AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003011

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003011.t1 MTR_2g024380 41.311 305 45 4 1 171 165 469 1.17e-60 195
MS.gene003011.t1 MTR_2g024350 75.000 88 22 0 84 171 139 226 2.74e-41 138
MS.gene003011.t1 MTR_6g053200 45.455 88 48 0 84 171 448 535 5.48e-17 77.8
MS.gene003011.t1 MTR_8g069935 39.831 118 51 5 68 171 351 462 2.30e-15 73.2
MS.gene003011.t1 MTR_7g104980 51.136 88 42 1 84 171 128 214 4.16e-14 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAAATCCAGTTTCAGAATA+AGG 0.301581 2.2:+61739399 None:intergenic
CACTAAGCAAATCGAGAAAA+AGG 0.306867 2.2:-61740515 MS.gene003011:intron
TTCACATAACAACGAGATTA+TGG 0.316402 2.2:-61739478 MS.gene003011:CDS
AACTTGCCTTATTCTGAAAC+TGG 0.331215 2.2:-61739405 MS.gene003011:CDS
ATCAATGCATGCAACAGGTT+TGG 0.338091 2.2:+61740584 None:intergenic
GAGTGTTAGGAAATTAAAAT+TGG 0.348469 2.2:+61740656 None:intergenic
TCAATGCATGCAACAGGTTT+GGG 0.360204 2.2:+61740585 None:intergenic
TTGGTCAGATGATTACTTAA+TGG 0.368705 2.2:-61739328 MS.gene003011:CDS
GTTGTTGTTCCGCGAGTGTT+AGG 0.379748 2.2:+61740643 None:intergenic
GATTTGCTTAGTGCAATTGA+TGG 0.391574 2.2:+61740525 None:intergenic
ATCCACAAATGTTAGAAACT+TGG 0.408052 2.2:-61739502 MS.gene003011:CDS
GTGATATCAATGCATGCAAC+AGG 0.433021 2.2:+61740579 None:intergenic
GACCCAGCTTCTTCGACAAC+GGG 0.441727 2.2:+61739525 None:intergenic
ACCCAAGTTTCTAACATTTG+TGG 0.449992 2.2:+61739500 None:intergenic
TCCACAAATGTTAGAAACTT+GGG 0.479230 2.2:-61739501 MS.gene003011:CDS
TTACCCGTTGTCGAAGAAGC+TGG 0.488577 2.2:-61739528 MS.gene003011:CDS
GTTAGGAAATTAAAATTGGT+GGG 0.494516 2.2:+61740660 None:intergenic
AGCAATGCTCAAGTTGTTGT+CGG 0.499521 2.2:-61739435 MS.gene003011:CDS
ATGGACTTCAACCGCCTCAA+TGG 0.514519 2.2:-61739309 MS.gene003011:CDS
TGTTAGGAAATTAAAATTGG+TGG 0.530065 2.2:+61740659 None:intergenic
TGATAACAAACATAACAGCT+TGG 0.533538 2.2:-61739347 MS.gene003011:CDS
AGATTGTCCAGCAAGAAGAA+AGG 0.551728 2.2:-61739782 MS.gene003011:intron
TACCCGTTGTCGAAGAAGCT+GGG 0.554513 2.2:-61739527 MS.gene003011:CDS
TGACCCAGCTTCTTCGACAA+CGG 0.566165 2.2:+61739524 None:intergenic
TTAGGAAATTAAAATTGGTG+GGG 0.575907 2.2:+61740661 None:intergenic
TTATTACAAATGTAGCACTT+TGG 0.580718 2.2:-61739806 MS.gene003011:CDS
ATGAACACTAGTGTTTGTCA+TGG 0.581670 2.2:+61740698 None:intergenic
GACTTCAACCGCCTCAATGG+TGG 0.595091 2.2:-61739306 MS.gene003011:CDS
