AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030307

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030307.t1 MTR_6g090515 96.335 191 7 0 1 191 30 220 1.69e-130 365
MS.gene030307.t1 MTR_8g102030 85.864 191 25 2 1 191 34 222 1.34e-93 272
MS.gene030307.t1 MTR_8g102020 72.775 191 35 2 1 191 32 205 1.37e-71 216
MS.gene030307.t1 MTR_1g090490 30.000 180 107 4 4 165 36 214 3.34e-13 65.9
MS.gene030307.t1 MTR_1g090490 30.000 180 107 4 4 165 36 214 3.43e-13 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030307.t1 AT2G19830 83.854 192 23 3 1 191 10 194 1.71e-97 281
MS.gene030307.t1 AT2G19830 83.854 192 23 3 1 191 29 213 3.00e-97 281
MS.gene030307.t1 AT4G29160 86.667 180 23 1 13 191 13 192 3.21e-96 277
MS.gene030307.t1 AT4G29160 86.667 180 23 1 13 191 40 219 1.03e-95 277
MS.gene030307.t1 AT4G29160 86.667 180 23 1 13 191 40 219 1.03e-95 277
MS.gene030307.t1 AT5G04850 30.935 139 88 1 10 140 35 173 3.02e-12 63.5
MS.gene030307.t1 AT3G10640 30.220 182 101 4 10 165 35 216 1.01e-11 62.0
MS.gene030307.t1 AT3G10640 30.488 164 93 4 33 175 1 164 6.22e-11 58.9
MS.gene030307.t1 AT5G09260 31.250 144 94 2 15 157 41 180 8.70e-11 59.3

Find 43 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAGAAATGCTTGAGAAAA+AGG 0.221659 6.2:-88733254 None:intergenic
TCCTCAGGAGTCGGCTTTGC+AGG 0.229972 6.2:+88731924 None:intergenic
AGATGAATTGGCAGCTTTGC+AGG 0.277136 6.2:-88731901 MS.gene030307:CDS
TTGAATCTGCTTCATGTTCT+CGG 0.295683 6.2:+88732625 None:intergenic
GGAAAATGTACTCCTTAAAA+AGG 0.296574 6.2:-88733233 MS.gene030307:CDS
CACCAAAAGAAAGAACAAAA+AGG 0.308755 6.2:-88733179 MS.gene030307:CDS
GGAAGCAGAACTTGAAGAAT+TGG 0.338385 6.2:-88732045 MS.gene030307:CDS
CCCACAGTGCATGTCCCAGC+TGG 0.344057 6.2:-88731969 MS.gene030307:CDS
CGTGCAGGTTGCCTCCCAGC+TGG 0.353565 6.2:+88731954 None:intergenic
GGAGTCGGCTTTGCAGGAAC+AGG 0.397015 6.2:+88731930 None:intergenic
GACTCCTGAGGAAGATGAAT+TGG 0.412289 6.2:-88731913 MS.gene030307:CDS
TTGTTCTTTACAGGACGAAT+TGG 0.437007 6.2:-88732066 MS.gene030307:intron
GGAGCAGGAGCTGTAGTTGC+TGG 0.442696 6.2:+88731990 None:intergenic
AAATCAGCAGCTGCACCAAT+TGG 0.448641 6.2:+88732587 None:intergenic
TAATAGATGATAATGTTAGA+AGG 0.453601 6.2:-88732879 MS.gene030307:intron
CCAGTTGCGTATTCATGACC+AGG 0.454482 6.2:-88732986 MS.gene030307:intron
CCAGCTGGGACATGCACTGT+GGG 0.462898 6.2:+88731969 None:intergenic
GCAGATTCAAGAAGCATTGT+CGG 0.464581 6.2:-88732612 MS.gene030307:CDS
AGAATTGGAGAGTGCTGAGT+TGG 0.466125 6.2:-88732030 MS.gene030307:CDS
ACGGTAGATGCGTTAAGAAC+AGG 0.469044 6.2:-88732837 MS.gene030307:CDS
TTCAATGTTTGAAGAGGAAG+AGG 0.475427 6.2:-88733044 MS.gene030307:CDS
TGCTAAAGCCACCACGGAAA+CGG 0.478535 6.2:-88732856 MS.gene030307:CDS
