AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene68806


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68806.t1 MTR_3g116830 96.629 178 6 0 1 178 1 178 4.12e-128 357
MS.gene68806.t1 MTR_1g054750 26.437 174 94 5 32 171 12 185 4.30e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68806.t1 AT2G21620 76.404 178 41 1 1 178 1 177 7.64e-93 268
MS.gene68806.t1 AT2G21620 73.913 184 41 2 1 178 1 183 3.25e-90 262

Find 43 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCTTGTTCATGCTGTTTC+TGG 0.024473 3.2:-92363636 MS.gene68806:intron
TAAACCTGCAGCTGTGGTTT+TGG 0.252116 3.2:-92362665 MS.gene68806:CDS
GCACCTGTTGTGATCGTTCC+TGG 0.338638 3.2:-92362444 MS.gene68806:CDS
TCAAAAGCATGTTTACTGTT+TGG 0.339328 3.2:+92363699 None:intergenic
CCAGAGCTTGAGAGGGAAAC+AGG 0.363491 3.2:-92363768 MS.gene68806:CDS
AGCTCTGGCTCAGGCACTAT+TGG 0.369995 3.2:+92363783 None:intergenic
ACTGTTTGGACCATGATCTA+TGG 0.408420 3.2:+92363713 None:intergenic
TTGAAACAAGCTTCTGCCTC+TGG 0.408871 3.2:+92362639 None:intergenic
GTGATGCATCAATGGTCTAA+TGG 0.411227 3.2:-92362329 None:intergenic
CCTGTTTCCCTCTCAAGCTC+TGG 0.412478 3.2:+92363768 None:intergenic
CGACTTAACCCAGGGATTGA+TGG 0.429955 3.2:-92363445 MS.gene68806:CDS
CTAATTTCTCCATCAATCCC+TGG 0.431733 3.2:+92363436 None:intergenic
TCCCTCTCAAGCTCTGGCTC+AGG 0.455326 3.2:+92363774 None:intergenic
TTTCCAGGAACGATCACAAC+AGG 0.474556 3.2:+92362441 None:intergenic
CAGGAGAAAGAAGAAGAGGA+AGG 0.480520 3.2:-92363749 MS.gene68806:CDS
GAGGCAGAAGCTTGTTTCAA+AGG 0.482260 3.2:-92362636 MS.gene68806:intron
GAAACAGGAGAAAGAAGAAG+AGG 0.483483 3.2:-92363753 MS.gene68806:CDS
CGGATAGTGCAAGGTGATGC+AGG 0.488351 3.2:-92362718 MS.gene68806:CDS
GTCCCCAAAACCACAGCTGC+AGG 0.501479 3.2:+92362661 None:intergenic
GTTGTGATCGTTCCTGGAAA+AGG 0.523884 3.2:-92362438 MS.gene68806:intron
GCCTTCTTCAGTGTGCTACA+AGG 0.527496 3.2:-92362504 MS.gene68806:intron
AGGAGAAAGAAGAAGAGGAA+GGG 0.532412 3.2:-92363748 MS.gene68806:CDS
TAAATTAATGGAGACAGTGA+TGG 0.533156 3.2:-92363856 None:intergenic
TAATTTCTCCATCAATCCCT+GGG 0.538350 3.2:+92363437 None:intergenic
TGCCTGAGCCAGAGCTTGAG+AGG 0.541192 3.2:-92363776 MS.gene68806:CDS
AGATGCTGGTGATGCATCAA+TGG 0.543889 3.2:-92362337 MS.gene68806:CDS
ATAGTATTAGCCATAGATCA+TGG 0.553466 3.2:-92363723 MS.gene68806:CDS
AACAGGTGAAAACAGTAGCT+CGG 0.557174 3.2:-92362738 MS.gene68806:intron
GAGGATTAAACCTGCAGCTG+TGG 0.569878 3.2:-92362671 MS.gene68806:CDS
