AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene92177

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene92177.t1 MTR_1g060700 89.342 319 14 10 1 308 178 487 0.0 539
MS.gene92177.t1 MTR_2g067000 86.495 311 26 4 1 308 1 298 0.0 501
MS.gene92177.t1 MTR_8g093500 58.491 53 22 0 178 230 125 177 9.39e-13 67.8
MS.gene92177.t1 MTR_3g101810 58.491 53 22 0 178 230 182 234 3.40e-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.gene92177.t1 AT1G30670 38.596 228 121 7 87 301 41 262 3.88e-30 115
MS.gene92177.t1 AT2G34820 39.662 237 108 8 87 301 66 289 1.39e-25 103
MS.gene92177.t1 AT3G21330 60.377 53 21 0 178 230 280 332 4.66e-13 69.3
MS.gene92177.t1 AT5G01305 50.000 58 29 0 178 235 48 105 4.60e-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 2.4:+27501612 None:intergenic
AGTTGGAATGCTTCAACTTA+TGG 0.195386 2.4:-27502639 MS.gene92177:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 2.4:+27502704 None:intergenic
AAAATGAAATCTTCCTCATT+TGG 0.263570 2.4:+27503025 None:intergenic
AATTTGGTGACAAACTCTTT+TGG 0.289383 2.4:+27501628 None:intergenic
CCTCATAGTATAACAGCTTT+TGG 0.301868 2.4:+27502972 None:intergenic
AAATGAAATCTTCCTCATTT+GGG 0.325640 2.4:+27503026 None:intergenic
GAAGCAAAAGGGTTAGGGTT+AGG 0.345524 2.4:+27502878 None:intergenic
AAGCAAAAGGGTTAGGGTTA+GGG 0.345934 2.4:+27502879 None:intergenic
TACAATTTCTCTTGAACAAA+TGG 0.348402 2.4:+27501673 None:intergenic
GAGAAGCTTCATTGAAATAG+TGG 0.359894 2.4:+27503188 None:intergenic
ATCAAAACCTACCATCCTTA+AGG 0.361760 2.4:-27501584 MS.gene92177:CDS
AAATAACACTATTCTTGCTT+TGG 0.365183 2.4:+27501523 None:intergenic
TCAAAGGAAGCAAAAGGGTT+AGG 0.369513 2.4:+27502872 None:intergenic
GCAGTTTGAATAGGTTGATA+AGG 0.385279 2.4:+27503274 None:intergenic
GAGCTTGGGAAGTTGGTTCC+TGG 0.392352 2.4:-27502731 MS.gene92177:CDS
GACACAAGAGCTTGGGAAGT+TGG 0.397999 2.4:-27502738 MS.gene92177:CDS
TTGATTATTTCAGGAAGAAA+AGG 0.406675 2.4:-27501737 MS.gene92177:intron
CAAGCTGTTTCAGACCCTTA+AGG 0.427556 2.4:+27501569 None:intergenic
TCAAAACCTACCATCCTTAA+GGG 0.456430 2.4:-27501583 MS.gene92177:CDS
AAGGGTCTGAAACAGCTTGT+TGG 0.460418 2.4:-27501565 MS.gene92177:CDS
CAAAGGAAGCAAAAGGGTTA+GGG 0.461232 2.4:+27502873 None:intergenic
TCTGCCTCAAAGGAAGCAAA+AGG 0.471457 2.4:+27502866 None:intergenic
AGTGGTGATTTCTGAGTTGT+TGG 0.472171 2.4:+27503249 None:intergenic