CCTGGTCATGAATACGCAAC+TGG 0.481018 6.2:+88732986 None:intergenic
GGGACATGCACTGTGGGAGC+AGG 0.482842 6.2:+88731975 None:intergenic
GAAGCATTGTCGGCTCCAAT+TGG 0.484568 6.2:-88732602 MS.gene030307:CDS
CGCATCTACCGTTTCCGTGG+TGG 0.487516 6.2:+88732848 None:intergenic
GGCAGCTTTGCAGGCTGAGA+TGG 0.492052 6.2:-88731892 MS.gene030307:CDS
TTTGCAGGAACAGGGCGTGC+AGG 0.497715 6.2:+88731939 None:intergenic
CTGTTCATTTATCTCGTCCA+TGG 0.501356 6.2:+88732649 None:intergenic
CCACAGTGCATGTCCCAGCT+GGG 0.512082 6.2:-88731968 MS.gene030307:CDS
GCTGCCAATTCATCTTCCTC+AGG 0.526016 6.2:+88731909 None:intergenic
AATTCATCTTCCTCAGGAGT+CGG 0.548839 6.2:+88731915 None:intergenic
GTGCAGGTTGCCTCCCAGCT+GGG 0.551247 6.2:+88731955 None:intergenic
CGGCAATTCAATGTTTGAAG+AGG 0.561917 6.2:-88733050 MS.gene030307:CDS
CCCAGCTGGGACATGCACTG+TGG 0.570484 6.2:+88731968 None:intergenic
AACAGGAGCAGCTACTATGA+AGG 0.577122 6.2:-88732820 MS.gene030307:CDS
TAACGCATCTACCGTTTCCG+TGG 0.584559 6.2:+88732845 None:intergenic
GAACAACAAGTTGAGCAGCT+TGG 0.596454 6.2:-88733015 MS.gene030307:CDS
GAGTCGGCTTTGCAGGAACA+GGG 0.596697 6.2:+88731931 None:intergenic
TCCTGCAAAGCCGACTCCTG+AGG 0.597589 6.2:-88731925 MS.gene030307:CDS
TGATGACGTCGACAAGACCA+TGG 0.612646 6.2:-88732666 MS.gene030307:CDS
CAGTGCATGTCCCAGCTGGG+AGG 0.671305 6.2:-88731965 MS.gene030307:CDS
AGAAGGTGCTAAAGCCACCA+CGG 0.700426 6.2:-88732862 MS.gene030307:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGCTTATTTATTTATGT+TGG - chr6.2:88732585-88732604 MS.gene030307:CDS 15.0%
!! ATGATTTATTTAATTGAGTT+TGG - chr6.2:88732418-88732437 MS.gene030307:intron 15.0%
!!! TCATTTTCTTAAAATATGAT+TGG + chr6.2:88732919-88732938 None:intergenic 15.0%
!! TTGATTACGTAAAAAAAATG+AGG + chr6.2:88732761-88732780 None:intergenic 20.0%
!!! CTTTTCACTTAATTTTGTTT+TGG - chr6.2:88732809-88732828 MS.gene030307:CDS 20.0%
!!! TAATAGATGATAATGTTAGA+AGG - chr6.2:88732252-88732271 MS.gene030307:intron 20.0%
!!! TTTAGTATTAGTTTAGACAA+TGG - chr6.2:88732184-88732203 MS.gene030307:intron 20.0%
! AATAAATTCAGAATGCTACA+CGG + chr6.2:88733047-88733066 None:intergenic 25.0%
! ACCAAAAGAAAGAACAAAAA+GGG - chr6.2:88731953-88731972 MS.gene030307:CDS 25.0%
! ATATACAAAACACTAATGCA+TGG - chr6.2:88732890-88732909 MS.gene030307:intron 25.0%
! CTGAATTTATTGTTCTTTAC+AGG - chr6.2:88733056-88733075 MS.gene030307:intron 25.0%
! TTCTAATTTCACTTAATCCA+TGG - chr6.2:88732029-88732048 MS.gene030307:CDS 25.0%
! TTTGTATATAAGTACTACTC+TGG + chr6.2:88732879-88732898 None:intergenic 25.0%
!! GTTTGATTATTTGTACCTTT+TGG - chr6.2:88732621-88732640 MS.gene030307:CDS 25.0%
AAAGAAAGAACAAAAAGGGT+AGG - chr6.2:88731957-88731976 MS.gene030307:CDS 30.0%
