AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70308

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70308.t1 MTR_8g092010 93.701 127 7 1 1 126 1 127 2.81e-84 243
MS.gene70308.t1 MTR_8g092010 93.701 127 7 1 1 126 1 127 1.66e-83 243
MS.gene70308.t1 MTR_3g095040 47.826 138 55 6 1 124 1 135 6.60e-25 94.7
MS.gene70308.t1 MTR_1g015140 38.776 98 58 1 28 125 25 120 9.57e-14 64.7
MS.gene70308.t1 MTR_3g104750 75.000 32 8 0 94 125 91 122 3.91e-12 60.5
MS.gene70308.t1 MTR_5g029850 50.877 57 22 1 74 124 12 68 5.50e-12 57.8
MS.gene70308.t1 MTR_4g013260 31.933 119 73 3 8 125 243 354 8.70e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70308.t1 AT5G64810 69.444 36 11 0 90 125 93 128 1.13e-12 62.4
MS.gene70308.t1 AT5G26170 71.875 32 9 0 94 125 100 131 4.82e-12 60.5

Find 27 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGAACAAAGTAGCTTTA+AGG 0.256918 4.1:+9406010 MS.gene70308:intron
AAGATCAGAGCTTGAGATTA+TGG 0.284446 4.1:+9405867 MS.gene70308:CDS
CTTGTTCTAAAGGCTATCTT+TGG 0.312484 4.1:-9405847 None:intergenic
GTAAACTCAGAAGAGGAATT+AGG 0.336749 4.1:-9405241 None:intergenic
TGAGTAGAGTGAGCAAAGTT+TGG 0.356689 4.1:-9405211 None:intergenic
TGCATCATTGAATTCTTGAT+TGG 0.365316 4.1:-9405368 None:intergenic
GAGTAGAGTGAGCAAAGTTT+GGG 0.391273 4.1:-9405210 None:intergenic
TTACATATTATTGTTCTTTG+AGG 0.400718 4.1:-9405392 None:intergenic
TGTTACCTTCTCTAATGATT+CGG 0.455426 4.1:-9405335 None:intergenic
AAGCTCTGATCTTGTTCTAA+AGG 0.476991 4.1:-9405857 None:intergenic
GGATACAAGTGGAGGAAGTA+CGG 0.476991 4.1:+9405895 MS.gene70308:CDS
GTGACCGAGATTCTTGATCA+AGG 0.501478 4.1:-9405306 None:intergenic
AAGCGAATTAAAGTAGAAGC+GGG 0.522259 4.1:+9405823 MS.gene70308:CDS
CAAAGTTTGGGGTAGCATGA+GGG 0.552088 4.1:-9405198 None:intergenic
GATACAAGTGGAGGAAGTAC+GGG 0.554483 4.1:+9405896 MS.gene70308:CDS
ATCACCTTGATCAAGAATCT+CGG 0.560454 4.1:+9405302 MS.gene70308:CDS
TGAAGAACAGTCCTAACCTA+AGG 0.563814 4.1:+9405929 MS.gene70308:CDS
TGAACAAAGTAGCTTTAAGG+TGG 0.569106 4.1:+9406013 MS.gene70308:intron
GCAAAGTTTGGGGTAGCATG+AGG 0.576767 4.1:-9405199 None:intergenic
AGATAGTGTAAACTCAGAAG+AGG 0.584693 4.1:-9405248 None:intergenic
AAGTACCGAATCATTAGAGA+AGG 0.606756 4.1:+9405330 MS.gene70308:CDS
AGTAGAGTGAGCAAAGTTTG+GGG 0.609244 4.1:-9405209 None:intergenic
GAGCTTGAGATTATGGACGA+TGG 0.615286 4.1:+9405874 MS.gene70308:CDS
TTATGGACGATGGATACAAG+TGG 0.616058 4.1:+9405884 MS.gene70308:CDS
TAAGCGAATTAAAGTAGAAG+CGG 0.631449 4.1:+9405822 MS.gene70308:CDS
TGGACGATGGATACAAGTGG+AGG 0.691711 4.1:+9405887 MS.gene70308:CDS
AGCGAATTAAAGTAGAAGCG+GGG 0.700406 4.1:+9405824 MS.gene70308:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCATTTAAAATTAAGAAAA+GGG + chr4.1:9405446-9405465 MS.gene70308:intron 10.0%
!! CAAATACAAAATGAAATTTA+AGG - chr4.1:9405995-9406014 None:intergenic 15.0%
!!! GTTCATTTAAAATTAAGAAA+AGG + chr4.1:9405445-9405464 MS.gene70308:intron 15.0%
!! TTACATATTATTGTTCTTTG+AGG - chr4.1:9405395-9405414 None:intergenic 20.0%
!! TTTGCAGAAAATACAAAAAT+GGG + chr4.1:9405797-9405816 MS.gene70308:intron 20.0%
!!! CTAATAAAGTGTACATATTT+TGG + chr4.1:9405756-9405775 MS.gene70308:intron 20.0%
!!! TTTTGCAGAAAATACAAAAA+TGG + chr4.1:9405796-9405815 MS.gene70308:intron 20.0%
! AACAAGAGCAATACAAATTA+AGG - chr4.1:9405428-9405447 None:intergenic 25.0%
! ACAAGAGCAATACAAATTAA+GGG - chr4.1:9405427-9405446 None:intergenic 25.0%
! ATTAATGAAGCATATACCAT+CGG + chr4.1:9405690-9405709 MS.gene70308:intron 25.0%
!! ATTTGAACAAAGTAGCTTTA+AGG + chr4.1:9406010-9406029 MS.gene70308:intron 25.0%
!! GTATTTCCTTTTATTACCTT+AGG - chr4.1:9405948-9405967 None:intergenic 25.0%
!! TTCAAAAGTGTACTTCTAAA+CGG - chr4.1:9405509-9405528 None:intergenic 25.0%
!!! TCTAAAAGTGTACATTTTGA+GGG + chr4.1:9405578-9405597 MS.gene70308:intron 25.0%
