AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene30431

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30431.t1 MTR_7g050670 90.604 298 28 0 1 298 1 298 0.0 561
MS.gene30431.t1 MTR_7g076570 68.456 298 92 1 1 298 29 324 3.26e-140 408
MS.gene30431.t1 MTR_7g076760 66.000 300 100 1 1 298 1 300 1.28e-139 406
MS.gene30431.t1 MTR_4g088845 66.779 298 99 0 1 298 1 298 7.99e-138 401
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30431.t1 AT1G61330 29.749 279 191 4 24 298 15 292 2.26e-30 121
MS.gene30431.t1 AT1G61320 26.351 296 213 5 7 298 9 303 9.82e-29 117

Find 62 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTCTTTCCTCAAGTAAT+TGG 0.148637 7.3:-53612916 None:intergenic
ACTACCAGAGGAAGCAATTT+TGG 0.163512 7.3:-53612939 None:intergenic
CCGATATAGCCAACAAAATT+TGG 0.166151 7.3:+53613102 MS.gene30431:CDS
TTCTCTTTCCTCAAGTAATT+GGG 0.333664 7.3:-53612915 None:intergenic
TCTCCTTTCACCAGGTTCTC+TGG 0.337812 7.3:+53614273 MS.gene30431:intron
TTTCCTCAAGTAATTGGGTT+TGG 0.353663 7.3:-53612910 None:intergenic
CCTTGAGCAATTCGAACAAT+TGG 0.372454 7.3:-53613634 None:intergenic
CACTTGGAACATCTGGCAAC+TGG 0.398110 7.3:-53613360 None:intergenic
GCTTGGTCGCCGCCGATGGA+TGG 0.400376 7.3:-53614104 None:intergenic
TGCAAACCACTTGGAACATC+TGG 0.406207 7.3:-53613367 None:intergenic
CAGTTACATATCAATCCTGT+TGG 0.415520 7.3:+53613181 MS.gene30431:CDS
GTTATAATTGCATGTTTGAT+TGG 0.417480 7.3:-53613001 None:intergenic
AATCGATTGTTGTGAGGACT+TGG 0.438503 7.3:+53613555 MS.gene30431:CDS
AGCAAAACTTCAATCCCAAC+AGG 0.438662 7.3:-53613196 None:intergenic
CATTTATTCAATTCGCATGA+AGG 0.441661 7.3:+53613139 MS.gene30431:CDS
CTGCAACAACCGTGTCTCCT+AGG 0.455321 7.3:+53613023 MS.gene30431:CDS
CTTGGTCGCCGCCGATGGAT+GGG 0.463021 7.3:-53614103 None:intergenic
CAAACACGGATGTGCGGTAG+AGG 0.463363 7.3:-53614319 None:intergenic
AGTCTCTATCAAACAAGAAT+CGG 0.472631 7.3:-53613072 None:intergenic
CCAATTGTTCGAATTGCTCA+AGG 0.473509 7.3:+53613634 MS.gene30431:CDS
TTGGTCGCCGCCGATGGATG+GGG 0.474116 7.3:-53614102 None:intergenic
GAACCCAAAATTGCTTCCTC+TGG 0.478922 7.3:+53612935 MS.gene30431:CDS
TGCAAAAGTTGCAAACCACT+TGG 0.484261 7.3:-53613376 None:intergenic
AGTTACATATCAATCCTGTT+GGG 0.495020 7.3:+53613182 MS.gene30431:CDS
AGATGCTTGGTCGCCGCCGA+TGG 0.496481 7.3:-53614108 None:intergenic
CTCAATAAGTTGAGGTGTAG+TGG 0.510982 7.3:-53613764 None:intergenic
CGACAAACCAACGCAAAAGA+AGG 0.512803 7.3:-53614244 None:intergenic