AGAATAGAGCACCACCATTG+AGG 0.605565 2.2:+61739295 None:intergenic
ATAGAGCACCACCATTGAGG+CGG 0.679111 2.2:+61739298 None:intergenic
ACTTGAGCATTGCTACTCTG+TGG 0.710623 2.2:+61739444 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAATATATAAAATAAT+AGG + chr2.2:61739510-61739529 None:intergenic 0.0%
!! CTTAAAAAAGTTATTTATTA+GGG + chr2.2:61740063-61740082 None:intergenic 10.0%
!! TTAAAAAAGTTATTTATTAG+GGG + chr2.2:61740062-61740081 None:intergenic 10.0%
!! GCTTAAAAAAGTTATTTATT+AGG + chr2.2:61740064-61740083 None:intergenic 15.0%
!! TTCTAATTAAATTCAACATA+TGG - chr2.2:61739878-61739897 MS.gene003011:intron 15.0%
!! TTTAATAAGAATGTTGTTAT+TGG - chr2.2:61740301-61740320 MS.gene003011:intron 15.0%
!! ACAACATTCTTATTAAATGT+TGG + chr2.2:61740298-61740317 None:intergenic 20.0%
!! ACTTATATTGTGATATATGA+AGG - chr2.2:61740253-61740272 MS.gene003011:intron 20.0%
!! TAAAGGAAGTAAAAACATAT+TGG + chr2.2:61740016-61740035 None:intergenic 20.0%
!! TAGAATTATATGCAATGAAT+AGG + chr2.2:61739863-61739882 None:intergenic 20.0%
! AACATATGGTATCTTAATCA+CGG - chr2.2:61739892-61739911 MS.gene003011:intron 25.0%
! ATAAATCCAGTTTCAGAATA+AGG + chr2.2:61740590-61740609 None:intergenic 25.0%
! CAGAAAACATAATAACCAAA+CGG - chr2.2:61739621-61739640 MS.gene003011:intron 25.0%
! GAAAAATATGGTACACTTAA+AGG + chr2.2:61740033-61740052 None:intergenic 25.0%
! GAGTGTTAGGAAATTAAAAT+TGG + chr2.2:61739333-61739352 None:intergenic 25.0%
! GTTAGGAAATTAAAATTGGT+GGG + chr2.2:61739329-61739348 None:intergenic 25.0%
! TATTCTTACGTAACTTAACT+CGG - chr2.2:61739565-61739584 MS.gene003011:intron 25.0%
! TGTTAGGAAATTAAAATTGG+TGG + chr2.2:61739330-61739349 None:intergenic 25.0%
! TTAGGAAATTAAAATTGGTG+GGG + chr2.2:61739328-61739347 None:intergenic 25.0%
! TTATTACAAATGTAGCACTT+TGG - chr2.2:61740180-61740199 MS.gene003011:intron 25.0%
!! AAATTTGTTTATGCTGAAAC+TGG - chr2.2:61740111-61740130 MS.gene003011:intron 25.0%
!! AATCAATGTTTAAAACTCGA+GGG + chr2.2:61739826-61739845 None:intergenic 25.0%
!! TGTTTTCTGTAAGAAAAGAA+AGG + chr2.2:61739610-61739629 None:intergenic 25.0%
!!! GAGTTTTAAACATTGATTGT+AGG - chr2.2:61739828-61739847 MS.gene003011:intron 25.0%
ATCCACAAATGTTAGAAACT+TGG - chr2.2:61740484-61740503 MS.gene003011:intron 30.0%
CTCTATAATAGTTCCATTTC+CGG + chr2.2:61740434-61740453 None:intergenic 30.0%
GTATGCATGATAAAAATGAG+CGG + chr2.2:61739435-61739454 None:intergenic 30.0%
TAGGGGCTTAAAGAAAAATA+TGG + chr2.2:61740045-61740064 None:intergenic 30.0%