TTGTGTAAATCTTCACTTGG+AGG 0.473071 2.4:+27501709 None:intergenic
CAGTTTGAATAGGTTGATAA+GGG 0.475268 2.4:+27503275 None:intergenic
TTGTTGGTAGCAGTTTGAAT+AGG 0.476845 2.4:+27503265 None:intergenic
GTTCAATGTGAGAAGAAAGT+TGG 0.488552 2.4:-27502824 MS.gene92177:CDS
CCAAAAGCTGTTATACTATG+AGG 0.493920 2.4:-27502972 MS.gene92177:CDS
GTGTTCATCTTTGGTCCACC+AGG 0.499817 2.4:+27502713 None:intergenic
ACTGAGAAGACACAAGAGCT+TGG 0.499993 2.4:-27502746 MS.gene92177:CDS
CTGAGAAGACACAAGAGCTT+GGG 0.500383 2.4:-27502745 MS.gene92177:CDS
AGAGTATCGCGGCTCGAGAA+AGG 0.514420 2.4:-27502781 MS.gene92177:CDS
TGTAAATCTTCACTTGGAGG+AGG 0.533936 2.4:+27501712 None:intergenic
CTTGGGAAGTTGGTTCCTGG+TGG 0.551828 2.4:-27502728 MS.gene92177:CDS
AGTTTGTGTAAATCTTCACT+TGG 0.555055 2.4:+27501706 None:intergenic
TTGTTCATGATGTTGAAAAG+TGG 0.560071 2.4:+27503231 None:intergenic
TCGCGGCTCGAGAAAGGAGA+AGG 0.564993 2.4:-27502775 MS.gene92177:CDS
GTGAGAAGAAAGTTGGTGAA+AGG 0.566992 2.4:-27502817 MS.gene92177:CDS
AAGTTTCTTCAAGCTCAAGT+TGG 0.567049 2.4:-27502656 MS.gene92177:CDS
ACTTATGGAAACATTTAGCA+AGG 0.569731 2.4:-27502624 MS.gene92177:intron
TTCAGACCCTTAAGGATGGT+AGG 0.578594 2.4:+27501577 None:intergenic
GAGTTGAAAAGCTCTTGTTG+TGG 0.596772 2.4:+27502935 None:intergenic
CTGCCTCAAAGGAAGCAAAA+GGG 0.606158 2.4:+27502867 None:intergenic
CTGTTTCAGACCCTTAAGGA+TGG 0.616344 2.4:+27501573 None:intergenic
AGTAGTTGATCATCTTGACA+AGG 0.655107 2.4:+27503106 None:intergenic
TATCTCGTCGCAGAGTATCG+CGG 0.698927 2.4:-27502792 MS.gene92177:CDS
GTAGTTGATCATCTTGACAA+GGG 0.704443 2.4:+27503107 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATTTTGTCTTTTTTATAT+TGG - chr2.4:27502622-27502641 MS.gene92177:intron 15.0%
!! GCAATTGTTATAAAAATTGA+TGG - chr2.4:27502685-27502704 MS.gene92177:CDS 20.0%
!! TCATTTGAGTAAAAACAATT+AGG + chr2.4:27501711-27501730 None:intergenic 20.0%
!! TTATTGTATAAAGTTACACT+AGG + chr2.4:27503043-27503062 None:intergenic 20.0%
!!! ACAATTGCTAAATATTTTCA+TGG + chr2.4:27502673-27502692 None:intergenic 20.0%
!!! TAAATAATGAGAGAGTATTT+AGG - chr2.4:27502800-27502819 MS.gene92177:CDS 20.0%
!!! TATTTTCATGGAGTAAAAAT+TGG + chr2.4:27502661-27502680 None:intergenic 20.0%
!!! TTTTGCTAATTGATTATTTC+AGG - chr2.4:27503098-27503117 MS.gene92177:CDS 20.0%
! AAAATGAAATCTTCCTCATT+TGG + chr2.4:27501822-27501841 None:intergenic 25.0%
