AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040271

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040271.t1 MTR_7g063520 58.594 256 49 4 1 201 1 254 8.71e-85 251
MS.gene040271.t1 MTR_5g080880 39.545 220 110 6 3 200 36 254 9.25e-41 141
MS.gene040271.t1 MTR_5g080870 34.272 213 112 8 3 200 20 219 1.89e-23 95.9
MS.gene040271.t1 MTR_4g006560 33.758 157 91 3 55 201 83 236 4.08e-19 82.4
MS.gene040271.t1 MTR_1g013120 35.032 157 90 6 55 201 79 233 4.95e-16 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040271.t1 AT5G02050 46.774 186 80 3 33 201 84 267 3.17e-48 159
MS.gene040271.t1 AT3G55605 39.157 166 82 3 53 201 95 258 3.90e-34 122
MS.gene040271.t1 AT2G39795 42.593 162 82 4 50 201 90 250 7.01e-33 119
MS.gene040271.t1 AT5G05990 37.500 176 86 3 48 200 84 258 1.49e-31 115
MS.gene040271.t1 AT2G39790 35.256 156 92 4 50 200 88 239 1.82e-21 88.6
MS.gene040271.t1 AT1G15870 30.380 158 102 3 51 201 85 241 3.96e-20 85.1
MS.gene040271.t1 AT1G80720 29.121 182 117 6 28 201 12 189 3.56e-17 76.3
MS.gene040271.t1 AT1G80720 29.121 182 117 6 28 201 64 241 4.51e-17 77.0

Find 39 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGGAGTGTGTCTGGAGTT+TGG 0.334459 7.1:-65801004 MS.gene040271:CDS
ATTTCTCAATGAAGCTCTTC+AGG 0.341876 7.1:+65800664 None:intergenic
ATGGAGTGTGTCTGGAGTTT+GGG 0.358455 7.1:-65801003 MS.gene040271:CDS
AAAATAGACACAACTAATAA+AGG 0.372853 7.1:+65801034 None:intergenic
GATAGCGCTGTGGAAGGTTC+TGG 0.396323 7.1:+65801541 None:intergenic
TTCTTTGTGGCAAAGGTTAA+CGG 0.402077 7.1:+65801517 None:intergenic
TATATAACGGACGTGGAATC+AGG 0.402815 7.1:-65800904 MS.gene040271:intron
CAAAGGAAATGGAGTGTGTC+TGG 0.417993 7.1:-65801011 MS.gene040271:CDS
CATGTTCAACAAAGACAAAA+AGG 0.444344 7.1:-65800709 MS.gene040271:CDS
CAAAAGGAGTGGTTTCTTTG+TGG 0.449205 7.1:+65801504 None:intergenic
GAGAGGGACTGCAGCGGCGG+TGG 0.453065 7.1:+65801592 None:intergenic
AGCTGGTCTTCAGATTCATC+AGG 0.457345 7.1:+65800929 None:intergenic
TTGCTGATGCACGGAGAGAA+AGG 0.458381 7.1:+65801570 None:intergenic
TTATCTTGGGTGTTATCCCT+CGG 0.469573 7.1:+65800751 None:intergenic
ACTCGAGAAAAGCGTTCTGC+AGG 0.478308 7.1:+65800784 None:intergenic
ATGAGGTTATGATTACTAGA+TGG 0.490856 7.1:-65800964 MS.gene040271:CDS
CTGCAGCGGCGGTGGCGCGA+CGG 0.501759 7.1:+65801600 None:intergenic
TTTGAGATTGTGGACAACCC+TGG 0.521588 7.1:-65801166 MS.gene040271:CDS
GGGTTGTCCACAATCTCAAA+AGG 0.524335 7.1:+65801169 None:intergenic
GAGTGGTTTCTTTGTGGCAA+AGG 0.529220 7.1:+65801510 None:intergenic
TGATGAATCTGAAGACCAGC+TGG 0.536120 7.1:-65800927 MS.gene040271:CDS
CACGTCCGTTATATACCAGC+TGG 0.563114 7.1:+65800912 None:intergenic
AGAAAGGAGAGGGACTGCAG+CGG 0.570549 7.1:+65801586 None:intergenic
TGGAGGAAGTTGCTGATGCA+CGG 0.579223 7.1:+65801561 None:intergenic
