AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99919

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99919.t1 MTR_8g447000 90.811 185 14 1 4 188 23 204 2.02e-98 290
MS.gene99919.t1 MTR_8g447000 90.811 185 14 1 4 188 23 204 2.65e-97 290
MS.gene99919.t1 MTR_2g063510 63.731 193 58 4 4 188 22 210 4.68e-59 189
MS.gene99919.t1 MTR_2g063510 63.731 193 58 4 4 188 22 210 3.85e-58 189
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99919.t1 AT5G44680 37.879 198 82 7 1 185 1 170 2.41e-20 89.0
MS.gene99919.t1 AT3G12710 55.670 97 25 5 95 188 50 131 2.75e-18 82.8

Find 40 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTTTGTTGCTGGAGGTCT+TGG 0.223812 4.2:-57347857 None:intergenic
GACTTTAACTTTGGTGAAAT+TGG 0.248820 4.2:-57347833 None:intergenic
GAATTTCTTCTTTCAAGATT+TGG 0.263831 4.2:-57347734 None:intergenic
GAAATCTTTGTTGAGTTTCT+TGG 0.269762 4.2:-57347929 None:intergenic
GATGGTAGTGAAAGTGATTT+TGG 0.288345 4.2:-57347773 None:intergenic
AACATGTCTTTCATTGATCT+TGG 0.300182 4.2:-57347687 None:intergenic
CATAAACTCGACAATGGGTT+TGG 0.305289 4.2:+57349425 MS.gene99919:CDS
AAAATGAAGATTGCTCATTA+TGG 0.312266 4.2:+57348100 MS.gene99919:CDS
AGTTATGAATTACCTGTATT+GGG 0.321034 4.2:-57348232 None:intergenic
CTCTTATCTTCATCCTCTTC+AGG 0.327384 4.2:-57349516 None:intergenic
TCATTGACTCTCTTTGTTGC+TGG 0.334398 4.2:-57347866 None:intergenic
TAGTTATGAATTACCTGTAT+TGG 0.336376 4.2:-57348233 None:intergenic
GGTCTTGGTGACTTTAACTT+TGG 0.354606 4.2:-57347842 None:intergenic
ATCACTACTGTGATTCTCTT+CGG 0.381388 4.2:-57349490 None:intergenic
TGGTGGTGTTGATGAAGTTT+TGG 0.386677 4.2:-57347813 None:intergenic
GATTCACCAGGGAGTATTGC+TGG 0.391119 4.2:+57348037 MS.gene99919:CDS
ATAAACTCGACAATGGGTTT+GGG 0.435027 4.2:+57349426 MS.gene99919:CDS
TCACTACTGTGATTCTCTTC+GGG 0.437036 4.2:-57349489 None:intergenic
GTTGGAAGTGGTGGTGATGA+TGG 0.454983 4.2:-57347791 None:intergenic
TTCTTCATAAACTCGACAAT+GGG 0.464944 4.2:+57349420 MS.gene99919:CDS
AGCTTTATTACACCCAATAC+AGG 0.478219 4.2:+57348220 MS.gene99919:CDS
TTGACTCTCTTTGTTGCTGG+AGG 0.493147 4.2:-57347863 None:intergenic
AGCTTTAAAGAAGGTTCTTG+TGG 0.521274 4.2:+57347971 MS.gene99919:CDS
GTGATTCTCTTCGGGTAGAT+CGG 0.525769 4.2:-57349481 None:intergenic
CAGTAGTGATCTACCTGAAG+AGG 0.545335 4.2:+57349503 MS.gene99919:CDS
TTTGAAATAAGATTGGTTGA+AGG 0.547752 4.2:-57348169 None:intergenic