TCAGAGATGGCTGCAGCCGA+TGG 0.516857 7.3:-53614155 None:intergenic
AGGTTCTCTGGATTCTTCAT+CGG 0.520483 7.3:+53614285 MS.gene30431:intron
CACTACACCTCAACTTATTG+AGG 0.526106 7.3:+53613765 MS.gene30431:CDS
GTAGTGCGCAAAAGTGTTGT+TGG 0.526510 7.3:-53614180 None:intergenic
TTCCTCTGGTAGTCTTTCTG+AGG 0.527967 7.3:+53612949 MS.gene30431:CDS
CACATCACTGAAGAAATGTC+TGG 0.537374 7.3:+53613421 MS.gene30431:CDS
CTCCTAGGTACAAAAGATCA+TGG 0.540463 7.3:+53613038 MS.gene30431:CDS
AGATGGCTGCAGCCGATGGG+TGG 0.548816 7.3:-53614151 None:intergenic
CAGACATTTCTTCAGTGATG+TGG 0.565836 7.3:-53613420 None:intergenic
CAGAGATGGCTGCAGCCGAT+GGG 0.575565 7.3:-53614154 None:intergenic
GGTGGAGTGTGAAGAGGAGA+TGG 0.575913 7.3:-53614133 None:intergenic
AGGAACAGAGATGGCTGCGG+CGG 0.577022 7.3:-53614221 None:intergenic
CAGAGATGGCTGCGGCGGAG+TGG 0.577597 7.3:-53614216 None:intergenic
CAATTGTTCGAATTGCTCAA+GGG 0.587482 7.3:+53613635 MS.gene30431:CDS
ATGCACTAACAAGGATCTAG+AGG 0.591437 7.3:+53613237 MS.gene30431:CDS
CAAACCAACGCAAAAGAAGG+AGG 0.596357 7.3:-53614241 None:intergenic
TGGTCGCCGCCGATGGATGG+GGG 0.598864 7.3:-53614101 None:intergenic
ATTCAATTGTGAAACCAGGT+TGG 0.602985 7.3:-53613279 None:intergenic
TTTGAGAATCGATTGTTGTG+AGG 0.603428 7.3:+53613549 MS.gene30431:CDS
CCGATGGGTGGAGTGTGAAG+AGG 0.604359 7.3:-53614139 None:intergenic
AGAGGAGATGGTGAGATGCT+TGG 0.609134 7.3:-53614121 None:intergenic
AAACCAAACCCAATTACTTG+AGG 0.614535 7.3:+53612907 MS.gene30431:CDS
GTAAATTCAATTGTGAAACC+AGG 0.629720 7.3:-53613283 None:intergenic
GCGGTGGTGATGATGATAAG+AGG 0.633081 7.3:-53614069 None:intergenic
CAGTTGCCAGATGTTCCAAG+TGG 0.634968 7.3:+53613361 MS.gene30431:CDS
ATCCTCAGAAAGACTACCAG+AGG 0.635655 7.3:-53612951 None:intergenic
CCTCTTCACACTCCACCCAT+CGG 0.639955 7.3:+53614139 MS.gene30431:CDS
AGGAGGAACAGAGATGGCTG+CGG 0.642938 7.3:-53614224 None:intergenic
ATATATACCTCAATAAGTTG+AGG 0.643108 7.3:-53613772 None:intergenic
AGTGTTGTTGGAATCAGAGA+TGG 0.654556 7.3:-53614168 None:intergenic
AAAAGAAGGAGGAACAGAGA+TGG 0.659532 7.3:-53614230 None:intergenic
CTTAATCAAACACGGATGTG+CGG 0.661449 7.3:-53614325 None:intergenic
GTTGCAAATATGCACTAACA+AGG 0.665849 7.3:+53613228 MS.gene30431:CDS
GGATGTGCGGTAGAGGACGA+AGG 0.696996 7.3:-53614312 None:intergenic
AAACAATCCTTAATCAAACA+CGG 0.698099 7.3:-53614333 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATAAATGCATATAGATT+TGG - chr7.3:53613912-53613931 None:intergenic 15.0%