CACCAAAAGAAAGAACAAAA+AGG - chr6.2:88731952-88731971 MS.gene030307:CDS 30.0%
CTACTCTGGACTTAAAATAT+AGG + chr6.2:88732865-88732884 None:intergenic 30.0%
GGAAAATGTACTCCTTAAAA+AGG - chr6.2:88731898-88731917 MS.gene030307:CDS 30.0%
TTCAGACAGATTACGAAAAA+TGG - chr6.2:88732731-88732750 MS.gene030307:intron 30.0%
TTGAATGTAACCACATGTAT+CGG - chr6.2:88732944-88732963 MS.gene030307:intron 30.0%
! ACCCTTTTTGTTCTTTCTTT+TGG + chr6.2:88731957-88731976 None:intergenic 30.0%
!! CTTTCTTTTGGTGTATTCTT+TGG + chr6.2:88731945-88731964 None:intergenic 30.0%
!!! TGATTTTTTGTTTTACGCAG+CGG - chr6.2:88732061-88732080 MS.gene030307:intron 30.0%
AAAAATCAAGTCACGTTCCA+TGG + chr6.2:88732049-88732068 None:intergenic 35.0%
CTTCAGATTGAACACATGTT+CGG + chr6.2:88732991-88733010 None:intergenic 35.0%
TTCAATGTTTGAAGAGGAAG+AGG - chr6.2:88732087-88732106 MS.gene030307:intron 35.0%
TTGAATCTGCTTCATGTTCT+CGG + chr6.2:88732509-88732528 None:intergenic 35.0%
TTGTTCTTTACAGGACGAAT+TGG - chr6.2:88733065-88733084 MS.gene030307:intron 35.0%
! AAACTCTGAAGAACAAGTAG+AGG + chr6.2:88732002-88732021 None:intergenic 35.0%
! ATGTGTTCAATCTGAAGTGT+TGG - chr6.2:88732994-88733013 MS.gene030307:CDS 35.0%
! TAATCTTCTTTTGCGTCTTC+TGG - chr6.2:88732217-88732236 MS.gene030307:intron 35.0%
!! TTGGTTCTGTTTCTTTCTAC+AGG - chr6.2:88732437-88732456 MS.gene030307:intron 35.0%
AATACAACTGTGTTCACACC+TGG + chr6.2:88732166-88732185 None:intergenic 40.0%
AATTCATCTTCCTCAGGAGT+CGG + chr6.2:88733219-88733238 None:intergenic 40.0%
AGTGCTGTACAATACTCTCT+CGG - chr6.2:88732652-88732671 MS.gene030307:CDS 40.0%
CAGCACTATACACAACCAAA+AGG + chr6.2:88732639-88732658 None:intergenic 40.0%
CGGCAATTCAATGTTTGAAG+AGG - chr6.2:88732081-88732100 MS.gene030307:intron 40.0%
CTGTTCATTTATCTCGTCCA+TGG + chr6.2:88732485-88732504 None:intergenic 40.0%
GGAAGCAGAACTTGAAGAAT+TGG - chr6.2:88733086-88733105 MS.gene030307:intron 40.0%
TGTACTCCTTAAAAAGGCCA+CGG - chr6.2:88731904-88731923 MS.gene030307:CDS 40.0%
!! GCAGATTCAAGAAGCATTGT+CGG - chr6.2:88732519-88732538 MS.gene030307:intron 40.0%
!! TGTTCAATCTGAAGTGTTGG+TGG - chr6.2:88732997-88733016 MS.gene030307:CDS 40.0%
AAATCAGCAGCTGCACCAAT+TGG + chr6.2:88732547-88732566 None:intergenic 45.0%
AACAGGAGCAGCTACTATGA+AGG - chr6.2:88732311-88732330 MS.gene030307:intron 45.0%
ACGGTAGATGCGTTAAGAAC+AGG - chr6.2:88732294-88732313 MS.gene030307:intron 45.0%
AGATGAATTGGCAGCTTTGC+AGG - chr6.2:88733230-88733249 MS.gene030307:CDS 45.0%
GACTCCTGAGGAAGATGAAT+TGG - chr6.2:88733218-88733237 MS.gene030307:CDS 45.0%
GTGCTGTACAATACTCTCTC+GGG - chr6.2:88732653-88732672 MS.gene030307:CDS 45.0%
! GAACAACAAGTTGAGCAGCT+TGG - chr6.2:88732116-88732135 MS.gene030307:intron 45.0%