! AAATGAAATCTTCCTCATTT+GGG + chr2.4:27501821-27501840 None:intergenic 25.0%
! ACTCAAATGATTACAAGAAA+GGG + chr2.4:27502456-27502475 None:intergenic 25.0%
! ATCATTATGATTGCTCAATT+TGG + chr2.4:27503235-27503254 None:intergenic 25.0%
! GAAAAACATGCAAATTCAAT+CGG + chr2.4:27502374-27502393 None:intergenic 25.0%
! TACAATTTCTCTTGAACAAA+TGG + chr2.4:27503174-27503193 None:intergenic 25.0%
! TACTCAAATGATTACAAGAA+AGG + chr2.4:27502457-27502476 None:intergenic 25.0%
! TATTGTGGTAAATATCTAGA+TGG - chr2.4:27502543-27502562 MS.gene92177:intron 25.0%
! TGTTATTATGTCATGTATTG+TGG - chr2.4:27502528-27502547 MS.gene92177:intron 25.0%
! TTGATTATTTCAGGAAGAAA+AGG - chr2.4:27503107-27503126 MS.gene92177:CDS 25.0%
!! TGAACAACATCAACAATTTT+TGG + chr2.4:27502005-27502024 None:intergenic 25.0%
!!! ATGCTACTTGATTTTGTTTT+TGG - chr2.4:27502429-27502448 MS.gene92177:intron 25.0%
AAACTCATCCACAAAAAAGT+TGG + chr2.4:27501937-27501956 None:intergenic 30.0%
AAAGACAAAATTGAGACAGT+AGG + chr2.4:27502615-27502634 None:intergenic 30.0%
ACTTATGGAAACATTTAGCA+AGG - chr2.4:27502220-27502239 MS.gene92177:intron 30.0%
AGTTTGTGTAAATCTTCACT+TGG + chr2.4:27503141-27503160 None:intergenic 30.0%
GAAAAAAAGGGTTAAGGAAA+CGG - chr2.4:27502757-27502776 MS.gene92177:CDS 30.0%
TAATATCCTTCCAAGTGTTT+GGG + chr2.4:27502938-27502957 None:intergenic 30.0%
TTAATATCCTTCCAAGTGTT+TGG + chr2.4:27502939-27502958 None:intergenic 30.0%
TTGTTCATGATGTTGAAAAG+TGG + chr2.4:27501616-27501635 None:intergenic 30.0%
! AATTGATGGATGCAATTGTT+AGG - chr2.4:27502699-27502718 MS.gene92177:CDS 30.0%
! GAATGAAATTTTCCCAAATG+AGG - chr2.4:27501806-27501825 MS.gene92177:intron 30.0%
! TATTTAGTTTCCCAAACACT+TGG - chr2.4:27502925-27502944 MS.gene92177:CDS 30.0%
! TTCAACTGTTTTATGTCCTT+AGG - chr2.4:27502334-27502353 MS.gene92177:intron 30.0%
!! AATTTGGTGACAAACTCTTT+TGG + chr2.4:27503219-27503238 None:intergenic 30.0%
!! ACTTTTTCTTCTCAAAACGA+TGG - chr2.4:27501771-27501790 MS.gene92177:intron 30.0%
!! CAGTTTGAATAGGTTGATAA+GGG + chr2.4:27501572-27501591 None:intergenic 30.0%
!!! ATCGTTTTGAGAAGAAAAAG+TGG + chr2.4:27501772-27501791 None:intergenic 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG - chr2.4:27502188-27502207 MS.gene92177:intron 35.0%
AGTAGTTGATCATCTTGACA+AGG + chr2.4:27501741-27501760 None:intergenic 35.0%
