AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43517


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43517.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 5.14e-31 115
MS.gene43517.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 3.20e-21 88.6
MS.gene43517.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 4.20e-18 80.1
MS.gene43517.t1 MTR_4g112730 57.971 69 28 1 143 211 2 69 7.91e-18 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 60 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGATCAATGGAACAAATTA+AGG 0.196151 5.3:-8159169 MS.gene43517:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 5.3:-8159189 MS.gene43517:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 5.3:+8158873 None:intergenic
CAAAAGATCCCAAGATCTTA+TGG 0.237847 5.3:-8159247 MS.gene43517:CDS
GATTCTTGAGGGAGAAGATT+TGG 0.253340 5.3:-8159366 MS.gene43517:CDS
GACAAAATTAAGGCAAGATT+TGG 0.257188 5.3:-8159224 MS.gene43517:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 5.3:+8159415 None:intergenic
CACGACCTCCACCACGAAAA+TGG 0.277262 5.3:+8158757 None:intergenic
GATCTTATGGGACAAAATTA+AGG 0.310971 5.3:-8159234 MS.gene43517:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 5.3:-8158979 MS.gene43517:CDS
ATTCTTGAGGGAGAAGATTT+GGG 0.333151 5.3:-8159365 MS.gene43517:CDS
AGACAGGTAGTGTCATTCTT+TGG 0.342502 5.3:+8158501 None:intergenic
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 5.3:-8159345 MS.gene43517:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 5.3:+8158658 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 5.3:+8158823 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 5.3:-8158813 MS.gene43517:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 5.3:-8159223 MS.gene43517:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 5.3:-8159066 MS.gene43517:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 5.3:-8159181 MS.gene43517:CDS
CGTGGTGGAGGTCGTGGAAG+AGG 0.449888 5.3:-8158750 MS.gene43517:CDS
TCCTGCATGCTTTAGCCCAA+TGG 0.457473 5.3:+8158601 None:intergenic
AAAAGATCCCAAGATCTTAT+GGG 0.458748 5.3:-8159246 MS.gene43517:CDS
AACCATCAGTTGCGTCCTAC+AGG 0.459311 5.3:-8158909 MS.gene43517:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 5.3:-8159075 MS.gene43517:CDS
ATCTGTGGATGGAAAGGAAA+GGG 0.491819 5.3:-8158547 MS.gene43517:CDS
ATCAAGCACCACATTGATGA+TGG 0.492315 5.3:-8159293 MS.gene43517:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.495634 5.3:-8158624 MS.gene43517:CDS
CTGGCGACAACTACATAACC+TGG 0.502097 5.3:-8159433 MS.gene43517:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 5.3:+8159178 None:intergenic
ATGCGGAAAGAAAGGCCATT+GGG 0.516896 5.3:-8158616 MS.gene43517:CDS
CAAAGAATCTGTGGATGGAA+AGG 0.532926 5.3:-8158553 MS.gene43517:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 5.3:+8159179 None:intergenic
CGTGGACGAGGTAGAAATCA+TGG 0.535808 5.3:-8158786 MS.gene43517:CDS
GGACTCGATAAGATTCTTGA+GGG 0.539399 5.3:-8159377 MS.gene43517:CDS
GCCATTGGGCTAAAGCATGC+AGG 0.539769 5.3:-8158602 MS.gene43517:CDS
CCCTCTAGAAATCATGATGA+TGG 0.541875 5.3:-8158648 MS.gene43517:CDS
TTCCTGTAGGACGCAACTGA+TGG 0.562606 5.3:+8158907 None:intergenic
AAAATCAGCAGCCTCAAGAC+AGG 0.562896 5.3:+8158485 None:intergenic
TTTGATTGGTCATATTTGAG+AGG 0.564015 5.3:+8158711 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 5.3:-8159399 MS.gene43517:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 5.3:-8159398 MS.gene43517:CDS
