AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35329

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35329.t1 MTR_2g084510 68.116 138 39 1 28 165 110 242 7.77e-58 181
MS.gene35329.t1 MTR_2g084510 93.220 59 4 0 4 62 1 59 2.26e-36 126
MS.gene35329.t1 MTR_2g084525 72.662 139 33 1 27 165 110 243 1.23e-47 155
MS.gene35329.t1 MTR_2g084525 88.333 60 7 0 3 62 1 60 4.72e-35 123
MS.gene35329.t1 MTR_2g060500 74.194 62 16 0 1 62 5 66 3.41e-29 105
MS.gene35329.t1 MTR_2g060540 74.194 62 16 0 1 62 5 66 3.90e-29 105
MS.gene35329.t1 MTR_2g084495 74.576 59 15 0 3 61 1 59 5.86e-28 104
MS.gene35329.t1 MTR_2g084495 48.485 132 51 4 38 165 112 230 7.38e-21 85.9
MS.gene35329.t1 MTR_2g083710 65.574 61 21 0 1 61 1 61 1.90e-24 90.5
MS.gene35329.t1 MTR_1g062160 30.288 208 94 9 1 164 1 201 2.08e-15 70.9
MS.gene35329.t1 MTR_7g102790 29.048 210 95 9 1 164 1 202 9.79e-13 63.9
MS.gene35329.t1 MTR_4g078170 28.205 195 101 7 7 164 16 208 1.47e-12 63.5
MS.gene35329.t1 MTR_5g007230 27.041 196 95 8 7 164 22 207 9.54e-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.gene35329.t1 AT1G43000 34.000 100 59 4 2 101 5 97 4.77e-12 62.0
MS.gene35329.t1 AT1G43000 26.027 219 99 9 2 164 12 223 4.79e-12 62.4

Find 20 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATTTCTTCCATCTCTTT+AGG 0.173263 2.1:-17066872 None:intergenic
CCATTTCTTCCATCTCTTTA+GGG 0.175139 2.1:-17066871 None:intergenic
AAGAATGCTTTCTCTGTCTT+TGG 0.205190 2.1:-17067044 None:intergenic
CAAAGATCATCAAGTAATTC+AGG 0.304180 2.1:+17066143 MS.gene35329:CDS
CCCTAAAGAGATGGAAGAAA+TGG 0.314047 2.1:+17066871 MS.gene35329:CDS
TCTATACAAGATTCACATAA+TGG 0.352887 2.1:-17066111 None:intergenic
ACCTTGGCTTGTAAACTTGC+TGG 0.395128 2.1:+17065999 MS.gene35329:CDS
TTAGAAGACGCGAGAATTGA+TGG 0.420130 2.1:+17066977 MS.gene35329:CDS
AAAGAAAGGGAATAGCTCAT+AGG 0.424904 2.1:+17067110 MS.gene35329:CDS
AGACAGAGAAAGCATTCTTC+CGG 0.471091 2.1:+17067048 MS.gene35329:CDS
GAAGCCGGTGAACGATTAAC+CGG 0.479886 2.1:-17067067 None:intergenic
AAGAAAGGGAATAGCTCATA+GGG 0.490291 2.1:+17067111 MS.gene35329:CDS
CGCGAGAATTGATGGGAAAG+AGG 0.502155 2.1:+17066985 MS.gene35329:CDS
GCCAGCAAGTTTACAAGCCA+AGG 0.514131 2.1:-17066000 None:intergenic
AATTGATGGGAAAGAGGATG+AGG 0.516719 2.1:+17066991 MS.gene35329:CDS
AGGATATGATGTGTGTACCT+TGG 0.542052 2.1:+17065983 MS.gene35329:intron
ATATCTAGAGCAATCAATCA+AGG 0.554194 2.1:+17066898 MS.gene35329:CDS
TTTGGCTTGCGAAGTGAAGC+CGG 0.566900 2.1:-17067082 None:intergenic
TCTTCCGGTTAATCGTTCAC+CGG 0.571810 2.1:+17067063 MS.gene35329:CDS
