AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38010.t1 MTR_5g096790 87.021 339 17 2 1 328 1 323 0.0 587
MS.gene38010.t1 MTR_5g096700 42.151 344 151 10 6 327 8 325 5.80e-75 234
MS.gene38010.t1 MTR_3g061090 43.429 350 149 10 1 327 1 324 1.37e-72 228
MS.gene38010.t1 MTR_5g096700 45.035 282 123 6 57 327 6 266 1.08e-68 216
MS.gene38010.t1 MTR_3g061090 50.833 240 101 5 100 327 18 252 2.51e-65 207
MS.gene38010.t1 MTR_3g088560 34.393 346 174 12 7 327 4 321 2.38e-49 167
MS.gene38010.t1 MTR_1g029850 33.430 344 182 11 7 327 5 324 8.65e-49 166
MS.gene38010.t1 MTR_3g088560 40.260 231 120 5 111 327 25 251 1.05e-43 151
MS.gene38010.t1 MTR_3g088560 40.260 231 120 5 111 327 40 266 1.65e-43 151
MS.gene38010.t1 MTR_3g088560 43.333 180 97 3 151 327 22 199 3.13e-40 140
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38010.t1 AT1G55760 41.143 350 156 10 1 327 1 323 2.00e-69 219
MS.gene38010.t1 AT1G21780 36.628 344 167 12 7 327 5 320 8.69e-54 179
MS.gene38010.t1 AT1G21780 36.628 344 167 12 7 327 5 320 8.69e-54 179

Find 49 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCAATATCTAGTGGAATT+TGG 0.233852 5.1:-77173645 MS.gene38010:CDS
TTGGTAAAATACATGAAATC+TGG 0.300649 5.1:-77173626 MS.gene38010:CDS
GATTTGCAGTCTTGAGATCT+AGG 0.320253 5.1:+77174275 None:intergenic
TCAAGATATCTAAATGGAAT+TGG 0.352470 5.1:-77175215 MS.gene38010:intron
GCGAAACTGATGCATTTAAC+TGG 0.358814 5.1:-77174351 MS.gene38010:CDS
AAGCTTTCAAGATATCTAAA+TGG 0.359355 5.1:-77175221 MS.gene38010:CDS
TATGTTTGCACAAGATTCTA+AGG 0.372257 5.1:-77173931 MS.gene38010:CDS
CCCACGGATTCCACTTTGAA+TGG 0.379615 5.1:+77175315 None:intergenic
GCATATAATTTGATAGTAAC+CGG 0.381945 5.1:+77174938 None:intergenic
TTTAGATATCTTGAAAGCTT+CGG 0.402228 5.1:+77175224 None:intergenic
GAATCATAGTTTCGAGCTAT+TGG 0.408610 5.1:-77173808 MS.gene38010:CDS
ATGAATGCTTGACAAACTTC+AGG 0.409567 5.1:+77173870 None:intergenic
ATCTAGCTGTTCTTGCTGCC+CGG 0.416939 5.1:-77173971 MS.gene38010:CDS
CGGAATTTGAAAGATGCAAT+TGG 0.422404 5.1:+77174893 None:intergenic
CCGTGGGTTACGTCGCTCAA+TGG 0.441645 5.1:-77175299 MS.gene38010:CDS
TGCAATTGGTGGATTATTTG+TGG 0.455591 5.1:+77174907 None:intergenic
TTCCGATAGAGTCAAGAATA+CGG 0.466943 5.1:+77174873 None:intergenic
TTCCGTATTCTTGACTCTAT+CGG 0.469882 5.1:-77174875 MS.gene38010:CDS
TGGTAAAATACATGAAATCT+GGG 0.484453 5.1:-77173625 MS.gene38010:CDS
TTGGTTGCTGCTGAGAAATA+CGG 0.484832 5.1:-77173789 MS.gene38010:CDS
TACAATCAAGCTCGTATCAT+CGG 0.487102 5.1:-77174012 MS.gene38010:CDS
TGGAATAACCTTCGCAGAGA+CGG 0.491897 5.1:-77174846 MS.gene38010:CDS
GGAATAACCTTCGCAGAGAC+GGG 0.508589 5.1:-77174845 MS.gene38010:intron
TCTGCATCGTTGTGGAAAAG+AGG 0.517234 5.1:+77174397 None:intergenic
AATTTGAAAGATGCAATTGG+TGG 0.524532 5.1:+77174896 None:intergenic
ACACAGGATGTTGTAACATC+AGG 0.530431 5.1:+77174310 None:intergenic
TTAACTAAGGAAGAAATTCA+CGG 0.535488 5.1:+77173547 None:intergenic
GTTAAATGCATCAGTTTCGC+TGG 0.535589 5.1:+77174354 None:intergenic
TTCTCTTAACATTCGAACAA+GGG 0.536373 5.1:+77174052 None:intergenic
TATATTCAAACATAGGTGAC+CGG 0.536701 5.1:+77173952 None:intergenic
AGCGCAACTAATCTTCAAGT+AGG 0.555426 5.1:+77173665 None:intergenic