TAAGCGAATTAAAGTAGAAG+CGG + chr4.1:9405822-9405841 MS.gene70308:CDS 30.0%
TCCTAACCTAAGGTAATAAA+AGG + chr4.1:9405939-9405958 MS.gene70308:intron 30.0%
TGCATCATTGAATTCTTGAT+TGG - chr4.1:9405371-9405390 None:intergenic 30.0%
TGTTACCTTCTCTAATGATT+CGG - chr4.1:9405338-9405357 None:intergenic 30.0%
! TCAAAAGTGTACTTCTAAAC+GGG - chr4.1:9405508-9405527 None:intergenic 30.0%
! TCCTTTTATTACCTTAGGTT+AGG - chr4.1:9405943-9405962 None:intergenic 30.0%
!! AGTGTACATATTTTGGATTG+TGG + chr4.1:9405763-9405782 MS.gene70308:intron 30.0%
!! ATCGGTTTTTAAGAAACTAC+GGG - chr4.1:9405485-9405504 None:intergenic 30.0%
!! GATCGGTTTTTAAGAAACTA+CGG - chr4.1:9405486-9405505 None:intergenic 30.0%
!! GTCTAAAAGTGTACATTTTG+AGG + chr4.1:9405577-9405596 MS.gene70308:intron 30.0%
!! GTGTACATATTTTGGATTGT+GGG + chr4.1:9405764-9405783 MS.gene70308:intron 30.0%
!! TGTACATATTTTGGATTGTG+GGG + chr4.1:9405765-9405784 MS.gene70308:intron 30.0%
!!! TGCATGATTGCATTTTTTCA+AGG - chr4.1:9405639-9405658 None:intergenic 30.0%
AAGATCAGAGCTTGAGATTA+TGG + chr4.1:9405867-9405886 MS.gene70308:CDS 35.0%
AAGCGAATTAAAGTAGAAGC+GGG + chr4.1:9405823-9405842 MS.gene70308:CDS 35.0%
AGATAGTGTAAACTCAGAAG+AGG - chr4.1:9405251-9405270 None:intergenic 35.0%
ATCACCTTGATCAAGAATCT+CGG + chr4.1:9405302-9405321 MS.gene70308:CDS 35.0%
CAAATGAAGTAATGAACCGA+TGG - chr4.1:9405709-9405728 None:intergenic 35.0%
GCAATACAAATTAAGGGAGA+AGG - chr4.1:9405421-9405440 None:intergenic 35.0%
GTAAACTCAGAAGAGGAATT+AGG - chr4.1:9405244-9405263 None:intergenic 35.0%
! AAGCTCTGATCTTGTTCTAA+AGG - chr4.1:9405860-9405879 None:intergenic 35.0%
!! AAGTACCGAATCATTAGAGA+AGG + chr4.1:9405330-9405349 MS.gene70308:CDS 35.0%
!! AAGTGTACATTTTGAGGGAT+CGG + chr4.1:9405583-9405602 MS.gene70308:intron 35.0%
!! CTTGTTCTAAAGGCTATCTT+TGG - chr4.1:9405850-9405869 None:intergenic 35.0%
!! GGATCGGTTTTTAGAAATCA+TGG + chr4.1:9405599-9405618 MS.gene70308:intron 35.0%
!! TCGGTTTTTAAGAAACTACG+GGG - chr4.1:9405484-9405503 None:intergenic 35.0%
!! TGAACAAAGTAGCTTTAAGG+TGG + chr4.1:9406013-9406032 MS.gene70308:intron 35.0%
AGCGAATTAAAGTAGAAGCG+GGG + chr4.1:9405824-9405843 MS.gene70308:CDS 40.0%
AGTAGAGTGAGCAAAGTTTG+GGG - chr4.1:9405212-9405231 None:intergenic 40.0%
AGTGTACTTCTAAACGGGAT+CGG - chr4.1:9405503-9405522 None:intergenic 40.0%
GAGTAGAGTGAGCAAAGTTT+GGG - chr4.1:9405213-9405232 None:intergenic 40.0%
TGAAGAACAGTCCTAACCTA+AGG + chr4.1:9405929-9405948 MS.gene70308:CDS 40.0%
TGAGTAGAGTGAGCAAAGTT+TGG - chr4.1:9405214-9405233 None:intergenic 40.0%
TTATGGACGATGGATACAAG+TGG + chr4.1:9405884-9405903 MS.gene70308:CDS 40.0%
GAGCTTGAGATTATGGACGA+TGG + chr4.1:9405874-9405893 MS.gene70308:CDS 45.0%
GGATACAAGTGGAGGAAGTA+CGG + chr4.1:9405895-9405914 MS.gene70308:CDS 45.0%
GTGACCGAGATTCTTGATCA+AGG - chr4.1:9405309-9405328 None:intergenic 45.0%
! CAAAGTTTGGGGTAGCATGA+GGG - chr4.1:9405201-9405220 None:intergenic 45.0%
! GATACAAGTGGAGGAAGTAC+GGG + chr4.1:9405896-9405915 MS.gene70308:CDS 45.0%
TGGACGATGGATACAAGTGG+AGG + chr4.1:9405887-9405906 MS.gene70308:CDS 50.0%
! GCAAAGTTTGGGGTAGCATG+AGG - chr4.1:9405202-9405221 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 9405178 9406052 9405178 ID=MS.gene70308
chr4.1 mRNA 9405178 9406052 9405178 ID=MS.gene70308.t1;Parent=MS.gene70308
chr4.1 exon 9405178 9405410 9405178 ID=MS.gene70308.t1.exon1;Parent=MS.gene70308.t1
chr4.1 CDS 9405178 9405410 9405178 ID=cds.MS.gene70308.t1;Parent=MS.gene70308.t1
chr4.1 exon 9405804 9405950 9405804 ID=MS.gene70308.t1.exon2;Parent=MS.gene70308.t1
chr4.1 CDS 9405804 9405950 9405804 ID=cds.MS.gene70308.t1;Parent=MS.gene70308.t1
chr4.1 exon 9406025 9406052 9406025 ID=MS.gene70308.t1.exon3;Parent=MS.gene70308.t1
chr4.1 CDS 9406025 9406052 9406025 ID=cds.MS.gene70308.t1;Parent=MS.gene70308.t1
Gene Sequence