TAGAAGACGCGAGAATTGAT+GGG 0.574916 2.1:+17066978 MS.gene35329:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATAAAAAAAAATATAAT+AGG - chr2.1:17066589-17066608 None:intergenic 0.0%
!!! ATTTTTAAATTTTGTTTCTT+AGG + chr2.1:17065963-17065982 MS.gene35329:intron 10.0%
!! AGAAAAAAATACAAAGAATT+AGG - chr2.1:17065936-17065955 None:intergenic 15.0%
!! ATAATATTTCGTAATGATCT+AGG + chr2.1:17066198-17066217 MS.gene35329:intron 20.0%
!! CTTTGATTAACCTTAAAAAA+AGG - chr2.1:17067139-17067158 None:intergenic 20.0%
!! GCTTGACATTATAATTAAAA+TGG - chr2.1:17065914-17065933 None:intergenic 20.0%
!!! ATTTTGTCTGCAATATTTTT+TGG - chr2.1:17066945-17066964 None:intergenic 20.0%
!!! TCCTTTTATTACTATTAATC+CGG + chr2.1:17066667-17066686 MS.gene35329:intron 20.0%
! AAGCCAAATTCAAAAAGAAA+GGG + chr2.1:17067097-17067116 MS.gene35329:CDS 25.0%
! GAGATGTGATATATATCTTA+TGG + chr2.1:17066516-17066535 MS.gene35329:intron 25.0%
! TAGTGAAATTTACAAACTTG+TGG + chr2.1:17066374-17066393 MS.gene35329:intron 25.0%
! TCCGGATTAATAGTAATAAA+AGG - chr2.1:17066671-17066690 None:intergenic 25.0%
! TCTATACAAGATTCACATAA+TGG - chr2.1:17066114-17066133 None:intergenic 25.0%
! TTGCAATGATATATCAGATA+AGG + chr2.1:17066322-17066341 MS.gene35329:intron 25.0%
! TTTGCGTTTATAAAAAAGGA+TGG + chr2.1:17066833-17066852 MS.gene35329:CDS 25.0%
!! ATTCCCTTTCTTTTTGAATT+TGG - chr2.1:17067103-17067122 None:intergenic 25.0%
ACTAGAGCTATTAATGACAT+AGG - chr2.1:17066418-17066437 None:intergenic 30.0%
ACTATTAATCCGGAGATTAA+AGG + chr2.1:17066677-17066696 MS.gene35329:intron 30.0%
AGGTTCAACATTGGAAAAAT+CGG + chr2.1:17066469-17066488 MS.gene35329:intron 30.0%
ATCAACGTAAGTACAATAAC+CGG - chr2.1:17066754-17066773 None:intergenic 30.0%
CAAAGATCATCAAGTAATTC+AGG + chr2.1:17066143-17066162 MS.gene35329:CDS 30.0%
CAAGCCAAATTCAAAAAGAA+AGG + chr2.1:17067096-17067115 MS.gene35329:CDS 30.0%
CAATGATATATCAGATAAGG+AGG + chr2.1:17066325-17066344 MS.gene35329:intron 30.0%
CCAGTTTGCGTTTATAAAAA+AGG + chr2.1:17066829-17066848 MS.gene35329:intron 30.0%
GTAGAAAAAGAAATGGAAGA+AGG + chr2.1:17067019-17067038 MS.gene35329:CDS 30.0%
! ACTTTTCTTTCAACCATTAC+CGG + chr2.1:17066724-17066743 MS.gene35329:intron 30.0%
! ATATCTAGAGCAATCAATCA+AGG + chr2.1:17066898-17066917 MS.gene35329:CDS 30.0%
! TTTTGTAAACCCTAAAGAGA+TGG + chr2.1:17066862-17066881 MS.gene35329:CDS 30.0%
!! TTTTTGGCCTTCTCTTTTTT+AGG - chr2.1:17066929-17066948 None:intergenic 30.0%
!!! CCTTTTTTATAAACGCAAAC+TGG - chr2.1:17066832-17066851 None:intergenic 30.0%
!!! CTCTACTTATTTTTGCTCTT+TGG + chr2.1:17066540-17066559 MS.gene35329:intron 30.0%