TCCACAAATGTTAGAAACTT+GGG - chr2.2:61740485-61740504 MS.gene003011:intron 30.0%
TCTTTAATAAATGATGCTGC+AGG - chr2.2:61740155-61740174 MS.gene003011:intron 30.0%
TGATAACAAACATAACAGCT+TGG - chr2.2:61740639-61740658 MS.gene003011:CDS 30.0%
TTCACATAACAACGAGATTA+TGG - chr2.2:61740508-61740527 MS.gene003011:intron 30.0%
TTGGTCAGATGATTACTTAA+TGG - chr2.2:61740658-61740677 MS.gene003011:CDS 30.0%
! AAACATTGATTGTAGGCATT+GGG - chr2.2:61739835-61739854 MS.gene003011:intron 30.0%
! AAATTTAGGTTTGCCTAATG+TGG - chr2.2:61740337-61740356 MS.gene003011:intron 30.0%
! CAATCAATGTTTAAAACTCG+AGG + chr2.2:61739827-61739846 None:intergenic 30.0%
! TAAACATTGATTGTAGGCAT+TGG - chr2.2:61739834-61739853 MS.gene003011:intron 30.0%
! TCAGCATAAACAAATTTTGC+AGG + chr2.2:61740108-61740127 None:intergenic 30.0%
!!! TTTTAATTTCCTAACACTCG+CGG - chr2.2:61739334-61739353 MS.gene003011:CDS 30.0%
AACTACAACATCACCACATT+AGG + chr2.2:61740353-61740372 None:intergenic 35.0%
AATAGTTCCATTTCCGGATA+AGG + chr2.2:61740428-61740447 None:intergenic 35.0%
ACATAATAACCAAACGGCAT+TGG - chr2.2:61739627-61739646 MS.gene003011:intron 35.0%
ACCCAAGTTTCTAACATTTG+TGG + chr2.2:61740489-61740508 None:intergenic 35.0%
AGGCAAACCTAAATTTGTGA+TGG + chr2.2:61740333-61740352 None:intergenic 35.0%
ATAGTTCCATTTCCGGATAA+GGG + chr2.2:61740427-61740446 None:intergenic 35.0%
ATGGACAGAAACCCATTAAA+GGG - chr2.2:61739692-61739711 MS.gene003011:intron 35.0%
CACTAAGCAAATCGAGAAAA+AGG - chr2.2:61739471-61739490 MS.gene003011:CDS 35.0%
GATGTTGTAGTTTGATCATC+CGG - chr2.2:61740361-61740380 MS.gene003011:intron 35.0%
GGCAAACCTAAATTTGTGAT+GGG + chr2.2:61740332-61740351 None:intergenic 35.0%
TATGGACAGAAACCCATTAA+AGG - chr2.2:61739691-61739710 MS.gene003011:intron 35.0%
TCAATCAAACATCCCTTATC+CGG - chr2.2:61740412-61740431 MS.gene003011:intron 35.0%
TGATTGATCAACGAGAACAT+GGG + chr2.2:61740399-61740418 None:intergenic 35.0%
TTGATTGATCAACGAGAACA+TGG + chr2.2:61740400-61740419 None:intergenic 35.0%
TTTAAATGTGCAGCTCATTG+TGG + chr2.2:61739968-61739987 None:intergenic 35.0%
! AAACCTAAATTTGTGATGGG+AGG + chr2.2:61740329-61740348 None:intergenic 35.0%
! GATTTGCTTAGTGCAATTGA+TGG + chr2.2:61739464-61739483 None:intergenic 35.0%
! TTTTCTACCTTTCTTCTTGC+TGG + chr2.2:61740214-61740233 None:intergenic 35.0%
! TTTTGAATGTGTGTGAACCT+TGG + chr2.2:61739727-61739746 None:intergenic 35.0%
!! AACTTGCCTTATTCTGAAAC+TGG - chr2.2:61740581-61740600 MS.gene003011:CDS 35.0%