AGTTGGAATGCTTCAACTTA+TGG - chr2.4:27502205-27502224 MS.gene92177:intron 35.0%
ATCAAAACCTACCATCCTTA+AGG - chr2.4:27503260-27503279 MS.gene92177:CDS 35.0%
CAAGTGTATATCAAATGAGC+TGG - chr2.4:27502828-27502847 MS.gene92177:CDS 35.0%
CCAAAAGCTGTTATACTATG+AGG - chr2.4:27501872-27501891 MS.gene92177:intron 35.0%
GAGAAGCTTCATTGAAATAG+TGG + chr2.4:27501659-27501678 None:intergenic 35.0%
GTAGTTGATCATCTTGACAA+GGG + chr2.4:27501740-27501759 None:intergenic 35.0%
GTGAGAGAAAAAAAGGGTTA+AGG - chr2.4:27502751-27502770 MS.gene92177:CDS 35.0%
GTGTGTGTGAGAGAAAAAAA+GGG - chr2.4:27502745-27502764 MS.gene92177:CDS 35.0%
GTTCAATGTGAGAAGAAAGT+TGG - chr2.4:27502020-27502039 MS.gene92177:intron 35.0%
TCAAAACCTACCATCCTTAA+GGG - chr2.4:27503261-27503280 MS.gene92177:CDS 35.0%
TGTGTGTGTGAGAGAAAAAA+AGG - chr2.4:27502744-27502763 MS.gene92177:CDS 35.0%
TTGTGTAAATCTTCACTTGG+AGG + chr2.4:27503138-27503157 None:intergenic 35.0%
! CCTCATAGTATAACAGCTTT+TGG + chr2.4:27501875-27501894 None:intergenic 35.0%
! GGAGTATTACATAAGACCTA+AGG + chr2.4:27502353-27502372 None:intergenic 35.0%
! TATAACAGCTTTTGGCGTTT+TGG + chr2.4:27501867-27501886 None:intergenic 35.0%
!! GCAGTTTGAATAGGTTGATA+AGG + chr2.4:27501573-27501592 None:intergenic 35.0%
!! TTGTTGGTAGCAGTTTGAAT+AGG + chr2.4:27501582-27501601 None:intergenic 35.0%
!!! AATTTTTGGTTCTGCCTCAA+AGG + chr2.4:27501991-27502010 None:intergenic 35.0%
!!! CAACTCAACCAACTTTTTTG+TGG - chr2.4:27501926-27501945 MS.gene92177:intron 35.0%
AAGCAAAAGGGTTAGGGTTA+GGG + chr2.4:27501968-27501987 None:intergenic 40.0%
AGGAAACGGTTACTAAGAAG+AGG - chr2.4:27502771-27502790 MS.gene92177:CDS 40.0%
AGTGGTGATTTCTGAGTTGT+TGG + chr2.4:27501598-27501617 None:intergenic 40.0%
ATCTCTGCTGTGTTCATCTT+TGG + chr2.4:27502143-27502162 None:intergenic 40.0%
ATTGAGACAGTAGGTAGTCA+TGG + chr2.4:27502606-27502625 None:intergenic 40.0%
CAAAGGAAGCAAAAGGGTTA+GGG + chr2.4:27501974-27501993 None:intergenic 40.0%
CGGTTACTAAGAAGAGGAAA+TGG - chr2.4:27502777-27502796 MS.gene92177:CDS 40.0%
GAGTTGAAAAGCTCTTGTTG+TGG + chr2.4:27501912-27501931 None:intergenic 40.0%
GGCTATGTAACTGTTCAACA+AGG - chr2.4:27502849-27502868 MS.gene92177:CDS 40.0%
TAGTTTCCCAAACACTTGGA+AGG - chr2.4:27502929-27502948 MS.gene92177:CDS 40.0%
TCAAAGGAAGCAAAAGGGTT+AGG + chr2.4:27501975-27501994 None:intergenic 40.0%
TGTAAATCTTCACTTGGAGG+AGG + chr2.4:27503135-27503154 None:intergenic 40.0%