AAAGAAAGGGAATAGCTCAT+AGG + chr2.1:17067110-17067129 MS.gene35329:CDS 35.0%
AAGAAAGGGAATAGCTCATA+GGG + chr2.1:17067111-17067130 MS.gene35329:CDS 35.0%
AAGAATGCTTTCTCTGTCTT+TGG - chr2.1:17067047-17067066 None:intergenic 35.0%
AAGTACAATAACCGGTATTC+CGG - chr2.1:17066746-17066765 None:intergenic 35.0%
CATTACATGCCTTTAATCTC+CGG - chr2.1:17066689-17066708 None:intergenic 35.0%
CCATTTCTTCCATCTCTTTA+GGG - chr2.1:17066874-17066893 None:intergenic 35.0%
CTAACAAGTCGAAAAATGAG+CGG + chr2.1:17066058-17066077 MS.gene35329:CDS 35.0%
GCGTTTATAAAAAAGGATGG+AGG + chr2.1:17066836-17066855 MS.gene35329:CDS 35.0%
GGAAGACGTAGAAAAAGAAA+TGG + chr2.1:17067012-17067031 MS.gene35329:CDS 35.0%
TACAAACTTGTGGATATCCT+CGG + chr2.1:17066384-17066403 MS.gene35329:intron 35.0%
TCCATTTCTTCCATCTCTTT+AGG - chr2.1:17066875-17066894 None:intergenic 35.0%
!!! TCATAGGGCACCTTTTTTTA+AGG + chr2.1:17067126-17067145 MS.gene35329:CDS 35.0%
AAACAAGAGAGCTCAGTAAG+AGG + chr2.1:17066449-17066468 MS.gene35329:intron 40.0%
AATAACCGGTATTCCGGTAA+TGG - chr2.1:17066740-17066759 None:intergenic 40.0%
AATTGATGGGAAAGAGGATG+AGG + chr2.1:17066991-17067010 MS.gene35329:CDS 40.0%
AGGATATGATGTGTGTACCT+TGG + chr2.1:17065983-17066002 MS.gene35329:intron 40.0%
CCCTAAAGAGATGGAAGAAA+TGG + chr2.1:17066871-17066890 MS.gene35329:CDS 40.0%
CTCAGTAAGAGGTTCAACAT+TGG + chr2.1:17066460-17066479 MS.gene35329:intron 40.0%
TAGAAGACGCGAGAATTGAT+GGG + chr2.1:17066978-17066997 MS.gene35329:CDS 40.0%
TGACATAGGTTTGAATTCCG+AGG - chr2.1:17066404-17066423 None:intergenic 40.0%
TGGAAAAATCGGTCACAGTA+GGG + chr2.1:17066480-17066499 MS.gene35329:intron 40.0%
TTAGAAGACGCGAGAATTGA+TGG + chr2.1:17066977-17066996 MS.gene35329:CDS 40.0%
TTCAACCATTACCGGAATAC+CGG + chr2.1:17066732-17066751 MS.gene35329:intron 40.0%
TTGGAAAAATCGGTCACAGT+AGG + chr2.1:17066479-17066498 MS.gene35329:intron 40.0%
! CGGAGATTAAAGGCATGTAA+TGG + chr2.1:17066687-17066706 MS.gene35329:intron 40.0%
! TGGCATGCAAGGTGAATTTT+TGG + chr2.1:17066560-17066579 MS.gene35329:intron 40.0%
! TTTTTGCTCTTTGGCATGCA+AGG + chr2.1:17066549-17066568 MS.gene35329:intron 40.0%
!! AGACAGAGAAAGCATTCTTC+CGG + chr2.1:17067048-17067067 MS.gene35329:CDS 40.0%
!! CGCTCATTTTTCGACTTGTT+AGG - chr2.1:17066060-17066079 None:intergenic 40.0%
GGAAAAATCGGTCACAGTAG+GGG + chr2.1:17066481-17066500 MS.gene35329:intron 45.0%
GGCATCGCCTAAAAAAGAGA+AGG + chr2.1:17066919-17066938 MS.gene35329:CDS 45.0%
TCTTCCGGTTAATCGTTCAC+CGG + chr2.1:17067063-17067082 MS.gene35329:CDS 45.0%
!! ACCTTGGCTTGTAAACTTGC+TGG + chr2.1:17065999-17066018 MS.gene35329:CDS 45.0%
