AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene008661

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008661.t1 MTR_3g465280 58.333 84 32 2 13 96 1 81 9.73e-26 101
MS.gene008661.t1 MTR_3g465280 47.917 96 47 3 1 95 83 176 1.48e-18 82.4
MS.gene008661.t1 MTR_4g079500 40.594 101 53 3 108 207 194 288 7.87e-14 69.7
MS.gene008661.t1 MTR_2g090900 38.614 101 55 3 108 207 191 285 2.04e-12 65.9
MS.gene008661.t1 MTR_2g090900 38.614 101 55 3 108 207 191 285 2.63e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008661.t1 AT2G42380 37.288 118 67 3 91 207 169 280 1.01e-14 72.0
MS.gene008661.t1 AT3G58120 36.975 119 67 4 90 207 185 296 7.17e-14 69.7
MS.gene008661.t1 AT2G42380 38.235 102 56 3 91 191 169 264 2.24e-12 65.1
MS.gene008661.t1 AT3G58120 37.864 103 56 4 90 191 185 280 1.74e-11 62.8

Find 43 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCAATTTCAAGTCTTAAT+TGG 0.217186 3.4:-60203823 None:intergenic
ACTTGATTATATTGCAGATT+TGG 0.251262 3.4:+60203166 MS.gene008661:CDS
ACATGACCAAGATCTGATTT+TGG 0.271978 3.4:-60202522 None:intergenic
GTATACCGTTTGAGCCTCTT+TGG 0.278573 3.4:-60202621 None:intergenic
TATGTACCAGTCATTCTCTT+TGG 0.297119 3.4:-60202309 None:intergenic
GAATAGGCTGAGGGAGCTTC+AGG 0.311474 3.4:+60203987 MS.gene008661:CDS
ATAAGAGAGCTGAGGTGAAT+AGG 0.348904 3.4:+60203971 MS.gene008661:CDS
ATGTACCAGTCATTCTCTTT+GGG 0.405085 3.4:-60202308 None:intergenic
TTCGACCATGGCAACCCTCT+TGG 0.419659 3.4:+60202412 MS.gene008661:CDS
ATGTTTGATTTCTTAGACGC+TGG 0.453635 3.4:-60202354 None:intergenic
TATTGCAGATTTGGAACAGA+TGG 0.461511 3.4:+60203175 MS.gene008661:CDS
AGTATACCAAAATCAGATCT+TGG 0.466062 3.4:+60202516 MS.gene008661:CDS
TTTCATAGGCTTCAACTTGT+GGG 0.474934 3.4:-60203769 None:intergenic
TCTTGGATGAGCATCGGCCT+TGG 0.498298 3.4:+60202429 MS.gene008661:CDS
TGGATCCAAAGAGGCTCAAA+CGG 0.512756 3.4:+60202616 MS.gene008661:CDS
CAATTTCAAGTCTTAATTGG+TGG 0.516892 3.4:-60203820 None:intergenic
AAACAAGAGGCAAGTAGCAG+TGG 0.526381 3.4:+60202453 MS.gene008661:CDS
GAGCTGAGGTGAATAGGCTG+AGG 0.526514 3.4:+60203977 MS.gene008661:CDS
GGCATCCCAAAGAGAATGAC+TGG 0.538746 3.4:+60202303 MS.gene008661:CDS
CTTCATCAGCATTTCGACCA+TGG 0.539881 3.4:+60202400 MS.gene008661:CDS
AGGCTTCAACTTGTGGGCGA+AGG 0.567374 3.4:-60203763 None:intergenic
TACATGTTGCAAACAGAAGA+GGG 0.569321 3.4:+60202330 MS.gene008661:CDS