! TCTTCTTTTGCGTCTTCTGG+TGG - chr6.2:88732220-88732239 MS.gene030307:intron 45.0%
!! AAGTGTTGGTGGTGCTACAT+TGG - chr6.2:88733008-88733027 MS.gene030307:CDS 45.0%
!! AGAATTGGAGAGTGCTGAGT+TGG - chr6.2:88733101-88733120 MS.gene030307:intron 45.0%
!! CAATACAGTGCCGATACATG+TGG + chr6.2:88732957-88732976 None:intergenic 45.0%
ATCGGCACTGTATTGCGTGT+CGG - chr6.2:88732962-88732981 MS.gene030307:intron 50.0%
CCAGTTGCGTATTCATGACC+AGG - chr6.2:88732145-88732164 MS.gene030307:intron 50.0%
CCTGGTCATGAATACGCAAC+TGG + chr6.2:88732148-88732167 None:intergenic 50.0%
GCTGCCAATTCATCTTCCTC+AGG + chr6.2:88733225-88733244 None:intergenic 50.0%
TAACGCATCTACCGTTTCCG+TGG + chr6.2:88732289-88732308 None:intergenic 50.0%
TGCTAAAGCCACCACGGAAA+CGG - chr6.2:88732275-88732294 MS.gene030307:intron 50.0%
! CTTCTGCCGTGGCCTTTTTA+AGG + chr6.2:88731913-88731932 None:intergenic 50.0%
! TCTTTTGCGTCTTCTGGTGG+TGG - chr6.2:88732223-88732242 MS.gene030307:intron 50.0%
! TGATGACGTCGACAAGACCA+TGG - chr6.2:88732465-88732484 MS.gene030307:intron 50.0%
!! AGAAGGTGCTAAAGCCACCA+CGG - chr6.2:88732269-88732288 MS.gene030307:intron 50.0%
!! GAAGCATTGTCGGCTCCAAT+TGG - chr6.2:88732529-88732548 MS.gene030307:intron 50.0%
!! TGTTGGTGGTGCTACATTGG+TGG - chr6.2:88733011-88733030 MS.gene030307:CDS 50.0%
!!! GGCTTTTTCAACTTCTGCCG+TGG + chr6.2:88731924-88731943 None:intergenic 50.0%
!!! TGCAGCTGCTGATTTTGACG+AGG - chr6.2:88732552-88732571 MS.gene030307:intron 50.0%
! GAGTCGGCTTTGCAGGAACA+GGG + chr6.2:88733203-88733222 None:intergenic 55.0%
CCACAGTGCATGTCCCAGCT+GGG - chr6.2:88733163-88733182 MS.gene030307:intron 60.0%
CCAGCTGGGACATGCACTGT+GGG + chr6.2:88733165-88733184 None:intergenic 60.0%
CGCATCTACCGTTTCCGTGG+TGG + chr6.2:88732286-88732305 None:intergenic 60.0%
GGAGCAGGAGCTGTAGTTGC+TGG + chr6.2:88733144-88733163 None:intergenic 60.0%
GGCAGCTTTGCAGGCTGAGA+TGG - chr6.2:88733239-88733258 MS.gene030307:CDS 60.0%
TTTGCAGGAACAGGGCGTGC+AGG + chr6.2:88733195-88733214 None:intergenic 60.0%
! GGAGTCGGCTTTGCAGGAAC+AGG + chr6.2:88733204-88733223 None:intergenic 60.0%
! TCCTCAGGAGTCGGCTTTGC+AGG + chr6.2:88733210-88733229 None:intergenic 60.0%
! TCCTGCAAAGCCGACTCCTG+AGG - chr6.2:88733206-88733225 MS.gene030307:CDS 60.0%
CAGTGCATGTCCCAGCTGGG+AGG - chr6.2:88733166-88733185 MS.gene030307:intron 65.0%
CCCACAGTGCATGTCCCAGC+TGG - chr6.2:88733162-88733181 MS.gene030307:intron 65.0%
CCCAGCTGGGACATGCACTG+TGG + chr6.2:88733166-88733185 None:intergenic 65.0%
GGGACATGCACTGTGGGAGC+AGG + chr6.2:88733159-88733178 None:intergenic 65.0%
GTGCAGGTTGCCTCCCAGCT+GGG + chr6.2:88733179-88733198 None:intergenic 65.0%
CGTGCAGGTTGCCTCCCAGC+TGG + chr6.2:88733180-88733199 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 88731884 88733269 88731884 ID=MS.gene030307