ATGGGTTTGGGTGATCTGAA+TGG 0.552337 4.2:+57349438 MS.gene99919:CDS
CTCAAGCCAGCAATACTCCC+TGG 0.554438 4.2:-57348043 None:intergenic
TTTAACTTTGGTGAAATTGG+TGG 0.559341 4.2:-57347830 None:intergenic
AAATCAAAGAGCTTTAAAGA+AGG 0.560833 4.2:+57347962 MS.gene99919:CDS
CTTCTTCATAAACTCGACAA+TGG 0.576133 4.2:+57349419 MS.gene99919:CDS
CAGGGAGTATTGCTGGCTTG+AGG 0.580636 4.2:+57348044 MS.gene99919:CDS
AGATCGGCAATCTTTGACAG+TGG 0.588722 4.2:-57349465 None:intergenic
TGGCTTGAGGAGAGAACAGA+TGG 0.590647 4.2:+57348057 MS.gene99919:CDS
AGATTGGTTGAAGGATGAAG+AGG 0.594939 4.2:-57348160 None:intergenic
AATTTGATCACTGATTCACC+AGG 0.605594 4.2:+57348025 MS.gene99919:CDS
AGGTTCTTGTGGTTCTACTG+AGG 0.640760 4.2:+57347982 MS.gene99919:CDS
TTTGGAACTCTGTTACATGT+TGG 0.645924 4.2:-57347716 None:intergenic
TGGCATTGCAGCATGCTCAG+AGG 0.687303 4.2:+57348077 MS.gene99919:CDS
ATTTGATCACTGATTCACCA+GGG 0.698236 4.2:+57348026 MS.gene99919:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATAAGATTAAAATCTA+AGG + chr4.2:57348776-57348795 MS.gene99919:intron 10.0%
!! TAAATAAGATTAAAATCTAA+GGG + chr4.2:57348777-57348796 MS.gene99919:intron 10.0%
!! AATGCTTTCTAATTAAATTA+AGG - chr4.2:57348867-57348886 None:intergenic 15.0%
!! AATTAAAAGAATGTTTAACA+TGG - chr4.2:57348353-57348372 None:intergenic 15.0%
!!! CTATTAATTTTTATTGTCTA+TGG + chr4.2:57349244-57349263 MS.gene99919:intron 15.0%
!!! TAGTTTTTTCAACATAATTT+TGG + chr4.2:57349386-57349405 MS.gene99919:CDS 15.0%
!!! TTTTTCATTTAAAAAATGAC+AGG + chr4.2:57349360-57349379 MS.gene99919:intron 15.0%
!! ACATGAAAAATATTGATAGA+AGG + chr4.2:57348467-57348486 MS.gene99919:intron 20.0%
!! AGGTATCTAATCTAATTAAA+AGG + chr4.2:57348487-57348506 MS.gene99919:intron 20.0%
!! TAAAGTTATAAACAGAAATG+AGG - chr4.2:57349063-57349082 None:intergenic 20.0%
!! TAACAAATGAAAATAAGAAC+AGG - chr4.2:57348443-57348462 None:intergenic 20.0%
!! TTTACACACATTACAAAATT+TGG - chr4.2:57349194-57349213 None:intergenic 20.0%
!!! ACTTGTTTTTGAAATAAGAT+TGG - chr4.2:57348179-57348198 None:intergenic 20.0%
!!! CTAGAAATATTATTTTGGAT+GGG + chr4.2:57349168-57349187 MS.gene99919:intron 20.0%
!!! TGAAGATAAGAGTTTTTTTA+TGG + chr4.2:57349527-57349546 MS.gene99919:CDS 20.0%
!!! TTATTGGCTAACATTAATTT+CGG - chr4.2:57348693-57348712 None:intergenic 20.0%
! AAAATGAAGATTGCTCATTA+TGG + chr4.2:57348100-57348119 MS.gene99919:CDS 25.0%
! AAAATGCTAGATATCAAGAA+TGG - chr4.2:57348844-57348863 None:intergenic 25.0%