!! CAATTTAAAAACACTAAAAT+TGG + chr7.3:53613324-53613343 MS.gene30431:CDS 15.0%
!! ATAGATATATTGCATGATAT+AGG - chr7.3:53613874-53613893 None:intergenic 20.0%
! ATATATACCTCAATAAGTTG+AGG - chr7.3:53613775-53613794 None:intergenic 25.0%
! GTTATAATTGCATGTTTGAT+TGG - chr7.3:53613004-53613023 None:intergenic 25.0%
! TAAAAAATTGAACGAAGAGT+TGG - chr7.3:53613601-53613620 None:intergenic 25.0%
!!! CTTCGTTCAATTTTTTATCA+TGG + chr7.3:53613604-53613623 MS.gene30431:CDS 25.0%
AGTCTCTATCAAACAAGAAT+CGG - chr7.3:53613075-53613094 None:intergenic 30.0%
AGTTACATATCAATCCTGTT+GGG + chr7.3:53613182-53613201 MS.gene30431:CDS 30.0%
CATTTATTCAATTCGCATGA+AGG + chr7.3:53613139-53613158 MS.gene30431:CDS 30.0%
GTAAATTCAATTGTGAAACC+AGG - chr7.3:53613286-53613305 None:intergenic 30.0%
TTCTCTTTCCTCAAGTAATT+GGG - chr7.3:53612918-53612937 None:intergenic 30.0%
! GATTGCATGTATTCTTTTGA+TGG - chr7.3:53613694-53613713 None:intergenic 30.0%
! TTGAAGTTTTGCTTAAGAGA+TGG + chr7.3:53613206-53613225 MS.gene30431:CDS 30.0%
!! CCAAATTTTGTTGGCTATAT+CGG - chr7.3:53613105-53613124 None:intergenic 30.0%
!!! TTGGGTTTGGTTTTCAAAAT+TGG - chr7.3:53612900-53612919 None:intergenic 30.0%
AAACCAAACCCAATTACTTG+AGG + chr7.3:53612907-53612926 MS.gene30431:CDS 35.0%
AAGGAGTGAGAATTGATCAA+AGG - chr7.3:53613956-53613975 None:intergenic 35.0%
ATTCAATTGTGAAACCAGGT+TGG - chr7.3:53613282-53613301 None:intergenic 35.0%
CAATTGTTCGAATTGCTCAA+GGG + chr7.3:53613635-53613654 MS.gene30431:CDS 35.0%
CAGTTACATATCAATCCTGT+TGG + chr7.3:53613181-53613200 MS.gene30431:CDS 35.0%
CCGATATAGCCAACAAAATT+TGG + chr7.3:53613102-53613121 MS.gene30431:CDS 35.0%
GTTCTCTTTCCTCAAGTAAT+TGG - chr7.3:53612919-53612938 None:intergenic 35.0%
GTTGCAAATATGCACTAACA+AGG + chr7.3:53613228-53613247 MS.gene30431:CDS 35.0%
TTTCCTCAAGTAATTGGGTT+TGG - chr7.3:53612913-53612932 None:intergenic 35.0%
TTTGAGAATCGATTGTTGTG+AGG + chr7.3:53613549-53613568 MS.gene30431:CDS 35.0%
! CTATTGCAGCCAAATTTTGT+TGG - chr7.3:53613114-53613133 None:intergenic 35.0%
AAAAGAAGGAGGAACAGAGA+TGG - chr7.3:53614233-53614252 None:intergenic 40.0%
AATCGATTGTTGTGAGGACT+TGG + chr7.3:53613555-53613574 MS.gene30431:CDS 40.0%
AGCAAAACTTCAATCCCAAC+AGG - chr7.3:53613199-53613218 None:intergenic 40.0%
AGGTTCTCTGGATTCTTCAT+CGG + chr7.3:53614285-53614304 MS.gene30431:intron 40.0%