TTTGGTTGCAGCCCTTCTAG+TGG 0.582793 5.3:-8158961 MS.gene43517:CDS
GATGCGGAAAGAAAGGCCAT+TGG 0.583841 5.3:-8158617 MS.gene43517:CDS
TTGTGCAATAATTTGATGCA+TGG 0.588693 5.3:+8159109 None:intergenic
TAAAAGATACAAAGAATCTG+TGG 0.594054 5.3:-8158562 MS.gene43517:CDS
AGATACAAAGAATCTGTGGA+TGG 0.602731 5.3:-8158558 MS.gene43517:CDS
GGGACTCGATAAGATTCTTG+AGG 0.606176 5.3:-8159378 MS.gene43517:CDS
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 5.3:+8158860 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 5.3:+8159024 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 5.3:-8158831 MS.gene43517:CDS
ACCATCATCATGATTTCTAG+AGG 0.616492 5.3:+8158647 None:intergenic
GGATACGACATTGTTCCTGT+AGG 0.627452 5.3:+8158894 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.642086 5.3:-8158837 MS.gene43517:CDS
CCATCATCATGATTTCTAGA+GGG 0.647682 5.3:+8158648 None:intergenic
GAATGACACTACCTGTCTTG+AGG 0.649563 5.3:-8158496 MS.gene43517:CDS
AATCTGTGGATGGAAAGGAA+AGG 0.653361 5.3:-8158548 MS.gene43517:CDS
GATGATGGTTGTTATAGATG+CGG 0.696569 5.3:-8158633 MS.gene43517:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 5.3:-8158828 MS.gene43517:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 5.3:+8159285 None:intergenic
AGATTTGGGAGATGTCCCAG+AGG 0.741186 5.3:-8159351 MS.gene43517:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCAAAATTTTAAGCATAAC+TGG - chr5.3:8158479-8158498 MS.gene43517:CDS 20.0%
! ACAAAATTAAGGCAAGATTT+GGG - chr5.3:8158708-8158727 MS.gene43517:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG - chr5.3:8158952-8158971 MS.gene43517:CDS 25.0%
! CAATCAAACAAAAATCATCA+GGG - chr5.3:8159235-8159254 MS.gene43517:CDS 25.0%
! TAAAAGATACAAAGAATCTG+TGG - chr5.3:8159369-8159388 MS.gene43517:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG - chr5.3:8158865-8158884 MS.gene43517:CDS 25.0%
!! ATTGCACAATTAGAATTTTG+TGG - chr5.3:8158836-8158855 MS.gene43517:CDS 25.0%
!! TATCTTTTACATAGATACTC+TGG + chr5.3:8159358-8159377 None:intergenic 25.0%
!!! CAACAACAGTTTTATAATCT+TGG + chr5.3:8158790-8158809 None:intergenic 25.0%
!!! TGTTGAAGGAGATTTTAATA+TGG - chr5.3:8159468-8159487 MS.gene43517:CDS 25.0%
AAAAGATCCCAAGATCTTAT+GGG - chr5.3:8158685-8158704 MS.gene43517:CDS 30.0%
AACAAAAATCATCAGGGTAA+AGG - chr5.3:8159241-8159260 MS.gene43517:CDS 30.0%
CCAATCAAACAAAAATCATC+AGG - chr5.3:8159234-8159253 MS.gene43517:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG - chr5.3:8158707-8158726 MS.gene43517:CDS 30.0%
GATCTTATGGGACAAAATTA+AGG - chr5.3:8158697-8158716 MS.gene43517:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG - chr5.3:8158762-8158781 MS.gene43517:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG - chr5.3:8158856-8158875 MS.gene43517:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG + chr5.3:8158755-8158774 None:intergenic 30.0%
TTGTGCAATAATTTGATGCA+TGG + chr5.3:8158825-8158844 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG + chr5.3:8158649-8158668 None:intergenic 30.0%
! AATTTTGTCCCATAAGATCT+TGG + chr5.3:8158696-8158715 None:intergenic 30.0%
! ATTTTGTCCCATAAGATCTT+GGG + chr5.3:8158695-8158714 None:intergenic 30.0%
! TTTGATTGGTCATATTTGAG+AGG + chr5.3:8159223-8159242 None:intergenic 30.0%