! AAATGAAAATAAGAACAGGT+TGG - chr4.2:57348439-57348458 None:intergenic 25.0%
! AAGAATGTTTAACATGGAAA+TGG - chr4.2:57348347-57348366 None:intergenic 25.0%
! AATGAAAATAAGAACAGGTT+GGG - chr4.2:57348438-57348457 None:intergenic 25.0%
! AGTTATGAATTACCTGTATT+GGG - chr4.2:57348235-57348254 None:intergenic 25.0%
! ATATGGTGTACTGTATATTT+AGG + chr4.2:57348519-57348538 MS.gene99919:intron 25.0%
! CTAATCTAATTAAAAGGAGT+AGG + chr4.2:57348493-57348512 MS.gene99919:intron 25.0%
! GAATTTCTTCTTTCAAGATT+TGG - chr4.2:57347737-57347756 None:intergenic 25.0%
! TAGTTATGAATTACCTGTAT+TGG - chr4.2:57348236-57348255 None:intergenic 25.0%
! TATTTCAAAAACAAGTGAAG+AGG + chr4.2:57348183-57348202 MS.gene99919:CDS 25.0%
!! TATTGGCTAACATTAATTTC+GGG - chr4.2:57348692-57348711 None:intergenic 25.0%
!! TTTGAAATAAGATTGGTTGA+AGG - chr4.2:57348172-57348191 None:intergenic 25.0%
!!! AAATCAAAGAGCTTTAAAGA+AGG + chr4.2:57347962-57347981 MS.gene99919:CDS 25.0%
!!! GCTAGAAATATTATTTTGGA+TGG + chr4.2:57349167-57349186 MS.gene99919:intron 25.0%
AACATGTCTTTCATTGATCT+TGG - chr4.2:57347690-57347709 None:intergenic 30.0%
AATGTTTAACATGGAAATGG+TGG - chr4.2:57348344-57348363 None:intergenic 30.0%
ATCTAATTAAAAGGAGTAGG+AGG + chr4.2:57348496-57348515 MS.gene99919:intron 30.0%
GAAATCTTTGTTGAGTTTCT+TGG - chr4.2:57347932-57347951 None:intergenic 30.0%
TATGTCCCACTTATAGATAT+AGG + chr4.2:57349309-57349328 MS.gene99919:intron 30.0%
TGATGAATTCAAGAATGACA+TGG - chr4.2:57348814-57348833 None:intergenic 30.0%
TTAACCATCACTTTACATAG+AGG + chr4.2:57349080-57349099 MS.gene99919:intron 30.0%
TTAACCTCTATGTAAAGTGA+TGG - chr4.2:57349087-57349106 None:intergenic 30.0%
TTCTTCATAAACTCGACAAT+GGG + chr4.2:57349420-57349439 MS.gene99919:CDS 30.0%
! AACAGAAATGAGGTATCTAA+TGG - chr4.2:57349053-57349072 None:intergenic 30.0%
! CGGAGCTAGAAATATTATTT+TGG + chr4.2:57349163-57349182 MS.gene99919:intron 30.0%
! GACTTTAACTTTGGTGAAAT+TGG - chr4.2:57347836-57347855 None:intergenic 30.0%
! TTTAACTTTGGTGAAATTGG+TGG - chr4.2:57347833-57347852 None:intergenic 30.0%
ACCCTCCTATATCTATAAGT+GGG - chr4.2:57349317-57349336 None:intergenic 35.0%
ATCACTACTGTGATTCTCTT+CGG - chr4.2:57349493-57349512 None:intergenic 35.0%
CTTCTTCATAAACTCGACAA+TGG + chr4.2:57349419-57349438 MS.gene99919:CDS 35.0%
TACCCTCCTATATCTATAAG+TGG - chr4.2:57349318-57349337 None:intergenic 35.0%