chr6.2 mRNA 88731884 88733269 88731884 ID=MS.gene030307.t1;Parent=MS.gene030307
chr6.2 exon 88733179 88733269 88733179 ID=MS.gene030307.t1.exon1;Parent=MS.gene030307.t1
chr6.2 CDS 88733179 88733269 88733179 ID=cds.MS.gene030307.t1;Parent=MS.gene030307.t1
chr6.2 exon 88732987 88733072 88732987 ID=MS.gene030307.t1.exon2;Parent=MS.gene030307.t1
chr6.2 CDS 88732987 88733072 88732987 ID=cds.MS.gene030307.t1;Parent=MS.gene030307.t1
chr6.2 exon 88732804 88732895 88732804 ID=MS.gene030307.t1.exon3;Parent=MS.gene030307.t1
chr6.2 CDS 88732804 88732895 88732804 ID=cds.MS.gene030307.t1;Parent=MS.gene030307.t1
chr6.2 exon 88732580 88732694 88732580 ID=MS.gene030307.t1.exon4;Parent=MS.gene030307.t1
chr6.2 CDS 88732580 88732694 88732580 ID=cds.MS.gene030307.t1;Parent=MS.gene030307.t1
chr6.2 exon 88731884 88732075 88731884 ID=MS.gene030307.t1.exon5;Parent=MS.gene030307.t1
chr6.2 CDS 88731884 88732075 88731884 ID=cds.MS.gene030307.t1;Parent=MS.gene030307.t1
Gene Sequence

>MS.gene030307

ATGCTTGAGAAAAAGGAAAATGTACTCCTTAAAAAGGCCACGGCAGAAGTTGAAAAAGCCAAAGAATACACCAAAAGAAAGAACAAAAAGGGTAGGTTGCTAGCTTAACTGAACTCCTCTACTTGTTCTTCAGAGTTTTCTGTAATTCTAATTTCACTTAATCCATGGAACGTGACTTGATTTTTTGTTTTACGCAGCGGCAATTCAATGTTTGAAGAGGAAGAGGTTATATGAACAACAAGTTGAGCAGCTTGGTAATTTCCAGTTGCGTATTCATGACCAGGTGTGAACACAGTTGTATTTAGTATTAGTTTAGACAATGGTTTAGAATATTAATCTTCTTTTGCGTCTTCTGGTGGTGGTTTTTGTAATAGATGATAATGTTAGAAGGTGCTAAAGCCACCACGGAAACGGTAGATGCGTTAAGAACAGGAGCAGCTACTATGAAGGCTATGCAGAAAGCAACGTATGTATTGCTATTATATACGATATATGATTCTAAGTCTTCAACAATCGAGCTGTTGATTATGATTTATGATTTATTTAATTGAGTTTGGTTCTGTTTCTTTCTACAGGAATATTGATGACGTCGACAAGACCATGGACGAGATAAATGAACAGACCGAGAACATGAAGCAGATTCAAGAAGCATTGTCGGCTCCAATTGGTGCAGCTGCTGATTTTGACGAGGTTATTCTCTCAAATGCTTATTTATTTATGTTGGTTGAAAACACAATGTTTGATTATTTGTACCTTTTGGTTGTGTATAGTGCTGTACAATACTCTCTCGGGACTCAATTATAAAGCAAAAAAAAAATATAATAAAAAATAATAAAAAAATACTAATTTCAGACAGATTACGAAAAATGGTTAACCTCATTTTTTTTACGTAATCAAAAAAAATACTCTCTTTTCTAAATACTCTCTTTTCACTTAATTTTGTTTTGGAACATAATTAATTGAATTAGTTAGATTTTGCCTATATTTTAAGTCCAGAGTAGTACTTATATACAAAACACTAATGCATGGACACCAATCATATTTTAAGAAAATGAAGTGATTGAATGTAACCACATGTATCGGCACTGTATTGCGTGTCGGACTCCGAACATGTGTTCAATCTGAAGTGTTGGTGGTGCTACATTGGTGGTAATGTATTTCCGTGTAGCATTCTGAATTTATTGTTCTTTACAGGACGAATTGGAAGCAGAACTTGAAGAATTGGAGAGTGCTGAGTTGGAAGAACAGCTTCTTCAGCCAGCAACTACAGCTCCTGCTCCCACAGTGCATGTCCCAGCTGGGAGGCAACCTGCACGCCCTGTTCCTGCAAAGCCGACTCCTGAGGAAGATGAATTGGCAGCTTTGCAGGCTGAGATGGCACTTTGA
Protein sequence

>MS.gene030307.t1

MLEKKENVLLKKATAEVEKAKEYTKRKNKKAAIQCLKRKRLYEQQVEQLGNFQLRIHDQMIMLEGAKATTETVDALRTGAATMKAMQKATNIDDVDKTMDEINEQTENMKQIQEALSAPIGAAADFDEDELEAELEELESAELEEQLLQPATTAPAPTVHVPAGRQPARPVPAKPTPEEDELAALQAEMAL