ATGCACTAACAAGGATCTAG+AGG + chr7.3:53613237-53613256 MS.gene30431:CDS 40.0%
CACATCACTGAAGAAATGTC+TGG + chr7.3:53613421-53613440 MS.gene30431:CDS 40.0%
CACTACACCTCAACTTATTG+AGG + chr7.3:53613765-53613784 MS.gene30431:CDS 40.0%
CAGACATTTCTTCAGTGATG+TGG - chr7.3:53613423-53613442 None:intergenic 40.0%
CCAATTGTTCGAATTGCTCA+AGG + chr7.3:53613634-53613653 MS.gene30431:CDS 40.0%
CCTTGAGCAATTCGAACAAT+TGG - chr7.3:53613637-53613656 None:intergenic 40.0%
CTCCTAGGTACAAAAGATCA+TGG + chr7.3:53613038-53613057 MS.gene30431:CDS 40.0%
TGCAAAAGTTGCAAACCACT+TGG - chr7.3:53613379-53613398 None:intergenic 40.0%
! ACTACCAGAGGAAGCAATTT+TGG - chr7.3:53612942-53612961 None:intergenic 40.0%
! AGTGTTGTTGGAATCAGAGA+TGG - chr7.3:53614171-53614190 None:intergenic 40.0%
! CACCATGATCTTTTGTACCT+AGG - chr7.3:53613043-53613062 None:intergenic 40.0%
! CTACCAGAGGAAGCAATTTT+GGG - chr7.3:53612941-53612960 None:intergenic 40.0%
! CTCAATAAGTTGAGGTGTAG+TGG - chr7.3:53613767-53613786 None:intergenic 40.0%
! GAGATGACTTTTTACCAACC+TGG + chr7.3:53613265-53613284 MS.gene30431:CDS 40.0%
! TCTTTTGTACCTAGGAGACA+CGG - chr7.3:53613035-53613054 None:intergenic 40.0%
!! AAGAAACGCGAGCTTGTTTT+GGG - chr7.3:53614043-53614062 None:intergenic 40.0%
AACGCGTGTGTTGTGTTTCA+AGG - chr7.3:53613975-53613994 None:intergenic 45.0%
AATCCAGAGAACCTGGTGAA+AGG - chr7.3:53614279-53614298 None:intergenic 45.0%
ATCCTCAGAAAGACTACCAG+AGG - chr7.3:53612954-53612973 None:intergenic 45.0%
CAAACCAACGCAAAAGAAGG+AGG - chr7.3:53614244-53614263 None:intergenic 45.0%
CGACAAACCAACGCAAAAGA+AGG - chr7.3:53614247-53614266 None:intergenic 45.0%
GAACCCAAAATTGCTTCCTC+TGG + chr7.3:53612935-53612954 MS.gene30431:CDS 45.0%
GATGAAGAATCCAGAGAACC+TGG - chr7.3:53614286-53614305 None:intergenic 45.0%
TGCAAACCACTTGGAACATC+TGG - chr7.3:53613370-53613389 None:intergenic 45.0%
TTCCTCTGGTAGTCTTTCTG+AGG + chr7.3:53612949-53612968 MS.gene30431:CDS 45.0%
! TGTTCCTCCTTCTTTTGCGT+TGG + chr7.3:53614237-53614256 MS.gene30431:CDS 45.0%
!! GAAGAAACGCGAGCTTGTTT+TGG - chr7.3:53614044-53614063 None:intergenic 45.0%
!! GTAGTGCGCAAAAGTGTTGT+TGG - chr7.3:53614183-53614202 None:intergenic 45.0%
AGAGGAGATGGTGAGATGCT+TGG - chr7.3:53614124-53614143 None:intergenic 50.0%
CACTTGGAACATCTGGCAAC+TGG - chr7.3:53613363-53613382 None:intergenic 50.0%
CAGTTGCCAGATGTTCCAAG+TGG + chr7.3:53613361-53613380 MS.gene30431:CDS 50.0%
CGTGTATCTCTCCTTTCACC+AGG + chr7.3:53614265-53614284 MS.gene30431:intron 50.0%