TAGCAGGTTGTATTATATGC+TGG - chr4.2:57349133-57349152 None:intergenic 35.0%
TCCCACTTATAGATATAGGA+GGG + chr4.2:57349313-57349332 MS.gene99919:intron 35.0%
TGGTGTACTGTATATTTAGG+AGG + chr4.2:57348522-57348541 MS.gene99919:intron 35.0%
TTAAAAGGAGTAGGAGGATA+TGG + chr4.2:57348502-57348521 MS.gene99919:intron 35.0%
TTCAAAAACAAGTGAAGAGG+AGG + chr4.2:57348186-57348205 MS.gene99919:CDS 35.0%
TTGTGATTCTTACTGTACGA+CGG - chr4.2:57348293-57348312 None:intergenic 35.0%
! ATAAACTCGACAATGGGTTT+GGG + chr4.2:57349426-57349445 MS.gene99919:CDS 35.0%
! TTTAACATGGAAATGGTGGA+AGG - chr4.2:57348340-57348359 None:intergenic 35.0%
! TTTGGAACTCTGTTACATGT+TGG - chr4.2:57347719-57347738 None:intergenic 35.0%
!! AATTTGATCACTGATTCACC+AGG + chr4.2:57348025-57348044 MS.gene99919:CDS 35.0%
!! AGCTTTAAAGAAGGTTCTTG+TGG + chr4.2:57347971-57347990 MS.gene99919:CDS 35.0%
!! AGCTTTATTACACCCAATAC+AGG + chr4.2:57348220-57348239 MS.gene99919:CDS 35.0%
!! ATTTGATCACTGATTCACCA+GGG + chr4.2:57348026-57348045 MS.gene99919:CDS 35.0%
!! GATGGTAGTGAAAGTGATTT+TGG - chr4.2:57347776-57347795 None:intergenic 35.0%
CTCTTATCTTCATCCTCTTC+AGG - chr4.2:57349519-57349538 None:intergenic 40.0%
GTCCCACTTATAGATATAGG+AGG + chr4.2:57349312-57349331 MS.gene99919:intron 40.0%
TAGCCAATAAAATCTCACCC+TGG + chr4.2:57348703-57348722 MS.gene99919:intron 40.0%
TCACTACTGTGATTCTCTTC+GGG - chr4.2:57349492-57349511 None:intergenic 40.0%
TGTGATTCTTACTGTACGAC+GGG - chr4.2:57348292-57348311 None:intergenic 40.0%
TTCACTGATCAAACGTGCAT+AGG - chr4.2:57348579-57348598 None:intergenic 40.0%
! AGATTGGTTGAAGGATGAAG+AGG - chr4.2:57348163-57348182 None:intergenic 40.0%
! CATAAACTCGACAATGGGTT+TGG + chr4.2:57349425-57349444 MS.gene99919:CDS 40.0%
! GGTCTTGGTGACTTTAACTT+TGG - chr4.2:57347845-57347864 None:intergenic 40.0%
!! TCATTGACTCTCTTTGTTGC+TGG - chr4.2:57347869-57347888 None:intergenic 40.0%
!!! GATGAAGTTTTGGTTGGAAG+TGG - chr4.2:57347806-57347825 None:intergenic 40.0%
!!! GGTGTTGATGAAGTTTTGGT+TGG - chr4.2:57347812-57347831 None:intergenic 40.0%
!!! TGGTGGTGTTGATGAAGTTT+TGG - chr4.2:57347816-57347835 None:intergenic 40.0%
AAGGTCAGTGAGGATGACAA+TGG - chr4.2:57348321-57348340 None:intergenic 45.0%
AGATCGGCAATCTTTGACAG+TGG - chr4.2:57349468-57349487 None:intergenic 45.0%
ATGGGTTTGGGTGATCTGAA+TGG + chr4.2:57349438-57349457 MS.gene99919:CDS 45.0%
CAACCTGCTACAATCACTAG+CGG + chr4.2:57349143-57349162 MS.gene99919:intron 45.0%
