AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene039033

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039033.t1 MTR_1g060700 89.655 319 13 10 1 308 178 487 0.0 540
MS.gene039033.t1 MTR_2g067000 86.817 311 25 4 1 308 1 298 0.0 502
MS.gene039033.t1 MTR_8g093500 58.491 53 22 0 178 230 125 177 9.30e-13 67.8
MS.gene039033.t1 MTR_3g101810 58.491 53 22 0 178 230 182 234 3.30e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039033.t1 AT1G30670 38.596 228 121 7 87 301 41 262 3.84e-30 115
MS.gene039033.t1 AT2G34820 40.084 237 107 8 87 301 66 289 5.51e-26 104
MS.gene039033.t1 AT3G21330 60.377 53 21 0 178 230 280 332 4.37e-13 69.3
MS.gene039033.t1 AT5G01305 50.000 58 29 0 178 235 48 105 4.69e-12 63.9

Find 48 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATTATGATTGCTCAATT+TGG 0.191234 2.2:+24324902 None:intergenic
AGTTGGAATGCTTCAACTTA+TGG 0.195386 2.2:-24325932 MS.gene039033:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 2.2:+24325997 None:intergenic
AAAATGAAATCTTCCTCATT+TGG 0.263570 2.2:+24326318 None:intergenic
AATTTGGTGACAAACTCTTT+TGG 0.289383 2.2:+24324918 None:intergenic
CCTCATAGTATAACAGCTTT+TGG 0.301868 2.2:+24326265 None:intergenic
AAATGAAATCTTCCTCATTT+GGG 0.325640 2.2:+24326319 None:intergenic
GAAGCAAAAGGGTTAGGGTT+AGG 0.345524 2.2:+24326171 None:intergenic
AAGCAAAAGGGTTAGGGTTA+GGG 0.345934 2.2:+24326172 None:intergenic
TACAATTTCTCTTGAACAAA+TGG 0.348402 2.2:+24324963 None:intergenic
GAGAAGCTTCATTGAAATAG+TGG 0.359894 2.2:+24326481 None:intergenic
ATCAAAACCTACCATCCTTA+AGG 0.361760 2.2:-24324874 MS.gene039033:CDS
AAATAACACTATTCTTGCTT+TGG 0.365183 2.2:+24324813 None:intergenic
TCAAAGGAAGCAAAAGGGTT+AGG 0.369513 2.2:+24326165 None:intergenic
GCAGTTTGAATAGGTTGATA+AGG 0.385279 2.2:+24326567 None:intergenic
GAGCTTGGGAAGTTGGTTCC+TGG 0.392352 2.2:-24326024 MS.gene039033:CDS
GACACAAGAGCTTGGGAAGT+TGG 0.397999 2.2:-24326031 MS.gene039033:CDS
TTGATTATTTCAGGAAGAAA+AGG 0.406675 2.2:-24325027 MS.gene039033:intron
CAAGCTGTTTCAGACCCTTA+AGG 0.427556 2.2:+24324859 None:intergenic
TCAAAACCTACCATCCTTAA+GGG 0.456430 2.2:-24324873 MS.gene039033:CDS
AAGGGTCTGAAACAGCTTGT+TGG 0.460418 2.2:-24324855 MS.gene039033:CDS
CAAAGGAAGCAAAAGGGTTA+GGG 0.461232 2.2:+24326166 None:intergenic
TCTGCCTCAAAGGAAGCAAA+AGG 0.471457 2.2:+24326159 None:intergenic