TCTCCTTTCACCAGGTTCTC+TGG + chr7.3:53614273-53614292 MS.gene30431:intron 50.0%
! GCGGTGGTGATGATGATAAG+AGG - chr7.3:53614072-53614091 None:intergenic 50.0%
AGGAGGAACAGAGATGGCTG+CGG - chr7.3:53614227-53614246 None:intergenic 55.0%
CAAACACGGATGTGCGGTAG+AGG - chr7.3:53614322-53614341 None:intergenic 55.0%
CCTCTTCACACTCCACCCAT+CGG + chr7.3:53614139-53614158 MS.gene30431:CDS 55.0%
CTGCAACAACCGTGTCTCCT+AGG + chr7.3:53613023-53613042 MS.gene30431:CDS 55.0%
GGTGGAGTGTGAAGAGGAGA+TGG - chr7.3:53614136-53614155 None:intergenic 55.0%
! GCGGAGTGGTTTTCGGTGAA+TGG - chr7.3:53614205-53614224 None:intergenic 55.0%
AGGAACAGAGATGGCTGCGG+CGG - chr7.3:53614224-53614243 None:intergenic 60.0%
CAACCCTCTCCCCCATCCAT+CGG + chr7.3:53614092-53614111 MS.gene30431:CDS 60.0%
CAGAGATGGCTGCAGCCGAT+GGG - chr7.3:53614157-53614176 None:intergenic 60.0%
CCGATGGGTGGAGTGTGAAG+AGG - chr7.3:53614142-53614161 None:intergenic 60.0%
GGATGTGCGGTAGAGGACGA+AGG - chr7.3:53614315-53614334 None:intergenic 60.0%
TCAGAGATGGCTGCAGCCGA+TGG - chr7.3:53614158-53614177 None:intergenic 60.0%
AGATGCTTGGTCGCCGCCGA+TGG - chr7.3:53614111-53614130 None:intergenic 65.0%
AGATGGCTGCAGCCGATGGG+TGG - chr7.3:53614154-53614173 None:intergenic 65.0%
CGATGGATGGGGGAGAGGGT+TGG - chr7.3:53614094-53614113 None:intergenic 65.0%
CTTGGTCGCCGCCGATGGAT+GGG - chr7.3:53614106-53614125 None:intergenic 65.0%
TGGATGGGGGAGAGGGTTGG+CGG - chr7.3:53614091-53614110 None:intergenic 65.0%
TTGGTCGCCGCCGATGGATG+GGG - chr7.3:53614105-53614124 None:intergenic 65.0%
! GGCTGCGGCGGAGTGGTTTT+CGG - chr7.3:53614212-53614231 None:intergenic 65.0%
CAGAGATGGCTGCGGCGGAG+TGG - chr7.3:53614219-53614238 None:intergenic 70.0%
CCCTCTCCCCCATCCATCGG+CGG + chr7.3:53614095-53614114 MS.gene30431:CDS 70.0%
CCGCCGATGGATGGGGGAGA+GGG - chr7.3:53614098-53614117 None:intergenic 70.0%
GCTTGGTCGCCGCCGATGGA+TGG - chr7.3:53614107-53614126 None:intergenic 70.0%
TGGTCGCCGCCGATGGATGG+GGG - chr7.3:53614104-53614123 None:intergenic 70.0%
! ATGGGGGAGAGGGTTGGCGG+TGG - chr7.3:53614088-53614107 None:intergenic 70.0%
GCCGCCGATGGATGGGGGAG+AGG - chr7.3:53614099-53614118 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 53612893 53614342 53612893 ID=MS.gene30431
chr7.3 mRNA 53612893 53614342 53612893 ID=MS.gene30431.t1;Parent=MS.gene30431
chr7.3 exon 53612893 53613786 53612893 ID=MS.gene30431.t1.exon1;Parent=MS.gene30431.t1