! TAACCCTTTTGCTTCCTTTG+AGG - chr2.4:27501974-27501993 MS.gene92177:intron 40.0%
!! GTGAGAAGAAAGTTGGTGAA+AGG - chr2.4:27502027-27502046 MS.gene92177:intron 40.0%
!! TAGGTGCTGAATCATGTCAT+GGG + chr2.4:27502974-27502993 None:intergenic 40.0%
ACTGAGAAGACACAAGAGCT+TGG - chr2.4:27502098-27502117 MS.gene92177:intron 45.0%
CTGAGAAGACACAAGAGCTT+GGG - chr2.4:27502099-27502118 MS.gene92177:intron 45.0%
CTGCCTCAAAGGAAGCAAAA+GGG + chr2.4:27501980-27501999 None:intergenic 45.0%
CTGTTTCAGACCCTTAAGGA+TGG + chr2.4:27503274-27503293 None:intergenic 45.0%
GAAGCAAAAGGGTTAGGGTT+AGG + chr2.4:27501969-27501988 None:intergenic 45.0%
TCTGCCTCAAAGGAAGCAAA+AGG + chr2.4:27501981-27502000 None:intergenic 45.0%
TTCAGACCCTTAAGGATGGT+AGG + chr2.4:27503270-27503289 None:intergenic 45.0%
! AAGGGTCTGAAACAGCTTGT+TGG - chr2.4:27503279-27503298 MS.gene92177:CDS 45.0%
! CAAGCTGTTTCAGACCCTTA+AGG + chr2.4:27503278-27503297 None:intergenic 45.0%
!! CTAGGTGCTGAATCATGTCA+TGG + chr2.4:27502975-27502994 None:intergenic 45.0%
!!! ATATTTTTTTTTAAAAAAAG+TGG + chr2.4:27502881-27502900 None:intergenic 5.0%
!!! TATTAATTTTATTATTTTCT+AGG + chr2.4:27502993-27503012 None:intergenic 5.0%
GACACAAGAGCTTGGGAAGT+TGG - chr2.4:27502106-27502125 MS.gene92177:intron 50.0%
GTGTTCATCTTTGGTCCACC+AGG + chr2.4:27502134-27502153 None:intergenic 50.0%
!! GGCGTTTTGGACAATGAAGC+TGG + chr2.4:27501854-27501873 None:intergenic 50.0%
!! TATCTCGTCGCAGAGTATCG+CGG - chr2.4:27502052-27502071 MS.gene92177:intron 50.0%
! CTTGGGAAGTTGGTTCCTGG+TGG - chr2.4:27502116-27502135 MS.gene92177:intron 55.0%
! GAGCTTGGGAAGTTGGTTCC+TGG - chr2.4:27502113-27502132 MS.gene92177:intron 55.0%
!! AGAGTATCGCGGCTCGAGAA+AGG - chr2.4:27502063-27502082 MS.gene92177:intron 55.0%
TCGCGGCTCGAGAAAGGAGA+AGG - chr2.4:27502069-27502088 MS.gene92177:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 27501531 27503335 27501531 ID=MS.gene92177
chr2.4 mRNA 27501531 27503335 27501531 ID=MS.gene92177.t1;Parent=MS.gene92177
chr2.4 exon 27502625 27503335 27502625 ID=MS.gene92177.t1.exon1;Parent=MS.gene92177.t1
chr2.4 CDS 27502625 27503335 27502625 ID=cds.MS.gene92177.t1;Parent=MS.gene92177.t1
chr2.4 exon 27501531 27501746 27501531 ID=MS.gene92177.t1.exon2;Parent=MS.gene92177.t1
chr2.4 CDS 27501531 27501746 27501531 ID=cds.MS.gene92177.t1;Parent=MS.gene92177.t1