CTCGAGTATCTCAAGATCCG+AGG 0.579948 7.1:-65800768 MS.gene040271:CDS
GAAGACCAGCTGGTATATAA+CGG 0.580921 7.1:-65800917 MS.gene040271:CDS
GTGAGAGGGTACAAAAGGAG+TGG 0.592163 7.1:+65801493 None:intergenic
AAGGAGAGGGACTGCAGCGG+CGG 0.602717 7.1:+65801589 None:intergenic
AACGGCGATAGCGCTGTGGA+AGG 0.604965 7.1:+65801535 None:intergenic
TCGAGTATCTCAAGATCCGA+GGG 0.613624 7.1:-65800767 MS.gene040271:CDS
CAGCTGGTATATAACGGACG+TGG 0.614053 7.1:-65800911 MS.gene040271:CDS
ATCTCAAAAGGAAAATAACC+AGG 0.622881 7.1:+65801181 None:intergenic
GATGATTGCTTTCCGTGATG+AGG 0.629611 7.1:-65800981 MS.gene040271:CDS
GGTTAACGGCGATAGCGCTG+TGG 0.644254 7.1:+65801531 None:intergenic
ATGCACGGAGAGAAAGGAGA+GGG 0.651299 7.1:+65801576 None:intergenic
AGCGCTGTGGAAGGTTCTGG+AGG 0.653512 7.1:+65801544 None:intergenic
TAGTAATCATAACCTCATCA+CGG 0.656663 7.1:+65800969 None:intergenic
CACTCACGTGAGTGACAACG+AGG 0.697712 7.1:-65801080 MS.gene040271:CDS
GATGCACGGAGAGAAAGGAG+AGG 0.703418 7.1:+65801575 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAACTTAAACTTAAAA+CGG + chr7.1:65800965-65800984 None:intergenic 10.0%
!! AATATTCATATGATTGAAAA+AGG + chr7.1:65801001-65801020 None:intergenic 15.0%
!!! GTTTTAAGTTTAAGTTTTTA+AGG - chr7.1:65800964-65800983 MS.gene040271:CDS 15.0%
!!! TGTAGGATTTAATAAATTTT+AGG - chr7.1:65800868-65800887 MS.gene040271:intron 15.0%
!! AAAATAGACACAACTAATAA+AGG + chr7.1:65801251-65801270 None:intergenic 20.0%
!! AAATCCTACAAGTAAATAAT+TGG + chr7.1:65800858-65800877 None:intergenic 20.0%
!!! CTTATTTTGTTTTTTCTGTT+TGG - chr7.1:65800814-65800833 MS.gene040271:intron 20.0%
!!! TTTTCCAATTATTTACTTGT+AGG - chr7.1:65800851-65800870 MS.gene040271:intron 20.0%
! AAAACAAAATAAGATGTGAG+AGG + chr7.1:65800807-65800826 None:intergenic 25.0%
! AAACAAAATAAGATGTGAGA+GGG + chr7.1:65800806-65800825 None:intergenic 25.0%
! TGCAAAAATTTGGTTATCTT+GGG + chr7.1:65801547-65801566 None:intergenic 25.0%
! TTGCAAAGTTAAATAACCAT+CGG + chr7.1:65800934-65800953 None:intergenic 25.0%
!! TGTTATCTTTTGCAGTAAAT+TGG - chr7.1:65801468-65801487 MS.gene040271:intron 25.0%
!! TTAGTTGTGTCTATTTTCAA+AGG - chr7.1:65801254-65801273 MS.gene040271:intron 25.0%
!!! TTATTTTCCTTTTGAGATTG+TGG - chr7.1:65801106-65801125 MS.gene040271:CDS 25.0%
!!! TTTTAGGTCAAATATCTCTT+TGG - chr7.1:65800884-65800903 MS.gene040271:intron 25.0%
ATCTCAAAAGGAAAATAACC+AGG + chr7.1:65801104-65801123 None:intergenic 30.0%
ATGAGGTTATGATTACTAGA+TGG - chr7.1:65801318-65801337 MS.gene040271:intron 30.0%
CAAAGACAAAAAGGAATACT+TGG - chr7.1:65801582-65801601 MS.gene040271:CDS 30.0%
CATGTATTGCTGCAAAAATT+TGG + chr7.1:65801557-65801576 None:intergenic 30.0%
CATGTTCAACAAAGACAAAA+AGG - chr7.1:65801573-65801592 MS.gene040271:CDS 30.0%
CTGCAAAAATTTGGTTATCT+TGG + chr7.1:65801548-65801567 None:intergenic 30.0%