GATGGAGAAATTAGCGGCTG+AGG 0.575246 3.2:-92363427 MS.gene68806:CDS
GGCACTATTGGTATCAGTGA+AGG 0.576088 3.2:+92363795 None:intergenic
GGGATTGATGGAGAAATTAG+CGG 0.601178 3.2:-92363433 MS.gene68806:CDS
AACCAGAAACAGCATGAACA+AGG 0.607545 3.2:+92363634 None:intergenic
GCCTGAGCCAGAGCTTGAGA+GGG 0.610344 3.2:-92363775 MS.gene68806:CDS
TGCAGGAAAAGTAATTTGCA+AGG 0.617105 3.2:-92362701 MS.gene68806:CDS
AACAGCATGAACAAGGTGGA+TGG 0.627059 3.2:+92363641 None:intergenic
ACAGTAGCTCGGATAGTGCA+AGG 0.631985 3.2:-92362727 MS.gene68806:CDS
ATTGTGTACGACTTAACCCA+GGG 0.659770 3.2:-92363453 MS.gene68806:CDS
AATTGTGTACGACTTAACCC+AGG 0.666749 3.2:-92363454 MS.gene68806:CDS
CAGAAACAGCATGAACAAGG+TGG 0.686182 3.2:+92363637 None:intergenic
CAACAGGTGCTGCTTTACAG+TGG 0.687014 3.2:+92362457 None:intergenic
AGTGTGCTACAAGGAAGCGT+CGG 0.687872 3.2:-92362495 MS.gene68806:CDS
TAATTTGCAAGGAAGCAGAG+AGG 0.695628 3.2:-92362690 MS.gene68806:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAACTTCAATTAATTTATA+TGG + chr3.2:92362630-92362649 None:intergenic 10.0%
!!! GATTTTTTTTTATTACTTTA+TGG - chr3.2:92362660-92362679 MS.gene68806:CDS 10.0%
!!! TTATTGTGAATTTATTTTTT+TGG - chr3.2:92363327-92363346 MS.gene68806:intron 10.0%
!! AAAAAACATATACAGAATAA+TGG + chr3.2:92363656-92363675 None:intergenic 15.0%
!! TCCAATTTGAAAAATTATAT+AGG - chr3.2:92362830-92362849 MS.gene68806:intron 15.0%
!!! AAAACTTATTCTTTTTCAAT+GGG - chr3.2:92363214-92363233 MS.gene68806:intron 15.0%
!!! AATTGAAGTTTTTGTTTTTA+TGG - chr3.2:92362638-92362657 MS.gene68806:CDS 15.0%
!!! TATTACAAGTTGATTTTATA+CGG + chr3.2:92363163-92363182 None:intergenic 15.0%
!!! TCCTATATAATTTTTCAAAT+TGG + chr3.2:92362834-92362853 None:intergenic 15.0%
!! ATCACATGTAAAAAAAACAA+TGG - chr3.2:92362964-92362983 MS.gene68806:intron 20.0%
!! GCATATCTTGAAATATTTAA+TGG - chr3.2:92363013-92363032 MS.gene68806:intron 20.0%
!! TAAAATCAACTTGTAATACA+AGG - chr3.2:92363165-92363184 MS.gene68806:intron 20.0%
!! TATCTTGAAATATTTAATGG+AGG - chr3.2:92363016-92363035 MS.gene68806:intron 20.0%
!! TCACATGTAAAAAAAACAAT+GGG - chr3.2:92362965-92362984 MS.gene68806:intron 20.0%
!! TTCATAAGTAAATAGGAAAA+CGG + chr3.2:92362809-92362828 None:intergenic 20.0%
!!! CAAAACTTATTCTTTTTCAA+TGG - chr3.2:92363213-92363232 MS.gene68806:intron 20.0%
! AAAAGTTTAATCAACCATCA+TGG - chr3.2:92363071-92363090 MS.gene68806:intron 25.0%
! ACAAATTGTGGTTAATGATT+TGG + chr3.2:92362907-92362926 None:intergenic 25.0%