!!! TTTTTATATTATGTTTTAAA+CGG + chr2.1:17066599-17066618 MS.gene35329:intron 5.0%
CGCGAGAATTGATGGGAAAG+AGG + chr2.1:17066985-17067004 MS.gene35329:CDS 50.0%
GAAGCCGGTGAACGATTAAC+CGG - chr2.1:17067070-17067089 None:intergenic 50.0%
GCCAGCAAGTTTACAAGCCA+AGG - chr2.1:17066003-17066022 None:intergenic 50.0%
!! TTTGGCTTGCGAAGTGAAGC+CGG - chr2.1:17067085-17067104 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 17065897 17067165 17065897 ID=MS.gene35329
chr2.1 mRNA 17065897 17067165 17065897 ID=MS.gene35329.t1;Parent=MS.gene35329
chr2.1 exon 17065897 17065899 17065897 ID=MS.gene35329.t1.exon1;Parent=MS.gene35329.t1
chr2.1 CDS 17065897 17065899 17065897 ID=cds.MS.gene35329.t1;Parent=MS.gene35329.t1
chr2.1 exon 17065985 17066164 17065985 ID=MS.gene35329.t1.exon2;Parent=MS.gene35329.t1
chr2.1 CDS 17065985 17066164 17065985 ID=cds.MS.gene35329.t1;Parent=MS.gene35329.t1
chr2.1 exon 17066833 17067165 17066833 ID=MS.gene35329.t1.exon3;Parent=MS.gene35329.t1
chr2.1 CDS 17066833 17067165 17066833 ID=cds.MS.gene35329.t1;Parent=MS.gene35329.t1
Gene Sequence

>MS.gene35329

ATGGTAATATCTATCCATTTTAATTATAATGTCAAGCCTAATTCTTTGTATTTTTTTCTTAATGCAATTTTTAAATTTTGTTTCTTAGGATATGATGTGTGTACCTTGGCTTGTAAACTTGCTGGCAATCACTTCATTTTTCGCAACATGTGAAACTCATCCTAACAAGTCGAAAAATGAGCGGAACAAGTTCTGTCTCGACTGCAATGAAAATCCATTATGTGAATCTTGTATAGAATCTCGTCACAAAGATCATCAAGTAATTCAGGTGAGTGTTGTTTAATTTGATTACTAGATCTGTATAATATTTCGTAATGATCTAGGTATCTGTGCTATATCTCTTTCTCTTCGATTTGTTTTTGTTACACTTGAGCAATTTTAATTAATTTTTTTTTACTATGTTATGTAAATATGAACTCTTATATTTGCAATGATATATCAGATAAGGAGGTCATCATATAATGAAGTAGTGAAGACTAGTGAAATTTACAAACTTGTGGATATCCTCGGAATTCAAACCTATGTCATTAATAGCTCTAGTGTTGTATACTTAAACAAGAGAGCTCAGTAAGAGGTTCAACATTGGAAAAATCGGTCACAGTAGGGGCTCTTTTTGTAAGAGATGTGATATATATCTTATGGACTCTACTTATTTTTGCTCTTTGGCATGCAAGGTGAATTTTTGGTCTCCTATTATATTTTTTTTTATATTATGTTTTAAACGGTAAAAAATAGTTCAATATATGAAAAACTAGTATATTTTATTCTACTCCTTTTATTACTATTAATCCGGAGATTAAAGGCATGTAATGGATATTATAACTTATACTTTTCTTTCAACCATTACCGGAATACCGGTTATTGTACTTACGTTGATTTTGTTTTCTTTTTGAAAGAATGATTAATTAATGTTGTATTGTATGTATATGATACCAGTTTGCGTTTATAAAAAAGGATGGAGGCTTTTTTGTAAACCCTAAAGAGATGGAAGAAATGGAAAGATATCTAGAGCAATCAATCAAGGCATCGCCTAAAAAAGAGAAGGCCAAAAAATATTGCAGACAAAATCTGAAACGAAAATTAGAAGACGCGAGAATTGATGGGAAAGAGGATGAGGAAGACGTAGAAAAAGAAATGGAAGAAGGCGCCAAAGACAGAGAAAGCATTCTTCCGGTTAATCGTTCACCGGCTTCACTTCGCAAGCCAAATTCAAAAAGAAAGGGAATAGCTCATAGGGCACCTTTTTTTAAGGTTAATCAAAGACTATGA
Protein sequence

>MS.gene35329.t1

MDMMCVPWLVNLLAITSFFATCETHPNKSKNERNKFCLDCNENPLCESCIESRHKDHQVIQFAFIKKDGGFFVNPKEMEEMERYLEQSIKASPKKEKAKKYCRQNLKRKLEDARIDGKEDEEDVEKEMEEGAKDRESILPVNRSPASLRKPNSKRKGIAHRAPFFKVNQRL