chr7.3 CDS 53612893 53613786 53612893 ID=cds.MS.gene30431.t1;Parent=MS.gene30431.t1
chr7.3 exon 53614051 53614258 53614051 ID=MS.gene30431.t1.exon2;Parent=MS.gene30431.t1
chr7.3 CDS 53614051 53614258 53614051 ID=cds.MS.gene30431.t1;Parent=MS.gene30431.t1
chr7.3 exon 53614287 53614342 53614287 ID=MS.gene30431.t1.exon3;Parent=MS.gene30431.t1
chr7.3 CDS 53614287 53614342 53614287 ID=cds.MS.gene30431.t1;Parent=MS.gene30431.t1
Gene Sequence

>MS.gene30431

ATGGCCAATTTTGAAAACCAAACCCAATTACTTGAGGAAAGAGAACCCAAAATTGCTTCCTCTGGTAGTCTTTCTGAGGATATGATTCAAATCATTTTCACTTTTTTACCAATCAAACATGCAATTATAACTGCAACAACCGTGTCTCCTAGGTACAAAAGATCATGGTGTCATAATCGCCGATTCTTGTTTGATAGAGACTTATGTTTCCGATATAGCCAACAAAATTTGGCTGCAATAGTTGATCATTTATTCAATTCGCATGAAGGTGACGAAATTAAAACGTTTCAGTTACATATCAATCCTGTTGGGATTGAAGTTTTGCTTAAGAGATGGTTGCAAATATGCACTAACAAGGATCTAGAGGATCTTGAGATGACTTTTTACCAACCTGGTTTCACAATTGAATTTACTGTTTTTAACGCACTGCACAATTTAAAAACACTAAAATTGGCTCAATGTGTGATCCAGTTGCCAGATGTTCCAAGTGGTTTGCAACTTTTGCAAAAGCTAAAGCTAGCTAACATCCACATCACTGAAGAAATGTCTGGTATGTTGATTGAGCATTGTAAGATGCTTGAAATGATTGTTTTAATTAATTGCTCTACAATTAAGAAATTGAAATTAATTGCTAGACAAAATAAATATTTCAAAAATTTGAGAATCGATTGTTGTGAGGACTTGGAAGAGATTGAAATCGATTCACCAACTCTTCGTTCAATTTTTTATCATGGAAAATTTCCAATTGTTCGAATTGCTCAAGGGATGCAATTGTACGATGCTTTCTTTCGCTTTACACCATCAAAAGAATACATGCAATCTACTCAGCTAGAAGCTCTTGCTAAAGATTTCTCACATGTCAGCATTCTCACCACTACACCTCAACTTATTGAGGTATATATATAAACAAGCATATGCTTATTCTTATTTATTTACATTTCACTATTTACTATTTTATTTAATTACTTACAAACTACTCCTATATCATGCAATATATCTATATACATTTTTTTTGACCAAATCTATATGCATTTATTATTATTATTTGAATTTATTGATGCCTTTGATCAATTCTCACTCCTTGAAACACAACACACGCGTTGATCAATTCTCACTCCTTGAAACACAACACACGCGTTTCTTCTTTCCCAAAACAAGCTCGCGTTTCTTCTTCTTCCTCTTATCATCATCACCACCGCCAACCCTCTCCCCCATCCATCGGCGGCGACCAAGCATCTCACCATCTCCTCTTCACACTCCACCCATCGGCTGCAGCCATCTCTGATTCCAACAACACTTTTGCGCACTACCATTCACCGAAAACCACTCCGCCGCAGCCATCTCTGTTCCTCCTTCTTTTGCGTTGGTTTGTCGTGTATCTCTCCTTTCACCAGGTTCTCTGGATTCTTCATCGGAACGCCTTCGTCCTCTACCGCACATCCGTGTTTGA
Protein sequence

>MS.gene30431.t1

MANFENQTQLLEEREPKIASSGSLSEDMIQIIFTFLPIKHAIITATTVSPRYKRSWCHNRRFLFDRDLCFRYSQQNLAAIVDHLFNSHEGDEIKTFQLHINPVGIEVLLKRWLQICTNKDLEDLEMTFYQPGFTIEFTVFNALHNLKTLKLAQCVIQLPDVPSGLQLLQKLKLANIHITEEMSGMLIEHCKMLEMIVLINCSTIKKLKLIARQNKYFKNLRIDCCEDLEEIEIDSPTLRSIFYHGKFPIVRIAQGMQLYDAFFRFTPSKEYMQSTQLEALAKDFSHVSILTTTPQLIELAFLLLPLIIITTANPLPHPSAATKHLTISSSHSTHRLQPSLIPTTLLRTTIHRKPLRRSHLCSSFFCVGSLDSSSERLRPLPHIRV