TACAAAACTATCGTACAAGA+AGG + chr7.1:65800911-65800930 None:intergenic 30.0%
TAGTAATCATAACCTCATCA+CGG + chr7.1:65801316-65801335 None:intergenic 30.0%
! AGTTGAAAAATCTTTTCTCC+AGG + chr7.1:65801137-65801156 None:intergenic 30.0%
! GTGTCTATTTTCAAAGGAAA+TGG - chr7.1:65801260-65801279 MS.gene040271:intron 30.0%
! GTTGAAAAATCTTTTCTCCA+GGG + chr7.1:65801136-65801155 None:intergenic 30.0%
AATAACCAGGAAATTCAAGC+TGG + chr7.1:65801091-65801110 None:intergenic 35.0%
AGTGACAGAGAACTTAATGA+CGG + chr7.1:65801054-65801073 None:intergenic 35.0%
ATTTCTCAATGAAGCTCTTC+AGG + chr7.1:65801621-65801640 None:intergenic 35.0%
TTCTTTGTGGCAAAGGTTAA+CGG + chr7.1:65800768-65800787 None:intergenic 35.0%
! ACAAAAAGGAATACTTGGTG+TGG - chr7.1:65801587-65801606 MS.gene040271:CDS 35.0%
! TTTTTCCAGCTTGAATTTCC+TGG - chr7.1:65801083-65801102 MS.gene040271:CDS 35.0%
CAAAAGGAGTGGTTTCTTTG+TGG + chr7.1:65800781-65800800 None:intergenic 40.0%
GAAGACCAGCTGGTATATAA+CGG - chr7.1:65801365-65801384 MS.gene040271:intron 40.0%
! AAGATGTGAGAGGGTACAAA+AGG + chr7.1:65800797-65800816 None:intergenic 40.0%
! TTATCTTGGGTGTTATCCCT+CGG + chr7.1:65801534-65801553 None:intergenic 40.0%
!! TATATAACGGACGTGGAATC+AGG - chr7.1:65801378-65801397 MS.gene040271:intron 40.0%
!!! GTACGATAGTTTTGTACCGA+TGG - chr7.1:65800915-65800934 MS.gene040271:CDS 40.0%
CAAAGGAAATGGAGTGTGTC+TGG - chr7.1:65801271-65801290 MS.gene040271:intron 45.0%
GAGTGGTTTCTTTGTGGCAA+AGG + chr7.1:65800775-65800794 None:intergenic 45.0%
GATGATTGCTTTCCGTGATG+AGG - chr7.1:65801301-65801320 MS.gene040271:intron 45.0%
GGGTTGTCCACAATCTCAAA+AGG + chr7.1:65801116-65801135 None:intergenic 45.0%
TCGAGTATCTCAAGATCCGA+GGG - chr7.1:65801515-65801534 MS.gene040271:CDS 45.0%
TGATGAATCTGAAGACCAGC+TGG - chr7.1:65801355-65801374 MS.gene040271:intron 45.0%
! AATGGAGTGTGTCTGGAGTT+TGG - chr7.1:65801278-65801297 MS.gene040271:intron 45.0%
! ATGGAGTGTGTCTGGAGTTT+GGG - chr7.1:65801279-65801298 MS.gene040271:intron 45.0%
! TTTGAGATTGTGGACAACCC+TGG - chr7.1:65801116-65801135 MS.gene040271:CDS 45.0%
!! AGCTGGTCTTCAGATTCATC+AGG + chr7.1:65801356-65801375 None:intergenic 45.0%
ATGCACGGAGAGAAAGGAGA+GGG + chr7.1:65800709-65800728 None:intergenic 50.0%
CACGTCCGTTATATACCAGC+TGG + chr7.1:65801373-65801392 None:intergenic 50.0%
CTCGAGTATCTCAAGATCCG+AGG - chr7.1:65801514-65801533 MS.gene040271:CDS 50.0%
TGGAGGAAGTTGCTGATGCA+CGG + chr7.1:65800724-65800743 None:intergenic 50.0%
TTGCTGATGCACGGAGAGAA+AGG + chr7.1:65800715-65800734 None:intergenic 50.0%
! GTGAGAGGGTACAAAAGGAG+TGG + chr7.1:65800792-65800811 None:intergenic 50.0%
!! ACTCGAGAAAAGCGTTCTGC+AGG + chr7.1:65801501-65801520 None:intergenic 50.0%
!! CAGCTGGTATATAACGGACG+TGG - chr7.1:65801371-65801390 MS.gene040271:intron 50.0%