GGTAGTGCATCTGCAGATGT+TGG 0.573551 3.4:+60202567 MS.gene008661:CDS
TACTTGCCTCTTGTTTACCA+AGG 0.574650 3.4:-60202446 None:intergenic
CTCATCCAAGAGGGTTGCCA+TGG 0.587878 3.4:-60202417 None:intergenic
GCATCTGCAGATGTTGGTGT+TGG 0.594426 3.4:+60202573 MS.gene008661:CDS
ATGGTTAGACCCTTCTCACA+TGG 0.603263 3.4:+60202375 MS.gene008661:CDS
GATTGAGAATAAGAGAGCTG+AGG 0.610144 3.4:+60203963 MS.gene008661:CDS
TTTCTGAAGCACAAAACAAG+AGG 0.611292 3.4:+60204019 MS.gene008661:CDS
AGCTGAGGTGAATAGGCTGA+GGG 0.614102 3.4:+60203978 MS.gene008661:CDS
AGGCCGATGCTCATCCAAGA+GGG 0.614873 3.4:-60202426 None:intergenic
GTTCAAGACTCAACAACCGC+TGG 0.617215 3.4:-60203796 None:intergenic
ATACATGTTGCAAACAGAAG+AGG 0.617735 3.4:+60202329 MS.gene008661:CDS
GATGAAGATCCATGTGAGAA+GGG 0.623366 3.4:-60202384 None:intergenic
AAAGAAAGGATACTTCAAGA+AGG 0.624481 3.4:+60203854 MS.gene008661:CDS
CAACCCTCTTGGATGAGCAT+CGG 0.637743 3.4:+60202423 MS.gene008661:CDS
CATCGGCCTTGGTAAACAAG+AGG 0.639464 3.4:+60202440 MS.gene008661:CDS
TGATGAAGATCCATGTGAGA+AGG 0.644091 3.4:-60202385 None:intergenic
AGCGTCTAAGAAATCAAACA+TGG 0.676949 3.4:+60202356 MS.gene008661:CDS
GAGAAGAAACACATCAGTGG+TGG 0.678185 3.4:+60202546 MS.gene008661:CDS
AAGGCCGATGCTCATCCAAG+AGG 0.678512 3.4:-60202427 None:intergenic
GTTGAGAAGAAACACATCAG+TGG 0.702052 3.4:+60202543 MS.gene008661:CDS
AAGCCTATGAAAATCACCAG+CGG 0.745418 3.4:+60203780 MS.gene008661:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTTAAAAATTCATAATTA+AGG + chr3.4:60204117-60204136 MS.gene008661:intron 10.0%
!! ATTAAAATAAATCTATCTGT+TGG + chr3.4:60202930-60202949 MS.gene008661:intron 15.0%
!! TTTCAATTTCAATTTCAATT+TGG - chr3.4:60203370-60203389 None:intergenic 15.0%
!!! ATATTATATTGATTTTGTGT+AGG - chr3.4:60203063-60203082 None:intergenic 15.0%
!!! ATTTTTTTTTTGGATAGATA+TGG - chr3.4:60203691-60203710 None:intergenic 15.0%
!!! GAATTTTTAAACAACAATTT+AGG - chr3.4:60204110-60204129 None:intergenic 15.0%
!! AAGCAATAAAAAAAATCAGT+TGG + chr3.4:60202663-60202682 MS.gene008661:intron 20.0%
!! CAAATCAACTATATTAGATA+GGG - chr3.4:60202999-60203018 None:intergenic 20.0%
!! TCAAATCAACTATATTAGAT+AGG - chr3.4:60203000-60203019 None:intergenic 20.0%
!! TCATGTATCAACTTATAATT+TGG + chr3.4:60203557-60203576 MS.gene008661:intron 20.0%
!!! GATAGAAATTTTGATTCTTA+AGG + chr3.4:60202704-60202723 MS.gene008661:intron 20.0%
!!! TACTAATGTTATTAGTTTTG+TGG - chr3.4:60202500-60202519 None:intergenic 20.0%