! ATTGGACTTCATAAGTAAAT+AGG + chr3.2:92362816-92362835 None:intergenic 25.0%
! CAATAGCATAATTAAGTCAA+GGG - chr3.2:92362991-92363010 MS.gene68806:intron 25.0%
! CACATGTAAAAAAAACAATG+GGG - chr3.2:92362966-92362985 MS.gene68806:intron 25.0%
! CATACTAATCATAAGTAGAA+TGG + chr3.2:92363416-92363435 None:intergenic 25.0%
! GGGATTATTAATACATGTAA+AGG + chr3.2:92363251-92363270 None:intergenic 25.0%
! TAATGAGTGATAAACAATAG+AGG + chr3.2:92363357-92363376 None:intergenic 25.0%
! TCAATAGCATAATTAAGTCA+AGG - chr3.2:92362990-92363009 MS.gene68806:intron 25.0%
AGTTATCAATAAATGCTGCA+AGG + chr3.2:92363272-92363291 None:intergenic 30.0%
ATAGTATTAGCCATAGATCA+TGG - chr3.2:92362458-92362477 MS.gene68806:CDS 30.0%
ATGAGAAGTTAAGAAAGTGA+AGG + chr3.2:92362581-92362600 None:intergenic 30.0%
GAGGTCAAAGATACTAATTA+CGG - chr3.2:92363035-92363054 MS.gene68806:intron 30.0%
GATTAGTATGATGTGAAAAC+AGG - chr3.2:92363426-92363445 MS.gene68806:CDS 30.0%
GTTATCAATAAATGCTGCAA+GGG + chr3.2:92363271-92363290 None:intergenic 30.0%
TTCAATCCCTTTCTATATCT+CGG - chr3.2:92363606-92363625 MS.gene68806:intron 30.0%
! ACAGTAAACATGCTTTTGAT+TGG - chr3.2:92362486-92362505 MS.gene68806:CDS 30.0%
! GCAGCATTTATTGATAACTT+TGG - chr3.2:92363273-92363292 MS.gene68806:intron 30.0%
! TCAAAAGCATGTTTACTGTT+TGG + chr3.2:92362485-92362504 None:intergenic 30.0%
!! ATACTAATTACGGTGGATTA+GGG - chr3.2:92363045-92363064 MS.gene68806:intron 30.0%
!! CAGTAAACATGCTTTTGATT+GGG - chr3.2:92362487-92362506 MS.gene68806:CDS 30.0%
CTCATTACTACTCTATTTCC+TGG - chr3.2:92363370-92363389 MS.gene68806:intron 35.0%
GTCAAAGATACTAATTACGG+TGG - chr3.2:92363038-92363057 MS.gene68806:intron 35.0%
TAATTTCTCCATCAATCCCT+GGG + chr3.2:92362747-92362766 None:intergenic 35.0%
TACTCTATTTCCTGGCAAAT+TGG - chr3.2:92363378-92363397 MS.gene68806:intron 35.0%
! GATACTAATTACGGTGGATT+AGG - chr3.2:92363044-92363063 MS.gene68806:intron 35.0%
! TGCAGGAAAAGTAATTTGCA+AGG - chr3.2:92363480-92363499 MS.gene68806:intron 35.0%
!!! TTCTTTTTCAATGGGAGACT+TGG - chr3.2:92363222-92363241 MS.gene68806:intron 35.0%
AAATGGACAACTCCGTGAAT+GGG + chr3.2:92362932-92362951 None:intergenic 40.0%
AACAGGTGAAAACAGTAGCT+CGG - chr3.2:92363443-92363462 MS.gene68806:CDS 40.0%
AACCAGAAACAGCATGAACA+AGG + chr3.2:92362550-92362569 None:intergenic 40.0%
AATTGTGTACGACTTAACCC+AGG - chr3.2:92362727-92362746 MS.gene68806:CDS 40.0%
ACTGTTTGGACCATGATCTA+TGG + chr3.2:92362471-92362490 None:intergenic 40.0%