!! CCTGATGATTTTTGTTTGAT+TGG + chr5.3:8159237-8159256 None:intergenic 30.0%
AAAGGTAAAAACATCCAGGA+AGG - chr5.3:8159259-8159278 MS.gene43517:CDS 35.0%
AAAGTTGTGGCGTTTATTTC+AGG + chr5.3:8159061-8159080 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG - chr5.3:8158532-8158551 MS.gene43517:CDS 35.0%
AGATACAAAGAATCTGTGGA+TGG - chr5.3:8159373-8159392 MS.gene43517:CDS 35.0%
ATTCTTGAGGGAGAAGATTT+GGG - chr5.3:8158566-8158585 MS.gene43517:CDS 35.0%
ATTGAGTATCTTGCATGTGA+GGG - chr5.3:8158533-8158552 MS.gene43517:CDS 35.0%
CAAAAGATCCCAAGATCTTA+TGG - chr5.3:8158684-8158703 MS.gene43517:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG + chr5.3:8158756-8158775 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG - chr5.3:8159307-8159326 MS.gene43517:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG - chr5.3:8159067-8159086 MS.gene43517:CDS 35.0%
! ACCATCATCATGATTTCTAG+AGG + chr5.3:8159287-8159306 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG - chr5.3:8159068-8159087 MS.gene43517:CDS 35.0%
! ATTTTGTTCAGCCACTAGAA+GGG + chr5.3:8158984-8159003 None:intergenic 35.0%
! CCATCATCATGATTTCTAGA+GGG + chr5.3:8159286-8159305 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG + chr5.3:8158519-8158538 None:intergenic 35.0%
! GATGATGGTTGTTATAGATG+CGG - chr5.3:8159298-8159317 MS.gene43517:CDS 35.0%
! TATTTTGTTCAGCCACTAGA+AGG + chr5.3:8158985-8159004 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG + chr5.3:8158598-8158617 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG + chr5.3:8158599-8158618 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG - chr5.3:8158742-8158761 MS.gene43517:CDS 35.0%
AATCTGTGGATGGAAAGGAA+AGG - chr5.3:8159383-8159402 MS.gene43517:CDS 40.0%
ACGCCCTTGATTAAAAGTTG+TGG + chr5.3:8159074-8159093 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG - chr5.3:8158638-8158657 MS.gene43517:CDS 40.0%
ATCTGTGGATGGAAAGGAAA+GGG - chr5.3:8159384-8159403 MS.gene43517:CDS 40.0%
CAAAGAATCTGTGGATGGAA+AGG - chr5.3:8159378-8159397 MS.gene43517:CDS 40.0%
GATTCTTGAGGGAGAAGATT+TGG - chr5.3:8158565-8158584 MS.gene43517:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG + chr5.3:8158910-8158929 None:intergenic 40.0%
GGACTCGATAAGATTCTTGA+GGG - chr5.3:8158554-8158573 MS.gene43517:CDS 40.0%
GGGTAAAGGTAAAAACATCC+AGG - chr5.3:8159255-8159274 MS.gene43517:CDS 40.0%
! ACAACTTTTAATCAAGGGCG+TGG - chr5.3:8159073-8159092 MS.gene43517:CDS 40.0%
! AGACAGGTAGTGTCATTCTT+TGG + chr5.3:8159433-8159452 None:intergenic 40.0%
! CCCTCTAGAAATCATGATGA+TGG - chr5.3:8159283-8159302 MS.gene43517:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG - chr5.3:8158750-8158769 MS.gene43517:CDS 40.0%
AAAATCAGCAGCCTCAAGAC+AGG + chr5.3:8159449-8159468 None:intergenic 45.0%
ATGCGGAAAGAAAGGCCATT+GGG - chr5.3:8159315-8159334 MS.gene43517:CDS 45.0%
GAATGACACTACCTGTCTTG+AGG - chr5.3:8159435-8159454 MS.gene43517:CDS 45.0%
GGATACGACATTGTTCCTGT+AGG + chr5.3:8159040-8159059 None:intergenic 45.0%
GGGACTCGATAAGATTCTTG+AGG - chr5.3:8158553-8158572 MS.gene43517:CDS 45.0%
GGTGGTTATAATCGCCAAAG+AGG - chr5.3:8159094-8159113 MS.gene43517:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG - chr5.3:8159100-8159119 MS.gene43517:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG - chr5.3:8159163-8159182 MS.gene43517:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG - chr5.3:8159076-8159095 MS.gene43517:CDS 45.0%