!!! TTTTATCTTATCTTGTTCTT+AGG + chr3.4:60203099-60203118 MS.gene008661:intron 20.0%
!!! TTTTGACAAAAGTTCTATTT+AGG + chr3.4:60202829-60202848 MS.gene008661:intron 20.0%
! ACACGTGAACATATATTAAT+AGG - chr3.4:60203266-60203285 None:intergenic 25.0%
! ACTTGATTATATTGCAGATT+TGG + chr3.4:60203166-60203185 MS.gene008661:CDS 25.0%
!!! CATTTATCGGATTTTTTTTC+AGG - chr3.4:60202778-60202797 None:intergenic 25.0%
!!! CTTCACAGGTATTTTTTTTT+TGG - chr3.4:60203701-60203720 None:intergenic 25.0%
!!! TTGAGATATTTTTTACATGC+AGG + chr3.4:60203727-60203746 MS.gene008661:intron 25.0%
!!! TTTTTTTGGATAGATATGGT+GGG - chr3.4:60203687-60203706 None:intergenic 25.0%
!!! TTTTTTTTGGATAGATATGG+TGG - chr3.4:60203688-60203707 None:intergenic 25.0%
AAAGAAAGGATACTTCAAGA+AGG + chr3.4:60203854-60203873 MS.gene008661:CDS 30.0%
ACAGATGGAAAAATATTTGC+AGG + chr3.4:60203190-60203209 MS.gene008661:CDS 30.0%
AGTATACCAAAATCAGATCT+TGG + chr3.4:60202516-60202535 MS.gene008661:CDS 30.0%
ATAGATCGATTATGATCGAA+TGG - chr3.4:60203537-60203556 None:intergenic 30.0%
ATTGATGAACCTAAACAACA+AGG + chr3.4:60203651-60203670 MS.gene008661:intron 30.0%
CAGTTGGCAAGTTAAAAATA+TGG + chr3.4:60202679-60202698 MS.gene008661:intron 30.0%
TATCTCAAAATCATCTTCAC+AGG - chr3.4:60203715-60203734 None:intergenic 30.0%
TGATCAAGCAACACAAAAAT+TGG + chr3.4:60202596-60202615 MS.gene008661:CDS 30.0%
TTGATGAACCTAAACAACAA+GGG + chr3.4:60203652-60203671 MS.gene008661:intron 30.0%
TTGCTGTAAGAGAAAAAGAA+AGG + chr3.4:60203840-60203859 MS.gene008661:CDS 30.0%
TTGGCAAGTTAAAAATATGG+AGG + chr3.4:60202682-60202701 MS.gene008661:intron 30.0%
! CAATTTCAAGTCTTAATTGG+TGG - chr3.4:60203823-60203842 None:intergenic 30.0%
! CAGCAATTTCAAGTCTTAAT+TGG - chr3.4:60203826-60203845 None:intergenic 30.0%
! GTTCTATTTAGGCTTTATCA+TGG + chr3.4:60202840-60202859 MS.gene008661:intron 30.0%
!!! TTATTAGTTTTGTGGTCTTG+TGG - chr3.4:60202492-60202511 None:intergenic 30.0%
AAAATCCGATAAATGCGAGT+TGG + chr3.4:60202783-60202802 MS.gene008661:intron 35.0%
ACATACTCGTGTGAAACAAA+TGG - chr3.4:60203929-60203948 None:intergenic 35.0%
AGCGTCTAAGAAATCAAACA+TGG + chr3.4:60202356-60202375 MS.gene008661:CDS 35.0%
ATACATGTTGCAAACAGAAG+AGG + chr3.4:60202329-60202348 MS.gene008661:CDS 35.0%
ATGTACCAGTCATTCTCTTT+GGG - chr3.4:60202311-60202330 None:intergenic 35.0%
CACAAAAATTGGATCCAAAG+AGG + chr3.4:60202607-60202626 MS.gene008661:CDS 35.0%