CAATAAAATCTCACCCTGGC+CGG + chr4.2:57348707-57348726 MS.gene99919:intron 45.0%
CAGTAGTGATCTACCTGAAG+AGG + chr4.2:57349503-57349522 MS.gene99919:CDS 45.0%
CGTGCATAGGATTCGATTTC+AGG - chr4.2:57348566-57348585 None:intergenic 45.0%
GTGATTCTCTTCGGGTAGAT+CGG - chr4.2:57349484-57349503 None:intergenic 45.0%
TTGACTCTCTTTGTTGCTGG+AGG - chr4.2:57347866-57347885 None:intergenic 45.0%
! AGGTTCTTGTGGTTCTACTG+AGG + chr4.2:57347982-57348001 MS.gene99919:CDS 45.0%
!!! GAAGTTTTGGTTGGAAGTGG+TGG - chr4.2:57347803-57347822 None:intergenic 45.0%
ACCTACCACCCCATGATTTC+CGG - chr4.2:57348729-57348748 None:intergenic 50.0%
CTCTTTGTTGCTGGAGGTCT+TGG - chr4.2:57347860-57347879 None:intergenic 50.0%
TGGCTTGAGGAGAGAACAGA+TGG + chr4.2:57348057-57348076 MS.gene99919:CDS 50.0%
! CGGCCAGGGTGAGATTTTAT+TGG - chr4.2:57348709-57348728 None:intergenic 50.0%
! GAAATGGTGGAAGGTCAGTG+AGG - chr4.2:57348331-57348350 None:intergenic 50.0%
! GTTGGAAGTGGTGGTGATGA+TGG - chr4.2:57347794-57347813 None:intergenic 50.0%
!! GATTCACCAGGGAGTATTGC+TGG + chr4.2:57348037-57348056 MS.gene99919:CDS 50.0%
CTCAAGCCAGCAATACTCCC+TGG - chr4.2:57348046-57348065 None:intergenic 55.0%
GCTCCGCTAGTGATTGTAGC+AGG - chr4.2:57349149-57349168 None:intergenic 55.0%
TCACCCTGGCCGGAAATCAT+GGG + chr4.2:57348717-57348736 MS.gene99919:intron 55.0%
TGGCATTGCAGCATGCTCAG+AGG + chr4.2:57348077-57348096 MS.gene99919:CDS 55.0%
!! CAGGGAGTATTGCTGGCTTG+AGG + chr4.2:57348044-57348063 MS.gene99919:CDS 55.0%
CACCCCATGATTTCCGGCCA+GGG - chr4.2:57348723-57348742 None:intergenic 60.0%
CACCCTGGCCGGAAATCATG+GGG + chr4.2:57348718-57348737 MS.gene99919:intron 60.0%
CTCACCCTGGCCGGAAATCA+TGG + chr4.2:57348716-57348735 MS.gene99919:intron 60.0%
GCCGGAAATCATGGGGTGGT+AGG + chr4.2:57348725-57348744 MS.gene99919:intron 60.0%
CCACCCCATGATTTCCGGCC+AGG - chr4.2:57348724-57348743 None:intergenic 65.0%
CCTGGCCGGAAATCATGGGG+TGG + chr4.2:57348721-57348740 MS.gene99919:intron 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 57347677 57349563 57347677 ID=MS.gene99919
chr4.2 mRNA 57347677 57349563 57347677 ID=MS.gene99919.t1;Parent=MS.gene99919
chr4.2 exon 57347677 57348241 57347677 ID=MS.gene99919.t1.exon1;Parent=MS.gene99919.t1
chr4.2 CDS 57347677 57348241 57347677 ID=cds.MS.gene99919.t1;Parent=MS.gene99919.t1
chr4.2 exon 57349382 57349563 57349382 ID=MS.gene99919.t1.exon2;Parent=MS.gene99919.t1