AAACATCCCTTATCCGGAAA+TGG - chr2.2:61740418-61740437 MS.gene003011:intron 40.0%
AGATTGTCCAGCAAGAAGAA+AGG - chr2.2:61740204-61740223 MS.gene003011:intron 40.0%
ATCAATGCATGCAACAGGTT+TGG + chr2.2:61739405-61739424 None:intergenic 40.0%
ATGAGCTTTCAAAAGACTCG+TGG - chr2.2:61739656-61739675 MS.gene003011:intron 40.0%
GCTCATTGTGGATAATTGAG+TGG + chr2.2:61739956-61739975 None:intergenic 40.0%
GTACCTCCCATCACAAATTT+AGG - chr2.2:61740323-61740342 MS.gene003011:intron 40.0%
GTGATATCAATGCATGCAAC+AGG + chr2.2:61739410-61739429 None:intergenic 40.0%
TCAATGCATGCAACAGGTTT+GGG + chr2.2:61739404-61739423 None:intergenic 40.0%
TGAGCTTTCAAAAGACTCGT+GGG - chr2.2:61739657-61739676 MS.gene003011:intron 40.0%
! AGCAATGCTCAAGTTGTTGT+CGG - chr2.2:61740551-61740570 MS.gene003011:CDS 40.0%
! ATGTTTAAAACTCGAGGGTG+CGG + chr2.2:61739821-61739840 None:intergenic 40.0%
ATGTGTGTGAACCTTGGATG+TGG + chr2.2:61739721-61739740 None:intergenic 45.0%
GGATGTGGAGACCCTTTAAT+GGG + chr2.2:61739706-61739725 None:intergenic 45.0%
TCGTGGGCATGAAGGAAATA+TGG - chr2.2:61739673-61739692 MS.gene003011:intron 45.0%
TGGATGTGGAGACCCTTTAA+TGG + chr2.2:61739707-61739726 None:intergenic 45.0%
TTAAAGGGTCTCCACATCCA+AGG - chr2.2:61739707-61739726 MS.gene003011:intron 45.0%
! ACTTGAGCATTGCTACTCTG+TGG + chr2.2:61740545-61740564 None:intergenic 45.0%
! AGAATAGAGCACCACCATTG+AGG + chr2.2:61740694-61740713 None:intergenic 45.0%
!! AGGGTGCGGTTGTTTGTTTT+AGG + chr2.2:61739807-61739826 None:intergenic 45.0%
!! AAATAATATCAATTTATTAT+TGG - chr2.2:61739988-61740007 MS.gene003011:intron 5.0%
ATGGACTTCAACCGCCTCAA+TGG - chr2.2:61740677-61740696 MS.gene003011:CDS 50.0%
CAAAAGACTCGTGGGCATGA+AGG - chr2.2:61739665-61739684 MS.gene003011:intron 50.0%
CATAGCACACCAATGCCGTT+TGG + chr2.2:61739639-61739658 None:intergenic 50.0%
TACCCGTTGTCGAAGAAGCT+GGG - chr2.2:61740459-61740478 MS.gene003011:intron 50.0%
TGACCCAGCTTCTTCGACAA+CGG + chr2.2:61740465-61740484 None:intergenic 50.0%
TTACCCGTTGTCGAAGAAGC+TGG - chr2.2:61740458-61740477 MS.gene003011:intron 50.0%
! ATAGAGCACCACCATTGAGG+CGG + chr2.2:61740691-61740710 None:intergenic 50.0%
! GTTGTTGTTCCGCGAGTGTT+AGG + chr2.2:61739346-61739365 None:intergenic 50.0%
GACCCAGCTTCTTCGACAAC+GGG + chr2.2:61740464-61740483 None:intergenic 55.0%
GACTTCAACCGCCTCAATGG+TGG - chr2.2:61740680-61740699 MS.gene003011:CDS 55.0%