TACATGTTGCAAACAGAAGA+GGG + chr3.4:60202330-60202349 MS.gene008661:CDS 35.0%
TAGAACCAACTCGCATTTAT+CGG - chr3.4:60202791-60202810 None:intergenic 35.0%
TATGTACCAGTCATTCTCTT+TGG - chr3.4:60202312-60202331 None:intergenic 35.0%
TTTCATAGGCTTCAACTTGT+GGG - chr3.4:60203772-60203791 None:intergenic 35.0%
! ACATGACCAAGATCTGATTT+TGG - chr3.4:60202525-60202544 None:intergenic 35.0%
! ATGTTTGATTTCTTAGACGC+TGG - chr3.4:60202357-60202376 None:intergenic 35.0%
! CAATTGCTCTAGATGTAGAA+CGG + chr3.4:60203425-60203444 MS.gene008661:intron 35.0%
! TATTGCAGATTTGGAACAGA+TGG + chr3.4:60203175-60203194 MS.gene008661:CDS 35.0%
! TTTTCATAGGCTTCAACTTG+TGG - chr3.4:60203773-60203792 None:intergenic 35.0%
!! AATGCGAGTTGGTTCTATTT+AGG + chr3.4:60202794-60202813 MS.gene008661:intron 35.0%
!! ATATGGATCCCTTGTTGTTT+AGG - chr3.4:60203663-60203682 None:intergenic 35.0%
!! TTTCTGAAGCACAAAACAAG+AGG + chr3.4:60204019-60204038 MS.gene008661:CDS 35.0%
AAGCCTATGAAAATCACCAG+CGG + chr3.4:60203780-60203799 MS.gene008661:CDS 40.0%
ATAAGAGAGCTGAGGTGAAT+AGG + chr3.4:60203971-60203990 MS.gene008661:CDS 40.0%
CTTAAGGCTAAACGTGTGAT+GGG + chr3.4:60202720-60202739 MS.gene008661:intron 40.0%
GATGAAGATCCATGTGAGAA+GGG - chr3.4:60202387-60202406 None:intergenic 40.0%
GATTGAGAATAAGAGAGCTG+AGG + chr3.4:60203963-60203982 MS.gene008661:CDS 40.0%
GTTGAGAAGAAACACATCAG+TGG + chr3.4:60202543-60202562 MS.gene008661:CDS 40.0%
TCTTAAGGCTAAACGTGTGA+TGG + chr3.4:60202719-60202738 MS.gene008661:intron 40.0%
TGATGAAGATCCATGTGAGA+AGG - chr3.4:60202388-60202407 None:intergenic 40.0%
! GGATAGATATGGTGGGAATA+TGG - chr3.4:60203680-60203699 None:intergenic 40.0%
! TACTTGCCTCTTGTTTACCA+AGG - chr3.4:60202449-60202468 None:intergenic 40.0%
AAACAAGAGGCAAGTAGCAG+TGG + chr3.4:60202453-60202472 MS.gene008661:CDS 45.0%
ATGGTTAGACCCTTCTCACA+TGG + chr3.4:60202375-60202394 MS.gene008661:CDS 45.0%
CTTCATCAGCATTTCGACCA+TGG + chr3.4:60202400-60202419 MS.gene008661:CDS 45.0%
GAGAAGAAACACATCAGTGG+TGG + chr3.4:60202546-60202565 MS.gene008661:CDS 45.0%
GTATACCGTTTGAGCCTCTT+TGG - chr3.4:60202624-60202643 None:intergenic 45.0%
TGGATCCAAAGAGGCTCAAA+CGG + chr3.4:60202616-60202635 MS.gene008661:CDS 45.0%
! CAACCGCTGGTGATTTTCAT+AGG - chr3.4:60203786-60203805 None:intergenic 45.0%
ACACCATTCGCTTTCGCGAT+TGG - chr3.4:60203311-60203330 None:intergenic 50.0%