AGTGGTGATTTCTGAGTTGT+TGG 0.472171 2.2:+24326542 None:intergenic
TTGTGTAAATCTTCACTTGG+AGG 0.473071 2.2:+24324999 None:intergenic
CAGTTTGAATAGGTTGATAA+GGG 0.475268 2.2:+24326568 None:intergenic
TTGTTGGTAGCAGTTTGAAT+AGG 0.476845 2.2:+24326558 None:intergenic
GTTCAATGTGAGAAGAAAGT+TGG 0.488552 2.2:-24326117 MS.gene039033:CDS
CCAAAAGCTGTTATACTATG+AGG 0.493920 2.2:-24326265 MS.gene039033:CDS
GTGTTCATCTTTGGTCCACC+AGG 0.499817 2.2:+24326006 None:intergenic
ACTGAGAAGACACAAGAGCT+TGG 0.499993 2.2:-24326039 MS.gene039033:CDS
CTGAGAAGACACAAGAGCTT+GGG 0.500383 2.2:-24326038 MS.gene039033:CDS
AGAGTATCGCGGCTCGAGAA+AGG 0.514420 2.2:-24326074 MS.gene039033:CDS
TGTAAATCTTCACTTGGAGG+AGG 0.533936 2.2:+24325002 None:intergenic
CTTGGGAAGTTGGTTCCTGG+TGG 0.551828 2.2:-24326021 MS.gene039033:CDS
AGTTTGTGTAAATCTTCACT+TGG 0.555055 2.2:+24324996 None:intergenic
TTGTTCATGATGTTGAAAAG+TGG 0.560071 2.2:+24326524 None:intergenic
TCGCGGCTCGAGAAAGGAGA+AGG 0.564993 2.2:-24326068 MS.gene039033:CDS
GTGAGAAGAAAGTTGGTGAA+AGG 0.566992 2.2:-24326110 MS.gene039033:CDS
AAGTTTCTTCAAGCTCAAGT+TGG 0.567049 2.2:-24325949 MS.gene039033:CDS
ACTTATGGAAACATTTAGCA+AGG 0.569731 2.2:-24325917 MS.gene039033:intron
TTCAGACCCTTAAGGATGGT+AGG 0.578594 2.2:+24324867 None:intergenic
GAGTTGAAAAGCTCTTGTTG+TGG 0.596772 2.2:+24326228 None:intergenic
CTGCCTCAAAGGAAGCAAAA+GGG 0.606158 2.2:+24326160 None:intergenic
CTGTTTCAGACCCTTAAGGA+TGG 0.616344 2.2:+24324863 None:intergenic
AGTAGTTGATCATCTTGACA+AGG 0.655107 2.2:+24326399 None:intergenic
TATCTCGTCGCAGAGTATCG+CGG 0.698927 2.2:-24326085 MS.gene039033:CDS
GTAGTTGATCATCTTGACAA+GGG 0.704443 2.2:+24326400 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATTTTGTCTTTTTTATAT+TGG - chr2.2:24325912-24325931 MS.gene039033:intron 15.0%
!! GCAATTGTTATAAAAATTGA+TGG - chr2.2:24325975-24325994 MS.gene039033:CDS 20.0%
!! TCATTTGAGTAAAAACAATT+AGG + chr2.2:24325001-24325020 None:intergenic 20.0%
!! TTATTGTATAAAGTTACACT+AGG + chr2.2:24326336-24326355 None:intergenic 20.0%
!!! ACAATTGCTAAATATTTTCA+TGG + chr2.2:24325963-24325982 None:intergenic 20.0%
!!! TAAATAATGAGAGAGTATTT+AGG - chr2.2:24326092-24326111 MS.gene039033:CDS 20.0%
!!! TATTTTCATGGAGTAAAAAT+TGG + chr2.2:24325951-24325970 None:intergenic 20.0%
!!! TTTTGCTAATTGATTATTTC+AGG - chr2.2:24326391-24326410 MS.gene039033:CDS 20.0%