AGAATGGCCGAGATATAGAA+AGG + chr3.2:92363616-92363635 None:intergenic 40.0%
AGGAGAAAGAAGAAGAGGAA+GGG - chr3.2:92362433-92362452 MS.gene68806:intron 40.0%
ATTCACGGAGTTGTCCATTT+AGG - chr3.2:92362932-92362951 MS.gene68806:intron 40.0%
ATTGTGTACGACTTAACCCA+GGG - chr3.2:92362728-92362747 MS.gene68806:CDS 40.0%
CACAATTTGTGTCCCATTCA+CGG - chr3.2:92362917-92362936 MS.gene68806:intron 40.0%
CTAATTTCTCCATCAATCCC+TGG + chr3.2:92362748-92362767 None:intergenic 40.0%
CTTCTTTGATTGACAGATGC+TGG - chr3.2:92363830-92363849 MS.gene68806:CDS 40.0%
GAAACAGGAGAAAGAAGAAG+AGG - chr3.2:92362428-92362447 MS.gene68806:intron 40.0%
GAACAACTTGTAAGCCATGA+TGG + chr3.2:92363088-92363107 None:intergenic 40.0%
GAATAGATTGCCAATTTGCC+AGG + chr3.2:92363391-92363410 None:intergenic 40.0%
GAATGGCCGAGATATAGAAA+GGG + chr3.2:92363615-92363634 None:intergenic 40.0%
GGGATTGATGGAGAAATTAG+CGG - chr3.2:92362748-92362767 MS.gene68806:intron 40.0%
GTGATTGACTACCACCTAAA+TGG + chr3.2:92362949-92362968 None:intergenic 40.0%
TAAATGGACAACTCCGTGAA+TGG + chr3.2:92362933-92362952 None:intergenic 40.0%
TAACTGCAGTGTGTAGAGAA+TGG + chr3.2:92363632-92363651 None:intergenic 40.0%
! TAATTTGCAAGGAAGCAGAG+AGG - chr3.2:92363491-92363510 MS.gene68806:intron 40.0%
! TAGTAATGCACACCTTTTCC+AGG + chr3.2:92363758-92363777 None:intergenic 40.0%
!! TTGTTCATGCTGTTTCTGGT+TGG - chr3.2:92362549-92362568 MS.gene68806:intron 40.0%
!!! TGAGGCTTTTGAAGTTGCAA+TGG - chr3.2:92362772-92362791 MS.gene68806:intron 40.0%
AACAGCATGAACAAGGTGGA+TGG + chr3.2:92362543-92362562 None:intergenic 45.0%
CAGAAACAGCATGAACAAGG+TGG + chr3.2:92362547-92362566 None:intergenic 45.0%
CAGGAGAAAGAAGAAGAGGA+AGG - chr3.2:92362432-92362451 MS.gene68806:intron 45.0%
CGTGAATGGGACACAAATTG+TGG + chr3.2:92362919-92362938 None:intergenic 45.0%
GGCACTATTGGTATCAGTGA+AGG + chr3.2:92362389-92362408 None:intergenic 45.0%
GTTGTGATCGTTCCTGGAAA+AGG - chr3.2:92363743-92363762 MS.gene68806:CDS 45.0%
TCCTTGTAGCACACTGAAGA+AGG + chr3.2:92363681-92363700 None:intergenic 45.0%
TTGAAACAAGCTTCTGCCTC+TGG + chr3.2:92363545-92363564 None:intergenic 45.0%
TTTCCAGGAACGATCACAAC+AGG + chr3.2:92363743-92363762 None:intergenic 45.0%
! AAACCTGCAGCTGTGGTTTT+GGG - chr3.2:92363517-92363536 MS.gene68806:intron 45.0%
! AGATGCTGGTGATGCATCAA+TGG - chr3.2:92363844-92363863 MS.gene68806:CDS 45.0%
! GAGGCAGAAGCTTGTTTCAA+AGG - chr3.2:92363545-92363564 MS.gene68806:intron 45.0%