AGAAAGGAGAGGGACTGCAG+CGG + chr7.1:65800699-65800718 None:intergenic 55.0%
CACTCACGTGAGTGACAACG+AGG - chr7.1:65801202-65801221 MS.gene040271:intron 55.0%
GATAGCGCTGTGGAAGGTTC+TGG + chr7.1:65800744-65800763 None:intergenic 55.0%
GATGCACGGAGAGAAAGGAG+AGG + chr7.1:65800710-65800729 None:intergenic 55.0%
AACGGCGATAGCGCTGTGGA+AGG + chr7.1:65800750-65800769 None:intergenic 60.0%
GGTTAACGGCGATAGCGCTG+TGG + chr7.1:65800754-65800773 None:intergenic 60.0%
! AGCGCTGTGGAAGGTTCTGG+AGG + chr7.1:65800741-65800760 None:intergenic 60.0%
AAGGAGAGGGACTGCAGCGG+CGG + chr7.1:65800696-65800715 None:intergenic 65.0%
GAGAGGGACTGCAGCGGCGG+TGG + chr7.1:65800693-65800712 None:intergenic 75.0%
! CTGCAGCGGCGGTGGCGCGA+CGG + chr7.1:65800685-65800704 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 65800662 65801642 65800662 ID=MS.gene040271
chr7.1 mRNA 65800662 65801642 65800662 ID=MS.gene040271.t1;Parent=MS.gene040271
chr7.1 exon 65801505 65801642 65801505 ID=MS.gene040271.t1.exon1;Parent=MS.gene040271.t1
chr7.1 CDS 65801505 65801642 65801505 ID=cds.MS.gene040271.t1;Parent=MS.gene040271.t1
chr7.1 exon 65800905 65801212 65800905 ID=MS.gene040271.t1.exon2;Parent=MS.gene040271.t1
chr7.1 CDS 65800905 65801212 65800905 ID=cds.MS.gene040271.t1;Parent=MS.gene040271.t1
chr7.1 exon 65800662 65800821 65800662 ID=MS.gene040271.t1.exon3;Parent=MS.gene040271.t1
chr7.1 CDS 65800662 65800821 65800662 ID=cds.MS.gene040271.t1;Parent=MS.gene040271.t1
Gene Sequence

>MS.gene040271

ATGGCTATGTACACTGCTCTCCGTCGCGCCACCGCCGCTGCAGTCCCTCTCCTTTCTCTCCGTGCATCAGCAACTTCCTCCAGAACCTTCCACAGCGCTATCGCCGTTAACCTTTGCCACAAAGAAACCACTCCTTTTGTACCCTCTCACATCTTATTTTGTTTTTTCTGTTTGGATTCTTCGTTTGTATTTTCCAATTATTTACTTGTAGGATTTAATAAATTTTAGGTCAAATATCTCTTTGGTCCTTCTTGTACGATAGTTTTGTACCGATGGTTATTTAACTTTGCAATGTTTATACCGTTTTAAGTTTAAGTTTTTAAGGTTTACATGTTACCTTTTTCAATCATATGAATATTTTATGTCAACACATTTGCTTTTGATATTAACCGTCATTAAGTTCTCTGTCACTTTTGTGTATTTTTTCCAGCTTGAATTTCCTGGTTATTTTCCTTTTGAGATTGTGGACAACCCTGGAGAAAAGATTTTTCAACTAAAAAGACAATTTGAAGATGAAACTATCACAGTTCAAGTTGACATCACTCACGTGAGTGACAACGAGGATGACAGCGAATCTTGCATCATTCCTTTATTAGTTGTGTCTATTTTCAAAGGAAATGGAGTGTGTCTGGAGTTTGGGATGATTGCTTTCCGTGATGAGGTTATGATTACTAGATGGTCACTAAAGAAGCCTGATGAATCTGAAGACCAGCTGGTATATAACGGACGTGGAATCAGGTAAGCATTTATCGATTGTCATTTAATTTTATCAAATGATAATGTCTCTATTACAGATTCTGAATGTTTGTTATCTTTTGCAGTAAATTGGATGAAAACCTGCAGAACGCTTTTCTCGAGTATCTCAAGATCCGAGGGATAACACCCAAGATAACCAAATTTTTGCAGCAATACATGTTCAACAAAGACAAAAAGGAATACTTGGTGTGGCTGAAGAACCTGAAGAGCTTCATTGAGAAATGA
Protein sequence

>MS.gene040271.t1

MAMYTALRRATAAAVPLLSLRASATSSRTFHSAIAVNLCHKETTPFLEFPGYFPFEIVDNPGEKIFQLKRQFEDETITVQVDITHVSDNEDDSESCIIPLLVVSIFKGNGVCLEFGMIAFRDEVMITRWSLKKPDESEDQLVYNGRGISKLDENLQNAFLEYLKIRGITPKITKFLQQYMFNKDKKEYLVWLKNLKSFIEK