! AAAATGAAATCTTCCTCATT+TGG + chr2.2:24325112-24325131 None:intergenic 25.0%
! AAACTCATCCACAAAAAAAT+TGG + chr2.2:24325227-24325246 None:intergenic 25.0%
! AAATGAAATCTTCCTCATTT+GGG + chr2.2:24325111-24325130 None:intergenic 25.0%
! ACTCAAATGATTACAAGAAA+GGG + chr2.2:24325746-24325765 None:intergenic 25.0%
! ATCATTATGATTGCTCAATT+TGG + chr2.2:24326528-24326547 None:intergenic 25.0%
! GAAAAACATGCAAATTCAAT+CGG + chr2.2:24325664-24325683 None:intergenic 25.0%
! TACAATTTCTCTTGAACAAA+TGG + chr2.2:24326467-24326486 None:intergenic 25.0%
! TACTCAAATGATTACAAGAA+AGG + chr2.2:24325747-24325766 None:intergenic 25.0%
! TATTGTGGTAAATATCTAGA+TGG - chr2.2:24325833-24325852 MS.gene039033:intron 25.0%
! TGTTATTATGTCATGTATTG+TGG - chr2.2:24325818-24325837 MS.gene039033:intron 25.0%
! TTGATTATTTCAGGAAGAAA+AGG - chr2.2:24326400-24326419 MS.gene039033:CDS 25.0%
!! TGAACAACATCAACAATTTT+TGG + chr2.2:24325295-24325314 None:intergenic 25.0%
!!! ATGCTACTTGATTTTGTTTT+TGG - chr2.2:24325719-24325738 MS.gene039033:intron 25.0%
AAAGACAAAATTGAGACAGT+AGG + chr2.2:24325905-24325924 None:intergenic 30.0%
ACTTATGGAAACATTTAGCA+AGG - chr2.2:24325510-24325529 MS.gene039033:intron 30.0%
AGTTTGTGTAAATCTTCACT+TGG + chr2.2:24326434-24326453 None:intergenic 30.0%
GAAAAAAAGGGTTAAGGAAA+CGG - chr2.2:24326049-24326068 MS.gene039033:CDS 30.0%
TAATATCCTTCCAAGTGTTT+GGG + chr2.2:24326231-24326250 None:intergenic 30.0%
TTAATATCCTTCCAAGTGTT+TGG + chr2.2:24326232-24326251 None:intergenic 30.0%
TTGTTCATGATGTTGAAAAG+TGG + chr2.2:24324906-24324925 None:intergenic 30.0%
! AATTGATGGATGCAATTGTT+AGG - chr2.2:24325989-24326008 MS.gene039033:CDS 30.0%
! GAATGAAATTTTCCCAAATG+AGG - chr2.2:24325096-24325115 MS.gene039033:intron 30.0%
! TATTTAGTTTCCCAAACACT+TGG - chr2.2:24326218-24326237 MS.gene039033:CDS 30.0%
! TTCAACTGTTTTATGTCCTT+AGG - chr2.2:24325624-24325643 MS.gene039033:intron 30.0%
!! AATTTGGTGACAAACTCTTT+TGG + chr2.2:24326512-24326531 None:intergenic 30.0%
!! ACTTTTTCTTCTCAAAACGA+TGG - chr2.2:24325061-24325080 MS.gene039033:intron 30.0%
!! CAGTTTGAATAGGTTGATAA+GGG + chr2.2:24324862-24324881 None:intergenic 30.0%
!!! ATCGTTTTGAGAAGAAAAAG+TGG + chr2.2:24325062-24325081 None:intergenic 30.0%
!!! CAACTCAACCAATTTTTTTG+TGG - chr2.2:24325216-24325235 MS.gene039033:intron 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG - chr2.2:24325478-24325497 MS.gene039033:intron 35.0%