Gene Sequence

>MS.gene92177

ATGGGAGCACTTAGCACATACTTTAACTATAATTGTTACCCTTATCAACCTATTCAAACTGCTACCAACAACTCAGAAATCACCACTTTTCAACATCATGAACAAGAACAACTTGTGCAACAAAACCACTATTTCAATGAAGCTTCTCTTTTAGATGAAAGCTTCATTTTTCAAACTCCTAATTGTTTTTACTCAAATGAGACTTACCCTTGTCAAGATGATCAACTACTTGTTGACTCCACTTTTTCTTCTCAAAACGATGGCTTCGTTACAATGAATGAAATTTTCCCAAATGAGGAAGATTTCATTTTCAACAACTACCAGCTTCATTGTCCAAAACGCCAAAAGCTGTTATACTATGAGGAGAAAAGAGAAGAGCCACAACAAGAGCTTTTCAACTCAACCAACTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTAACCCTTTTGCTTCCTTTGAGGCAGAACCAAAAATTGTTGATGTTGTTCAATGTGAGAAGAAAGTTGGTGAAAGGACTATCTCGTCGCAGAGTATCGCGGCTCGAGAAAGGAGAAGGAAGATAACTGAGAAGACACAAGAGCTTGGGAAGTTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTCATGCTGCTGCTAATTATGTCAAGTTTCTTCAAGCTCAAGTTGGAATGCTTCAACTTATGGAAACATTTAGCAAGGTAACTGTTTTTGCTTTTTTATTGTTGCAATGTTCTTATATTATTAGAGCTCATAATTGAAGTTAATTACTTTTCTTCACTTGAGTTTCGATTTCAACTGTTTTATGTCCTTAGGTCTTATGTAATACTCCGATTGAATTTGCATGTTTTTCTTTTGAATGATGTTTTTTGCTTTTTATATTATGCTATGCTACTTGATTTTGTTTTTGGACCCTTTCTTGTAATCATTTGAGTATATTTTGTTTGATCAAAATAATATTGAGTATGTATATGTCATTTATTGTAGTGTTATTATGTCATGTATTGTGGTAAATATCTAGATGGATGTTAATTCTTTTTTCATTTATGTATGTAATGTAATCCATGACTACCTACTGTCTCAATTTTGTCTTTTTTATATTGGTTTTTTTTTCTTACCAATTTTTACTCCATGAAAATATTTAGCAATTGTTATAAAAATTGATGGATGCAATTGTTAGGATTAAGAAAATGTTTGTTAGTGTGTGTGTGTGAGAGAAAAAAAGGGTTAAGGAAACGGTTACTAAGAAGAGGAAATGGTAAATAATGAGAGAGTATTTAGGAACAACAAGTGTATATCAAATGAGCTGGCTATGTAACTGTTCAACAAGGAATTATCCACTTTTTTTAAAAAAAAATATTCATTATTTTTACTTTCTTTATTGTATTTAGTTTCCCAAACACTTGGAAGGATATTAAAAAATTTATCATCCCATGACATGATTCAGCACCTAGAAAATAATAAAATTAATAGTGTAACATTTTTGTAAAAGCTGAATTCCTAGTGTAACTTTATACAATAAAATTAATTAATGCTTAGAATATTCATTCTCTTAGATTTTGCTAATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATTTACACAAACTAGTTGTTTCTCCATTTGTTCAAGAGAAATTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCAAATTGAGCAATCATAATGATGTTCAATCAAAACCTACCATCCTTAAGGGTCTGAAACAGCTTGTTGGAACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene92177.t1

MGALSTYFNYNCYPYQPIQTATNNSEITTFQHHEQEQLVQQNHYFNEASLLDESFIFQTPNCFYSNETYPCQDDQLLVDSTFSSQNDGFVTMNEIFPNEEDFIFNNYQLHCPKRQKLLYYEEKREEPQQELFNSTNFFVDEFMTNPNPNPFASFEAEPKIVDVVQCEKKVGERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLHAAANYVKFLQAQVGMLQLMETFSKEEKEPPPSEDLHKLVVSPFVQEKLYSEEKCFVPKEFVTKLSNHNDVQSKPTILKGLKQLVGTEIEKKPKQE