! ACATGGGCATTGCTGCTCTC+CGG + chr2.2:61740383-61740402 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 61739290 61740718 61739290 ID=MS.gene003011
chr2.2 mRNA 61739290 61740718 61739290 ID=MS.gene003011.t1;Parent=MS.gene003011
chr2.2 exon 61740516 61740718 61740516 ID=MS.gene003011.t1.exon1;Parent=MS.gene003011.t1
chr2.2 CDS 61740516 61740718 61740516 ID=cds.MS.gene003011.t1;Parent=MS.gene003011.t1
chr2.2 exon 61739783 61739831 61739783 ID=MS.gene003011.t1.exon2;Parent=MS.gene003011.t1
chr2.2 CDS 61739783 61739831 61739783 ID=cds.MS.gene003011.t1;Parent=MS.gene003011.t1
chr2.2 exon 61739290 61739556 61739290 ID=MS.gene003011.t1.exon3;Parent=MS.gene003011.t1
chr2.2 CDS 61739290 61739556 61739290 ID=cds.MS.gene003011.t1;Parent=MS.gene003011.t1
Gene Sequence

>MS.gene003011

ATGACAAACACTAGTGTTCATGAAATCAATCAATACCCCACCAATTTTAATTTCCTAACACTCGCGGAACAACAACTGATTCAACAAAACATCAACAATCAAGTGTCTGTTCCCAAACCTGTTGCATGCATTGATATCACAACCGCTCATTTTTATCATGCATACAAACATCCATCAATTGCACTAAGCAAATCGAGAAAAAGGTAAAGTATTTATTCCTATTATTTTATATATTTTAATTATAAATCAATTTTATCATGTCAAAATATTGAAAATATTCTTACGTAACTTAACTCGGTTGAACTAAAATCATTTTACCTTTCTTTTCTTACAGAAAACATAATAACCAAACGGCATTGGTGTGCTATGAGCTTTCAAAAGACTCGTGGGCATGAAGGAAATATGGACAGAAACCCATTAAAGGGTCTCCACATCCAAGGTTCACACACATTCAAAACTCTATCTTTAACATATTTCTCATTTCTTTCACATTAAAAACAATATAGTTTTGTTACCTAAAACAAACAACCGCACCCTCGAGTTTTAAACATTGATTGTAGGCATTGGGATCCTATTCATTGCATATAATTCTAATTAAATTCAACATATGGTATCTTAATCACGGCTGCGTTTGTGTTTCAAATTTGAAAACATCAAACATTGCCACTCAATTATCCACAATGAGCTGCACATTTAAAAAATAATATCAATTTATTATTGGTTCCAATATGTTTTTACTTCCTTTAAGTGTACCATATTTTTCTTTAAGCCCCTAATAAATAACTTTTTTAAGCATCGCAAATATTGTTGTAGCTCCTGCAAAATTTGTTTATGCTGAAACTGGTCTATGAATTATTATTTTTATTCTTTAATAAATGATGCTGCAGGAGTTATTACAAATGTAGCACTTTGGCAGATTGTCCAGCAAGAAGAAAGGTAGAAAAAAGCAAAACTCAAGAGAAGACTTATATTGTGATATATGAAGGAGAGCACAATCACGCAAAACCAACATTTAATAAGAATGTTGTTATTGGTACCTCCCATCACAAATTTAGGTTTGCCTAATGTGGTGATGTTGTAGTTTGATCATCCGGAGAGCAGCAATGCCCATGTTCTCGTTGATCAATCAAACATCCCTTATCCGGAAATGGAACTATTATAGAGTCAATTACCCGTTGTCGAAGAAGCTGGGTCATCCACAAATGTTAGAAACTTGGGTTCACATAACAACGAGATTATGGAGTTTGATGAGCCACAGAGTAGCAATGCTCAAGTTGTTGTCGGTGACTCAAACTTGCCTTATTCTGAAACTGGATTTATTAGAAGCTTTGATGATGATGACAATATTTTGATAACAAACATAACAGCTTGGTCAGATGATTACTTAATGGACTTCAACCGCCTCAATGGTGGTGCTCTATTCTCTTAG
Protein sequence

>MS.gene003011.t1

MTNTSVHEINQYPTNFNFLTLAEQQLIQQNINNQVSVPKPVACIDITTAHFYHAYKHPSIALSKSRKRSYYKCSTLADCPARRKSQLPVVEEAGSSTNVRNLGSHNNEIMEFDEPQSSNAQVVVGDSNLPYSETGFIRSFDDDDNILITNITAWSDDYLMDFNRLNGGALFS