AGTAGTTGATCATCTTGACA+AGG + chr2.2:24325031-24325050 None:intergenic 35.0%
AGTTGGAATGCTTCAACTTA+TGG - chr2.2:24325495-24325514 MS.gene039033:intron 35.0%
ATCAAAACCTACCATCCTTA+AGG - chr2.2:24326553-24326572 MS.gene039033:CDS 35.0%
CAAGTGTATATCAAATGAGC+TGG - chr2.2:24326120-24326139 MS.gene039033:CDS 35.0%
CCAAAAGCTGTTATACTATG+AGG - chr2.2:24325162-24325181 MS.gene039033:intron 35.0%
GAGAAGCTTCATTGAAATAG+TGG + chr2.2:24324949-24324968 None:intergenic 35.0%
GTAGTTGATCATCTTGACAA+GGG + chr2.2:24325030-24325049 None:intergenic 35.0%
GTGAGAGAAAAAAAGGGTTA+AGG - chr2.2:24326043-24326062 MS.gene039033:CDS 35.0%
GTGTGTGTGAGAGAAAAAAA+GGG - chr2.2:24326037-24326056 MS.gene039033:CDS 35.0%
GTTCAATGTGAGAAGAAAGT+TGG - chr2.2:24325310-24325329 MS.gene039033:intron 35.0%
TCAAAACCTACCATCCTTAA+GGG - chr2.2:24326554-24326573 MS.gene039033:CDS 35.0%
TGTGTGTGTGAGAGAAAAAA+AGG - chr2.2:24326036-24326055 MS.gene039033:CDS 35.0%
TTGTGTAAATCTTCACTTGG+AGG + chr2.2:24326431-24326450 None:intergenic 35.0%
! CCTCATAGTATAACAGCTTT+TGG + chr2.2:24325165-24325184 None:intergenic 35.0%
! GGAGTATTACATAAGACCTA+AGG + chr2.2:24325643-24325662 None:intergenic 35.0%
! TATAACAGCTTTTGGCGTTT+TGG + chr2.2:24325157-24325176 None:intergenic 35.0%
!! GCAGTTTGAATAGGTTGATA+AGG + chr2.2:24324863-24324882 None:intergenic 35.0%
!! TTGTTGGTAGCAGTTTGAAT+AGG + chr2.2:24324872-24324891 None:intergenic 35.0%
!!! AATTTTTGGTTCTGCCTCAA+AGG + chr2.2:24325281-24325300 None:intergenic 35.0%
AAGCAAAAGGGTTAGGGTTA+GGG + chr2.2:24325258-24325277 None:intergenic 40.0%
AGGAAACGGTTACTAAGAAG+AGG - chr2.2:24326063-24326082 MS.gene039033:CDS 40.0%
AGTGGTGATTTCTGAGTTGT+TGG + chr2.2:24324888-24324907 None:intergenic 40.0%
ATCTCTGCTGTGTTCATCTT+TGG + chr2.2:24325433-24325452 None:intergenic 40.0%
ATTGAGACAGTAGGTAGTCA+TGG + chr2.2:24325896-24325915 None:intergenic 40.0%
CAAAGGAAGCAAAAGGGTTA+GGG + chr2.2:24325264-24325283 None:intergenic 40.0%
CGGTTACTAAGAAGAGGAAA+TGG - chr2.2:24326069-24326088 MS.gene039033:CDS 40.0%
GAGTTGAAAAGCTCTTGTTG+TGG + chr2.2:24325202-24325221 None:intergenic 40.0%
GGCTATGTAACTGTTCAACA+AGG - chr2.2:24326141-24326160 MS.gene039033:CDS 40.0%
TAGTTTCCCAAACACTTGGA+AGG - chr2.2:24326222-24326241 MS.gene039033:CDS 40.0%
TCAAAGGAAGCAAAAGGGTT+AGG + chr2.2:24325265-24325284 None:intergenic 40.0%