chr4.2 CDS 57349382 57349563 57349382 ID=cds.MS.gene99919.t1;Parent=MS.gene99919.t1
Gene Sequence

>MS.gene99919

ATGTGCAGCTCCAAGATCAATGAAAGACATGTTCTTCAACCAACATGTAACAGAGTTCCAAATCTTGAAAGAAGAAATTCAATCAAGAAATTACAACCAAAATCACTTTCACTACCATCATCACCACCACTTCCAACCAAAACTTCATCAACACCACCAATTTCACCAAAGTTAAAGTCACCAAGACCTCCAGCAACAAAGAGAGTCAATGAAACTTATCTCTTAAATACAAGTTCTGAAAAAATTGTAGTACCAAGAAACTCAACAAAGATTTCAACTCTTAAAAAATCAAAGAGCTTTAAAGAAGGTTCTTGTGGTTCTACTGAGGCATCATTGAGTTACTCTTCAAATTTGATCACTGATTCACCAGGGAGTATTGCTGGCTTGAGGAGAGAACAGATGGCATTGCAGCATGCTCAGAGGAAAATGAAGATTGCTCATTATGGAAGATCAAAGTCTGCAAAATTTGAAAGTGTTGTTGTTCCTCTTCATCCTTCAACCAATCTTATTTCAAAAACAAGTGAAGAGGAGGAGAAAAGATGCAGCTTTATTACACCCAATACAGGTAATTCATAACTAATGTGTTTTCAAATATATCAAAGAAAAATACAACCCGTCGTACAGTAAGAATCACAACTAAACCATTGTCATCCTCACTGACCTTCCACCATTTCCATGTTAAACATTCTTTTAATTACTCAATGATATTGATATAAGACGATAGACTCTAAAATTCATTGTGTTTGATGTATGAAATACCCAACCTGTTCTTATTTTCATTTGTTATTTAACATGAAAAATATTGATAGAAGGTATCTAATCTAATTAAAAGGAGTAGGAGGATATGGTGTACTGTATATTTAGGAGGATTTAGTATATTCTTGTGCCTGAAATCGAATCCTATGCACGTTTGATCAGTGAAAATTATATTGATACAATCAAGCATAAGAAAACACGTTAATTAATTTAAGAGCAATGCTATTTATCAAGAAAGATTTTATCAAGAAATTGTCCCGAAATTAATGTTAGCCAATAAAATCTCACCCTGGCCGGAAATCATGGGGTGGTAGGTGTTATGTATTTTTTTTTTGAAACTTTAATAAATAAGATTAAAATCTAAGGGTGATTATTTTGCCATGTCATTCTTGAATTCATCAAGAAAATCCATTCTTGATATCTAGCATTTTCCTTAATTTAATTAGAAAGCATTGAAGTAAAAACAATACAAGAGTCTATTGATGTAAAAATAGAGTAAGTAACAAAGTAACAAACTCTGTAAAGTAACAAAGTTGATTTTAATTCTTAAAAAAAAAAAAATCAGTTTAGTCTTTAATTATATAAGATTGTGCTATGCATACTAATTGTATAAGTAACCATTAGATACCTCATTTCTGTTTATAACTTTAACCATCACTTTACATAGAGGTTAATAAAAATCAATCTCACACAAGAACCAGCATATAATACAACCTGCTACAATCACTAGCGGAGCTAGAAATATTATTTTGGATGGGCCAAATTTTGTAATGTGTGTAAATTTATACTTTTGATTAGTTAATTCGAACGACTATTAATTTTTATTGTCTATGGAACATGATTTATATCGATATTTTAAAGACATTTTAACATAATTATGTCCCACTTATAGATATAGGAGGGTAATAATTTTATTTTAGCTCATAGTTTTTCATTTAAAAAATGACAGGTTGTAGTTTTTTCAACATAATTTTGGCAATATTGTGCTTCTTCATAAACTCGACAATGGGTTTGGGTGATCTGAATGGAGAGCCACTGTCAAAGATTGCCGATCTACCCGAAGAGAATCACAGTAGTGATCTACCTGAAGAGGATGAAGATAAGAGTTTTTTTATGGAATGTTATTGTTAG
Protein sequence

>MS.gene99919.t1

MCSSKINERHVLQPTCNRVPNLERRNSIKKLQPKSLSLPSSPPLPTKTSSTPPISPKLKSPRPPATKRVNETYLLNTSSEKIVVPRNSTKISTLKKSKSFKEGSCGSTEASLSYSSNLITDSPGSIAGLRREQMALQHAQRKMKIAHYGRSKSAKFESVVVPLHPSTNLISKTSEEEEKRCSFITPNTGCSFFNIILAILCFFINSTMGLGDLNGEPLSKIADLPEENHSSDLPEEDEDKSFFMECYC