAGCTGCTCCCAACACCG+AGG - chr3.4:50439809-50439828 MS.gene035826:CDS 65.0%
CTGGGGTCTGCTCTGCACGG+AGG + chr3.4:50441300-50441319 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 50439798 50441491 50439798 ID=MS.gene035826
chr3.4 mRNA 50439798 50441491 50439798 ID=MS.gene035826.t1;Parent=MS.gene035826
chr3.4 exon 50441402 50441491 50441402 ID=MS.gene035826.t1.exon1;Parent=MS.gene035826.t1
chr3.4 CDS 50441402 50441491 50441402 ID=cds.MS.gene035826.t1;Parent=MS.gene035826.t1
chr3.4 exon 50439965 50440114 50439965 ID=MS.gene035826.t1.exon2;Parent=MS.gene035826.t1
chr3.4 CDS 50439965 50440114 50439965 ID=cds.MS.gene035826.t1;Parent=MS.gene035826.t1
chr3.4 exon 50439798 50439863 50439798 ID=MS.gene035826.t1.exon3;Parent=MS.gene035826.t1
chr3.4 CDS 50439798 50439863 50439798 ID=cds.MS.gene035826.t1;Parent=MS.gene035826.t1
Gene Sequence

>MS.gene035826

ATGTCGTCAGGTGCAGCTGCTCCCAACACCGAGGAAGACAAGAAGCCCGAAGCAGGTGGTGCTCACATCAACCTCAAAGTCAAAGGCCAGGTTCGTTTGTCTCTTCCTTCGATTCTAGGGTTTTTGTTTTTTATGAATCGTCTTATTCAAACGTATTCGATCGTTAATTTTTAGGGTTTTTTTTTGCCTTTGTTGTGTTTGTGATTGTTTGTTGAAGAACTAGGGTTTCTCTGGTTTAATTTGATTGCTATTTGTGTTATATAGCATAAGTATGAAAAATTTAAAAATAAAAAGAGAAATTTTATATGTTTAGATTAACGGGGAGTTCCACAAAATCACTGCGGAACTTTGATTTTGTGTAATTCCGTGTAGTTCTTATCAGAATCACTTGGTCACTGTGATTTTGCCAATTCCATCGTCAATCCAAACATAATTGAGACTGGAATTTATAGTGTTAATTTTATTGAATTATATACAATTTGTAAGGAATTTTTGTTTTGGAAATGATGCATTGATTTCGGTAAGATTTGTGCAATGTTATAATTAAATCACATCGCGCCGACCGCAATCCATAACGCAACATCAATATTTGCGAAATCCTTAACGCAGCCCCAACTTTGTTTAAAACGTTGGTTAGGGTCCTTTTTTTGGGTTTCTGTTATCAGTTTCATTAGGAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCGATCACTCTAACTTGTTTCCTGTACGATATTGTTGAAGAACTGGGGTTAATCTCACACTAGGAGTATATGATTTGGTGAAAATAGGATAATCACTAATGCTATTTTTTAAACATGTTTAAATTAACTGTGAGTTCGACAAACTCACGGTGGCACTTTGATTTAATGAAGTTCCAAAGTGTATTTTTTATCAAATCACTTGGTCACTGTGATTTTGCCAATTCCACCGTCAATCCAAACATTTTTATTGTATTTTTTATTGAATTTGTGTGTTGGACTGTTTGCATACCATATGTTAGGACTTTTTGGATTTCTGTTATTAGTTTCATTGGTAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCTACCACTCTAACTTGTCTCCTATATGGCTTGTTCAAAAAAAACATGTCTCCTATATGATATTGTTATCTTGTTCTTCGTTCGTTTCTTTATGTTGCATTCATGTAAAACATATTGGTCTAATCTTAAGTTATAACTTTTCAGAAATCGAAGTTATATTTGAAACTCTTGACATGGTTATAGTTTTCTATATTATTAGTCTTAGTTACTGTCAAAAGTTTTTAGTCATCATTGAAATTAGCATCAGAGTTATGTATGCTAATTTTTGGCATTTTAATATGTTCTAGGATGGGAATGAAGTGTTCTTCAGGATCAAGAGGAACACTCAACTGAAAAAGCTTATGAATGCTTACTGTGATCGTCAGTCTGTGGATTTCAATGCCATTGCTTTTCTATTTGATGGGCGTCGCCTCCGTGCAGAGCAGACCCCAGATGAGGTTTGTGTTTACGACATTTTTTCATCACTTTTTCTCTATCATAATGTTCAAATAAGTCTAACATTTGTGTTTTTATGACTTGAAAATATGTTTTGTTGCAGCTGGAAATGGAAGATGGGGACGAAATCGATGCCATGCTTCATCAGACAGGAGGTTCTGTTGTCTGA

Protein sequence

>MS.gene035826.t1

MSSGAAAPNTEEDKKPEAGGAHINLKVKGQDGNEVFFRIKRNTQLKKLMNAYCDRQSVDFNAIAFLFDGRRLRAEQTPDELEMEDGDEIDAMLHQTGGSVV