TGTAAATCTTCACTTGGAGG+AGG + chr2.2:24326428-24326447 None:intergenic 40.0%
! TAACCCTTTTGCTTCCTTTG+AGG - chr2.2:24325264-24325283 MS.gene039033:intron 40.0%
!! GTGAGAAGAAAGTTGGTGAA+AGG - chr2.2:24325317-24325336 MS.gene039033:intron 40.0%
!! TAGGTGCTGAATCATGTCAT+GGG + chr2.2:24326267-24326286 None:intergenic 40.0%
ACTGAGAAGACACAAGAGCT+TGG - chr2.2:24325388-24325407 MS.gene039033:intron 45.0%
CTGAGAAGACACAAGAGCTT+GGG - chr2.2:24325389-24325408 MS.gene039033:intron 45.0%
CTGCCTCAAAGGAAGCAAAA+GGG + chr2.2:24325270-24325289 None:intergenic 45.0%
CTGTTTCAGACCCTTAAGGA+TGG + chr2.2:24326567-24326586 None:intergenic 45.0%
GAAGCAAAAGGGTTAGGGTT+AGG + chr2.2:24325259-24325278 None:intergenic 45.0%
TCTGCCTCAAAGGAAGCAAA+AGG + chr2.2:24325271-24325290 None:intergenic 45.0%
TTCAGACCCTTAAGGATGGT+AGG + chr2.2:24326563-24326582 None:intergenic 45.0%
! AAGGGTCTGAAACAGCTTGT+TGG - chr2.2:24326572-24326591 MS.gene039033:CDS 45.0%
! CAAGCTGTTTCAGACCCTTA+AGG + chr2.2:24326571-24326590 None:intergenic 45.0%
!! CTAGGTGCTGAATCATGTCA+TGG + chr2.2:24326268-24326287 None:intergenic 45.0%
!!! TATTAATTTTATTATTTTCT+AGG + chr2.2:24326286-24326305 None:intergenic 5.0%
!!! TATTTTTTTTTTAAAAAAAG+TGG + chr2.2:24326173-24326192 None:intergenic 5.0%
GACACAAGAGCTTGGGAAGT+TGG - chr2.2:24325396-24325415 MS.gene039033:intron 50.0%
GTGTTCATCTTTGGTCCACC+AGG + chr2.2:24325424-24325443 None:intergenic 50.0%
!! GGCGTTTTGGACAATGAAGC+TGG + chr2.2:24325144-24325163 None:intergenic 50.0%
!! TATCTCGTCGCAGAGTATCG+CGG - chr2.2:24325342-24325361 MS.gene039033:intron 50.0%
! CTTGGGAAGTTGGTTCCTGG+TGG - chr2.2:24325406-24325425 MS.gene039033:intron 55.0%
! GAGCTTGGGAAGTTGGTTCC+TGG - chr2.2:24325403-24325422 MS.gene039033:intron 55.0%
!! AGAGTATCGCGGCTCGAGAA+AGG - chr2.2:24325353-24325372 MS.gene039033:intron 55.0%
TCGCGGCTCGAGAAAGGAGA+AGG - chr2.2:24325359-24325378 MS.gene039033:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 24324821 24326628 24324821 ID=MS.gene039033
chr2.2 mRNA 24324821 24326628 24324821 ID=MS.gene039033.t1;Parent=MS.gene039033
chr2.2 exon 24325918 24326628 24325918 ID=MS.gene039033.t1.exon1;Parent=MS.gene039033.t1
chr2.2 CDS 24325918 24326628 24325918 ID=cds.MS.gene039033.t1;Parent=MS.gene039033.t1
chr2.2 exon 24324821 24325036 24324821 ID=MS.gene039033.t1.exon2;Parent=MS.gene039033.t1