ACCATTCGCTTTCGCGATTG+GGG - chr3.4:60203309-60203328 None:intergenic 50.0%
AGCTGAGGTGAATAGGCTGA+GGG + chr3.4:60203978-60203997 MS.gene008661:CDS 50.0%
CAACCCTCTTGGATGAGCAT+CGG + chr3.4:60202423-60202442 MS.gene008661:CDS 50.0%
CACCATTCGCTTTCGCGATT+GGG - chr3.4:60203310-60203329 None:intergenic 50.0%
CATCGGCCTTGGTAAACAAG+AGG + chr3.4:60202440-60202459 MS.gene008661:CDS 50.0%
GCATCTGCAGATGTTGGTGT+TGG + chr3.4:60202573-60202592 MS.gene008661:CDS 50.0%
GGCATCCCAAAGAGAATGAC+TGG + chr3.4:60202303-60202322 MS.gene008661:CDS 50.0%
GGTAGTGCATCTGCAGATGT+TGG + chr3.4:60202567-60202586 MS.gene008661:CDS 50.0%
GTTCAAGACTCAACAACCGC+TGG - chr3.4:60203799-60203818 None:intergenic 50.0%
! TGCTCTAGATGTAGAACGGC+TGG + chr3.4:60203429-60203448 MS.gene008661:intron 50.0%
AAGGCCGATGCTCATCCAAG+AGG - chr3.4:60202430-60202449 None:intergenic 55.0%
AGGCCGATGCTCATCCAAGA+GGG - chr3.4:60202429-60202448 None:intergenic 55.0%
AGGCTTCAACTTGTGGGCGA+AGG - chr3.4:60203766-60203785 None:intergenic 55.0%
CTCATCCAAGAGGGTTGCCA+TGG - chr3.4:60202420-60202439 None:intergenic 55.0%
GAATAGGCTGAGGGAGCTTC+AGG + chr3.4:60203987-60204006 MS.gene008661:CDS 55.0%
GAGCTGAGGTGAATAGGCTG+AGG + chr3.4:60203977-60203996 MS.gene008661:CDS 55.0%
TCCCCAATCGCGAAAGCGAA+TGG + chr3.4:60203305-60203324 MS.gene008661:intron 55.0%
TTCGACCATGGCAACCCTCT+TGG + chr3.4:60202412-60202431 MS.gene008661:CDS 55.0%
!! TCTTGGATGAGCATCGGCCT+TGG + chr3.4:60202429-60202448 MS.gene008661:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 60202297 60204151 60202297 ID=MS.gene008661
chr3.4 mRNA 60202297 60204151 60202297 ID=MS.gene008661.t1;Parent=MS.gene008661
chr3.4 exon 60202297 60202660 60202297 ID=MS.gene008661.t1.exon1;Parent=MS.gene008661.t1
chr3.4 CDS 60202297 60202660 60202297 ID=cds.MS.gene008661.t1;Parent=MS.gene008661.t1
chr3.4 exon 60203129 60203211 60203129 ID=MS.gene008661.t1.exon2;Parent=MS.gene008661.t1
chr3.4 CDS 60203129 60203211 60203129 ID=cds.MS.gene008661.t1;Parent=MS.gene008661.t1
chr3.4 exon 60203749 60203875 60203749 ID=MS.gene008661.t1.exon3;Parent=MS.gene008661.t1
chr3.4 CDS 60203749 60203875 60203749 ID=cds.MS.gene008661.t1;Parent=MS.gene008661.t1
chr3.4 exon 60203959 60204040 60203959 ID=MS.gene008661.t1.exon4;Parent=MS.gene008661.t1
chr3.4 CDS 60203959 60204040 60203959 ID=cds.MS.gene008661.t1;Parent=MS.gene008661.t1