! TAAACCTGCAGCTGTGGTTT+TGG - chr3.2:92363516-92363535 MS.gene68806:intron 45.0%
!! CACCTTGTTCATGCTGTTTC+TGG - chr3.2:92362545-92362564 MS.gene68806:intron 45.0%
!! TCATGCTGTTTCTGGTTGGT+TGG - chr3.2:92362553-92362572 MS.gene68806:intron 45.0%
!! AAAAAAAATAAAAATAAACA+TGG - chr3.2:92362879-92362898 MS.gene68806:intron 5.0%
ACAGTAGCTCGGATAGTGCA+AGG - chr3.2:92363454-92363473 MS.gene68806:CDS 50.0%
CACGGAGTTGTCCATTTAGG+TGG - chr3.2:92362935-92362954 MS.gene68806:intron 50.0%
CGACTTAACCCAGGGATTGA+TGG - chr3.2:92362736-92362755 MS.gene68806:CDS 50.0%
GAGGATTAAACCTGCAGCTG+TGG - chr3.2:92363510-92363529 MS.gene68806:intron 50.0%
GATGGAGAAATTAGCGGCTG+AGG - chr3.2:92362754-92362773 MS.gene68806:intron 50.0%
GCCTTCTTCAGTGTGCTACA+AGG - chr3.2:92363677-92363696 MS.gene68806:CDS 50.0%
GTGAGCGTGTGTGTGTGTAT+GGG - chr3.2:92363567-92363586 MS.gene68806:intron 50.0%
! AGTGTGCTACAAGGAAGCGT+CGG - chr3.2:92363686-92363705 MS.gene68806:CDS 50.0%
!! AACCTGCAGCTGTGGTTTTG+GGG - chr3.2:92363518-92363537 MS.gene68806:intron 50.0%
!! CAACAGGTGCTGCTTTACAG+TGG + chr3.2:92363727-92363746 None:intergenic 50.0%
CCAGAGCTTGAGAGGGAAAC+AGG - chr3.2:92362413-92362432 MS.gene68806:intron 55.0%
CCTGTTTCCCTCTCAAGCTC+TGG + chr3.2:92362416-92362435 None:intergenic 55.0%
CGGATAGTGCAAGGTGATGC+AGG - chr3.2:92363463-92363482 MS.gene68806:CDS 55.0%
GCACCTGTTGTGATCGTTCC+TGG - chr3.2:92363737-92363756 MS.gene68806:CDS 55.0%
GGTGAGCGTGTGTGTGTGTA+TGG - chr3.2:92363566-92363585 MS.gene68806:intron 55.0%
! AGCTCTGGCTCAGGCACTAT+TGG + chr3.2:92362401-92362420 None:intergenic 55.0%
GCCTGAGCCAGAGCTTGAGA+GGG - chr3.2:92362406-92362425 MS.gene68806:intron 60.0%
GTCCCCAAAACCACAGCTGC+AGG + chr3.2:92363523-92363542 None:intergenic 60.0%
TGCCTGAGCCAGAGCTTGAG+AGG - chr3.2:92362405-92362424 MS.gene68806:intron 60.0%
! TCCCTCTCAAGCTCTGGCTC+AGG + chr3.2:92362410-92362429 None:intergenic 60.0%
!!! GCTGTGGTTTTGGGGACCAG+AGG - chr3.2:92363526-92363545 MS.gene68806:intron 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 92362332 92363871 92362332 ID=MS.gene68806
chr3.2 mRNA 92362332 92363871 92362332 ID=MS.gene68806.t1;Parent=MS.gene68806
chr3.2 exon 92363637 92363871 92363637 ID=MS.gene68806.t1.exon1;Parent=MS.gene68806.t1
chr3.2 CDS 92363637 92363871 92363637 ID=cds.MS.gene68806.t1;Parent=MS.gene68806.t1
chr3.2 exon 92363410 92363489 92363410 ID=MS.gene68806.t1.exon2;Parent=MS.gene68806.t1