>MS.gene70308

ATGGACTACTATTTTGTAAACCCTCATGCTACCCCAAACTTTGCTCACTCTACTCATATGATTCCTAATTCCTCTTCTGAGTTTACACTATCTGATTATCTTATGCTTGATGATATTTGTATTGATCACCTTGATCAAGAATCTCGGTCACAAAGTACCGAATCATTAGAGAAGGTAACATTCAATGATGCCAATCAAGAATTCAATGATGCAACCTCAAAGAACAATAATATGTAATTTCCTTCTCCCTTAATTTGTATTGCTCTTGTTCATTTAAAATTAAGAAAAGGGAGCTACTTTTATCCCCGTAGTTTCTTAAAAACCGATCCCGTTTAGAAGTACACTTTTGAACATGAAAAATATAGTTTCTTAAACGTGAACAAAATGATGTTTTTTATCGTCTAAAAGTGTACATTTTGAGGGATCGGTTTTTAGAAATCATGGCAATAAAGAAAGCTCCTTGAAAAAATGCAATCATGCACTATACAATGCGTAAGACTATTTATTGAAGAATTAATGAAGCATATACCATCGGTTCATTACTTCATTTGTATAAACATTACAGTTTTTTTTTTTTGCTAATAAAGTGTACATATTTTGGATTGTGGGGAATAATGTTTTTGCAGAAAATACAAAAATGGGATTAAGCGAATTAAAGTAGAAGCGGGGCCAAAGATAGCCTTTAGAACAAGATCAGAGCTTGAGATTATGGACGATGGATACAAGTGGAGGAAGTACGGGAAGAAGTCTGTGAAGAACAGTCCTAACCTAAGGTAATAAAAGGAAATACTATGTAAAAACTTAATTTCTTACACCTTAAATTTCATTTTGTATTTGAACAAAGTAGCTTTAAGGTGGAGAAATATCTTGCATAG
Protein sequence

>MS.gene70308.t1

MDYYFVNPHATPNFAHSTHMIPNSSSEFTLSDYLMLDDICIDHLDQESRSQSTESLEKVTFNDANQEFNDATSKNNNIKYKNGIKRIKVEAGPKIAFRTRSELEIMDDGYKWRKYGKKSVKNSPNLSFKVEKYLA