chr3.4 exon 60204139 60204151 60204139 ID=MS.gene008661.t1.exon5;Parent=MS.gene008661.t1
chr3.4 CDS 60204139 60204151 60204139 ID=cds.MS.gene008661.t1;Parent=MS.gene008661.t1
Gene Sequence

>MS.gene008661

ATGCAGGGCATCCCAAAGAGAATGACTGGTACATACATGTTGCAAACAGAAGAGGGACCAGCGTCTAAGAAATCAAACATGGTTAGACCCTTCTCACATGGATCTTCATCAGCATTTCGACCATGGCAACCCTCTTGGATGAGCATCGGCCTTGGTAAACAAGAGGCAAGTAGCAGTGGAGTAAAAGAAACTCCACAAGACCACAAAACTAATAACATTAGTATACCAAAATCAGATCTTGGTCATGTTGAGAAGAAACACATCAGTGGTGGTAGTGCATCTGCAGATGTTGGTGTTGGTGATCAAGCAACACAAAAATTGGATCCAAAGAGGCTCAAACGGTATACTTGTCTTACTTATGCTTGTAAGCAATAAAAAAAATCAGTTGGCAAGTTAAAAATATGGAGGATAGAAATTTTGATTCTTAAGGCTAAACGTGTGATGGGAATAATATATTTTTTTTATTACATTTTTTTTACCTGAAAAAAAATCCGATAAATGCGAGTTGGTTCTATTTAGGTTTTTTTTTTTTTTTTGACAAAAGTTCTATTTAGGCTTTATCATGGTCAACTGTGATTTTAATAATAAACTTAATTAATATTGTAATTGTTTTCATCTTATTTTTAATTAAAAATTAAAATAAATCTATCTGTTGGTTTAAGTTTCATGTTATTAGATTTATCATCTATGAATGTGATACCCTATCTAATATAGTTGATTTGATTGATTTTATTCTAATCAAATCTAAATCAGTTGTTTATTTCCTACACAAAATCAATATAATATATTTTAGATTTTCATCTTTTATCTTATCTTGTTCTTAGGATTGAAGCAAATCGAGCTGCTGCACAAAAATCGAGATTGAAAAAACTTGATTATATTGCAGATTTGGAACAGATGGAAAAATATTTGCAGGTTCACATCATTATTTATCATATCACGAAGATTGTAATTTATGCATTTTGTCCTATTAATATATGTTCACGTGTTTCGAAGAGACTTAAATTATCCCCAATCGCGAAAGCGAATGGTGTTTAGATGAGAATCAAACAACACAAATTCTAATTTCACCAAATTGAAATTGAAATTGAAATACACTTTATGTAATTTGTGTTGTTTGATCTTCATCAATTGCTCTAGATGTAGAACGGCTGGTTACGACTTCAAAAATTTCAATTTCTCGATTATTTGTATTAATTTGATGTAGATAAATACACTACGATCTTGTTGATTTGAACCATTCGATCATAATCGATCTATTCATGTATCAACTTATAATTTGGAATTCAATTGAAAAATTGACATGTGAGTCATTTGATCTAGATCTGATTGTTCAAATAGCATAACTCAACAAATTGATGAACCTAAACAACAAGGGATCCATATTCCCACCATATCTATCCAAAAAAAAAATACCTGTGAAGATGATTTTGAGATATTTTTTACATGCAGGCTGAGTTATCTTTCCTTCGCCCACAAGTTGAAGCCTATGAAAATCACCAGCGGTTGTTGAGTCTTGAACACCACCAATTAAGACTTGAAATTGCTGTAAGAGAAAAAGAAAGGATACTTCAAGAAGGTGATATTACTCATTTGTCTTTATATCTAGCATTTATTATCGTGTCTCTGCCATTTGTTTCACACGAGTATGTTTATTTTCAGTTGAGATTGAGAATAAGAGAGCTGAGGTGAATAGGCTGAGGGAGCTTCAGGAGAAACTAGTTTCTGAAGCACAAAACAAGAGGTATGTTGAAATGCTTACTAGTATTTTTAACAATATTTTTGTACTAATTATAATATGACTCATATGCCTAAATTGTTGTTTAAAAATTCATAATTAAGGTTTGTGTATTAA
Protein sequence

>MS.gene008661.t1

MQGIPKRMTGTYMLQTEEGPASKKSNMVRPFSHGSSSAFRPWQPSWMSIGLGKQEASSSGVKETPQDHKTNNISIPKSDLGHVEKKHISGGSASADVGVGDQATQKLDPKRLKRYTCLTYASNRAAAQKSRLKKLDYIADLEQMEKYLQAELSFLRPQVEAYENHQRLLSLEHHQLRLEIAVREKERILQEVEIENKRAEVNRLRELQEKLVSEAQNKRFVY