chr2.2 CDS 24324821 24325036 24324821 ID=cds.MS.gene039033.t1;Parent=MS.gene039033.t1
Gene Sequence

>MS.gene039033

ATGGGAGCACTTAGCACATACTTTAACTATAATTGTTACCCTTATCAACCTATTCAAACTGCTACCAACAACTCAGAAATCACCACTTTTCAACATCATGAACAAGAACAACTTGTGCAACAAAACCACTATTTCAATGAAGCTTCTCTTTTAGATGAAAGCTTCATTTTTCAAACTCCTAATTGTTTTTACTCAAATGAGACTTACCCTTGTCAAGATGATCAACTACTTGTTGACTCCACTTTTTCTTCTCAAAACGATGGCTTCGTTTCAATGAATGAAATTTTCCCAAATGAGGAAGATTTCATTTTCAACAACTACCAGCTTCATTGTCCAAAACGCCAAAAGCTGTTATACTATGAGGAGAAAAGAGAAGAGCCACAACAAGAGCTTTTCAACTCAACCAATTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTAACCCTTTTGCTTCCTTTGAGGCAGAACCAAAAATTGTTGATGTTGTTCAATGTGAGAAGAAAGTTGGTGAAAGGACTATCTCGTCGCAGAGTATCGCGGCTCGAGAAAGGAGAAGGAAGATAACTGAGAAGACACAAGAGCTTGGGAAGTTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTCATGCTGCTGCTAATTATGTCAAGTTTCTTCAAGCTCAAGTTGGAATGCTTCAACTTATGGAAACATTTAGCAAGGTAACTGTTTTTGCTTTTTTATTGTTGCAATGTTCTTATATTATTAGAGCTCATAATTGAAGTTAATTACTTTTCTTCACTTGAGTTTCGATTTCAACTGTTTTATGTCCTTAGGTCTTATGTAATACTCCGATTGAATTTGCATGTTTTTCTTTTGAATGATGTTTTTTGCTTTTTATATTATGCTATGCTACTTGATTTTGTTTTTGGACCCTTTCTTGTAATCATTTGAGTATATTTTGTTTGATCAAAATAATATTGAGTATGTATATGTCATTTATTGTAGTGTTATTATGTCATGTATTGTGGTAAATATCTAGATGGATGTTAATTCTTTTTTCATTTATGTATGTAATGTAATCCATGACTACCTACTGTCTCAATTTTGTCTTTTTTATATTGGTTTTTTTTTCTTACCAATTTTTACTCCATGAAAATATTTAGCAATTGTTATAAAAATTGATGGATGCAATTGTTAGGATTAAGAAAATGTTTGTTAGTGTGTGTGTGTGTGAGAGAAAAAAAGGGTTAAGGAAACGGTTACTAAGAAGAGGAAATGGTAAATAATGAGAGAGTATTTAGGAACAACAAGTGTATATCAAATGAGCTGGCTATGTAACTGTTCAACAAGGAATTATCCACTTTTTTTAAAAAAAAAATATTCATTATTTTTACTTTCTTTATTGTATTTAGTTTCCCAAACACTTGGAAGGATATTAAAAAATTTATCATCCCATGACATGATTCAGCACCTAGAAAATAATAAAATTAATAGTGTAACATTTTTGTAAAAGCTGAATTCCTAGTGTAACTTTATACAATAAAATTAATTAATGCTTAGAATATTCATTCTCTTAGATTTTGCTAATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATTTACACAAACTAGTTGTTTCTCCATTTGTTCAAGAGAAATTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCAAATTGAGCAATCATAATGATGTTCAATCAAAACCTACCATCCTTAAGGGTCTGAAACAGCTTGTTGGAACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene039033.t1

MGALSTYFNYNCYPYQPIQTATNNSEITTFQHHEQEQLVQQNHYFNEASLLDESFIFQTPNCFYSNETYPCQDDQLLVDSTFSSQNDGFVSMNEIFPNEEDFIFNNYQLHCPKRQKLLYYEEKREEPQQELFNSTNFFVDEFMTNPNPNPFASFEAEPKIVDVVQCEKKVGERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLHAAANYVKFLQAQVGMLQLMETFSKEEKEPPPSEDLHKLVVSPFVQEKLYSEEKCFVPKEFVTKLSNHNDVQSKPTILKGLKQLVGTEIEKKPKQE