!!! GAGGCTGCTGATTTTGTTGA+AGG - chr5.3:8159454-8159473 MS.gene43517:CDS 45.0%
AACCATCAGTTGCGTCCTAC+AGG - chr5.3:8159022-8159041 MS.gene43517:CDS 50.0%
AGATTTGGGAGATGTCCCAG+AGG - chr5.3:8158580-8158599 MS.gene43517:CDS 50.0%
CGTGGACGAGGTAGAAATCA+TGG - chr5.3:8159145-8159164 MS.gene43517:CDS 50.0%
CTGGCGACAACTACATAACC+TGG - chr5.3:8158498-8158517 MS.gene43517:CDS 50.0%
GATGCGGAAAGAAAGGCCAT+TGG - chr5.3:8159314-8159333 MS.gene43517:CDS 50.0%
TCCTGCATGCTTTAGCCCAA+TGG + chr5.3:8159333-8159352 None:intergenic 50.0%
TTCCTGTAGGACGCAACTGA+TGG + chr5.3:8159027-8159046 None:intergenic 50.0%
TTTGGTTGCAGCCCTTCTAG+TGG - chr5.3:8158970-8158989 MS.gene43517:CDS 50.0%
! CGAAACCATTTTCGTGGTGG+AGG - chr5.3:8159169-8159188 MS.gene43517:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG + chr5.3:8159276-8159295 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG - chr5.3:8159166-8159185 MS.gene43517:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG - chr5.3:8159127-8159146 MS.gene43517:CDS 50.0%
AATCGCCAAAGAGGACGTGG+TGG - chr5.3:8159103-8159122 MS.gene43517:CDS 55.0%
CACGACCTCCACCACGAAAA+TGG + chr5.3:8159177-8159196 None:intergenic 55.0%
CATAGCCACCACGTCCTCTT+TGG + chr5.3:8159111-8159130 None:intergenic 55.0%
GCCATTGGGCTAAAGCATGC+AGG - chr5.3:8159329-8159348 MS.gene43517:CDS 55.0%
GGGAGATGTCCCAGAGGAAT+TGG - chr5.3:8158586-8158605 MS.gene43517:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG - chr5.3:8159118-8159137 MS.gene43517:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG - chr5.3:8159121-8159140 MS.gene43517:CDS 55.0%
!! CATTTTCGTGGTGGAGGTCG+TGG - chr5.3:8159175-8159194 MS.gene43517:CDS 55.0%
!! CGTTTTGGTGGTCGTGGACG+AGG - chr5.3:8159133-8159152 MS.gene43517:CDS 60.0%
! CGTGGTGGAGGTCGTGGAAG+AGG - chr5.3:8159181-8159200 MS.gene43517:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 8158458 8159495 8158458 ID=MS.gene43517
chr5.3 mRNA 8158458 8159495 8158458 ID=MS.gene43517.t1;Parent=MS.gene43517
chr5.3 exon 8158458 8159495 8158458 ID=MS.gene43517.t1.exon1;Parent=MS.gene43517.t1
chr5.3 CDS 8158458 8159495 8158458 ID=cds.MS.gene43517.t1;Parent=MS.gene43517.t1
Gene Sequence

>MS.gene43517

ATGTCAAATGTTAAGCATCAATTCAAAATTTTAAGCATAACTGGCGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGATAAGATTCTTGAGGGAGAAGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCAAATGCAAAAGATCCCAAGATCTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCCATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGAGAATTTACTGAATACTCTGATTTGGTTGCAGCCCTTCTAGTGGCTGAACAAAATAACGAGCTGCTCATTAAAAACCATCAGTTGCGTCCTACAGGAACAATGTCGTATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGACGAGGTAGAAATCATGGTCGAAACCATTTTCGTGGTGGAGGTCGTGGAAGAGGTTATATGAATTACATGCCTCTCAAATATGACCAATCAAACAAAAATCATCAGGGTAAAGGTAAAAACATCCAGGAAGGTCCCTCTAGAAATCATGATGATGGTTGTTATAGATGCGGAAAGAAAGGCCATTGGGCTAAAGCATGCAGGACACCAGAGTATCTATGTAAAAGATACAAAGAATCTGTGGATGGAAAGGAAAGGGAAGTTAATTTTAATGAAATTGAACCAAAGAATGACACTACCTGTCTTGAGGCTGCTGATTTTGTTGAAGGAGATTTTAATATGGATTAA

Protein sequence

>MS.gene43517.t1

MSNVKHQFKILSITGDNYITWNNNLIEYLACEGLDKILEGEDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVAALLVAEQNNELLIKNHQLRPTGTMSYPEINATTFNQGRGGYNRQRGRGGYARFGGRGRGRNHGRNHFRGGGRGRGYMNYMPLKYDQSNKNHQGKGKNIQEGPSRNHDDGCYRCGKKGHWAKACRTPEYLCKRYKESVDGKEREVNFNEIEPKNDTTCLEAADFVEGDFNMD