chr3.2 CDS 92363410 92363489 92363410 ID=cds.MS.gene68806.t1;Parent=MS.gene68806.t1
chr3.2 exon 92362637 92362755 92362637 ID=MS.gene68806.t1.exon3;Parent=MS.gene68806.t1
chr3.2 CDS 92362637 92362755 92362637 ID=cds.MS.gene68806.t1;Parent=MS.gene68806.t1
chr3.2 exon 92362439 92362515 92362439 ID=MS.gene68806.t1.exon4;Parent=MS.gene68806.t1
chr3.2 CDS 92362439 92362515 92362439 ID=cds.MS.gene68806.t1;Parent=MS.gene68806.t1
chr3.2 exon 92362332 92362357 92362332 ID=MS.gene68806.t1.exon5;Parent=MS.gene68806.t1
chr3.2 CDS 92362332 92362357 92362332 ID=cds.MS.gene68806.t1;Parent=MS.gene68806.t1
Gene Sequence

>MS.gene68806

ATGGAGACAGTGATGGAAGATGTAGAAGAATACAACTACAGAGAAGTGAAGCTTCCTTCACTGATACCAATAGTGCCTGAGCCAGAGCTTGAGAGGGAAACAGGAGAAAGAAGAAGAGGAAGGGATATAGTATTAGCCATAGATCATGGTCCAAACAGTAAACATGCTTTTGATTGGGCTCTTATTCATCTATGCAGACTTGCTGATACCATCCACCTTGTTCATGCTGTTTCTGGTTGGTTGGCTCCTTCACTTTCTTAACTTCTCATATATTACTTTTTTAATTTATTTTGTTCCATATAAATTAATTGAAGTTTTTGTTTTTATGGATTTTTTTTTATTACTTTATGGATATTTATTTTGTTAATGAAATATTTTGCAGATGTGAAGAATCAAATTGTGTACGACTTAACCCAGGGATTGATGGAGAAATTAGCGGCTGAGGCTTTTGAAGTTGCAATGGTTAGTGTCTCTCCGTTTTCCTATTTACTTATGAAGTCCAATTTGAAAAATTATATAGGATAGAGTTAGAGTTGTTCAATTTGACAAAAAAAATAAAAATAAACATGGCTCCAAATCATTAACCACAATTTGTGTCCCATTCACGGAGTTGTCCATTTAGGTGGTAGTCAATCACATGTAAAAAAAACAATGGGGTTCAATAGCATAATTAAGTCAAGGGCATATCTTGAAATATTTAATGGAGGTCAAAGATACTAATTACGGTGGATTAGGGAAAAAAAGTTTAATCAACCATCATGGCTTACAAGTTGTTCAGTCACTTCATTTTTTAGATGATTAAGTTTTATATGAAGTCTGACGACTCATCCGTATAAAATCAACTTGTAATACAAGGAATGTCACTCTTTATAATCTGTTTACAAAACTTATTCTTTTTCAATGGGAGACTTGGAGTCCTTTACATGTATTAATAATCCCTTGCAGCATTTATTGATAACTTTGGTGCTTTATTAGTTGAATATGATGAATGCTAATTATTGTGAATTTATTTTTTTGGTTAACCTCTATTGTTTATCACTCATTACTACTCTATTTCCTGGCAAATTGGCAATCTATTCTTCCATTCTACTTATGATTAGTATGATGTGAAAACAGGTGAAAACAGTAGCTCGGATAGTGCAAGGTGATGCAGGAAAAGTAATTTGCAAGGAAGCAGAGAGGATTAAACCTGCAGCTGTGGTTTTGGGGACCAGAGGCAGAAGCTTGTTTCAAAGGTGAGCGTGTGTGTGTGTATGGGTGTACATTACATTCAATTCAATCCCTTTCTATATCTCGGCCATTCTCTACACACTGCAGTTATCCATTATTCTGTATATGTTTTTTTGCCTTCTTCAGTGTGCTACAAGGAAGCGTCGGTGAGTATTGCTTTCACCACTGTAAAGCAGCACCTGTTGTGATCGTTCCTGGAAAAGGTGTGCATTACTATTCTTTTTATCATTTTACTTTTACTCAAGTTTAGAATACTGAAGAAGTTTAGCTTCTTTGATTGACAGATGCTGGTGATGCATCAATGGTCTAA

Protein sequence

>MS.gene68806.t1

METVMEDVEEYNYREVKLPSLIPIVPEPELERETGERRRGRDIVLAIDHGPNSKHAFDWALIHLCRLADTIHLVHAVSDVKNQIVYDLTQGLMEKLAAEAFEVAMVKTVARIVQGDAGKVICKEAERIKPAAVVLGTRGRSLFQSVLQGSVGEYCFHHCKAAPVVIVPGKDAGDASMV