TTTCTCTTAACATTCGAACA+AGG 0.556453 5.1:+77174051 None:intergenic
TCTTGAAAGCTTCGGATGTG+TGG 0.556978 5.1:+77175232 None:intergenic
TCCATTCAAAGTGGAATCCG+TGG 0.560598 5.1:-77175316 MS.gene38010:CDS
GCAAACATATATTCAAACAT+AGG 0.563128 5.1:+77173945 None:intergenic
CGAAACTGATGCATTTAACT+GGG 0.567854 5.1:-77174350 MS.gene38010:CDS
CGGATGTGTGGATAAAGCTG+TGG 0.593373 5.1:+77175244 None:intergenic
GCGCAACTAATCTTCAAGTA+GGG 0.602481 5.1:+77173666 None:intergenic
TAGGAATTCAACTTCAACAC+AGG 0.603549 5.1:+77174294 None:intergenic
CCATTGAGCGACGTAACCCA+CGG 0.604930 5.1:+77175299 None:intergenic
CGGCGTTAATGATTTGAGAG+AGG 0.605267 5.1:-77173769 MS.gene38010:CDS
TAGTTGCGCTCAATATCTAG+TGG 0.608180 5.1:-77173652 MS.gene38010:CDS
ATAGAGAAACTAACTCAACT+AGG 0.608240 5.1:-77174088 MS.gene38010:CDS
GGATGTGTGGATAAAGCTGT+GGG 0.609946 5.1:+77175245 None:intergenic
CCATTCAAAGTGGAATCCGT+GGG 0.610952 5.1:-77175315 MS.gene38010:CDS
ATTGATAGAAATATGCAGCA+TGG 0.618155 5.1:+77173691 None:intergenic
ATATTCAAACATAGGTGACC+GGG 0.654376 5.1:+77173953 None:intergenic
GCTTGATTGTAGCGTCTGTG+TGG 0.704769 5.1:+77174024 None:intergenic
GATGTGTGGATAAAGCTGTG+GGG 0.847745 5.1:+77175246 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTTCAATTATATCATTA+AGG - chr5.1:77174120-77174139 MS.gene38010:intron 10.0%
!!! ATAATTTTAGTATTGATATT+AGG - chr5.1:77174711-77174730 MS.gene38010:intron 10.0%
!! ATTATAAGTATATATGTTTG+TGG + chr5.1:77174264-77174283 None:intergenic 15.0%
!!! TGTTTAAATTTTTTGAATGA+AGG - chr5.1:77174767-77174786 MS.gene38010:intron 15.0%
!!! TTTCATAGACAAAATTTTTT+AGG + chr5.1:77174387-77174406 None:intergenic 15.0%
!! ATGCTTATATCTATATGAAT+AGG - chr5.1:77174324-77174343 MS.gene38010:CDS 20.0%
!! ATTGAATAAAACAAGACATA+TGG - chr5.1:77174424-77174443 MS.gene38010:CDS 20.0%
!! CTCTAATCATAAAAATCATA+TGG - chr5.1:77173762-77173781 MS.gene38010:CDS 20.0%
!! TGCTTATATCTATATGAATA+GGG - chr5.1:77174325-77174344 MS.gene38010:CDS 20.0%
! AACAAGACATATGGTTAAAT+AGG - chr5.1:77174433-77174452 MS.gene38010:intron 25.0%
! AAGCTTTCAAGATATCTAAA+TGG - chr5.1:77173657-77173676 MS.gene38010:CDS 25.0%
! ACAGAAAAAATATACTTGAG+TGG - chr5.1:77175162-77175181 MS.gene38010:intron 25.0%
! ATCATAAAAATCATATGGTC+TGG - chr5.1:77173767-77173786 MS.gene38010:CDS 25.0%
! CTTTCAGAATGTAACAAATT+AGG + chr5.1:77174241-77174260 None:intergenic 25.0%
! GCAAACATATATTCAAACAT+AGG + chr5.1:77174936-77174955 None:intergenic 25.0%
! TCAAGATATCTAAATGGAAT+TGG - chr5.1:77173663-77173682 MS.gene38010:CDS 25.0%
! TGGTAAAATACATGAAATCT+GGG - chr5.1:77175253-77175272 MS.gene38010:CDS 25.0%
! TTACTTATAGAACTATGAGT+TGG - chr5.1:77174088-77174107 MS.gene38010:CDS 25.0%
! TTGGTAAAATACATGAAATC+TGG - chr5.1:77175252-77175271 MS.gene38010:CDS 25.0%
! TTTAGATATCTTGAAAGCTT+CGG + chr5.1:77173657-77173676 None:intergenic 25.0%
!! GCATATAATTTGATAGTAAC+CGG + chr5.1:77173943-77173962 None:intergenic 25.0%
!!! GTCTATGAAAATGTTGTTTT+TGG - chr5.1:77174397-77174416 MS.gene38010:CDS 25.0%
AATTTGAAAGATGCAATTGG+TGG + chr5.1:77173985-77174004 None:intergenic 30.0%
ATAGAGAAACTAACTCAACT+AGG - chr5.1:77174790-77174809 MS.gene38010:intron 30.0%
ATTGATAGAAATATGCAGCA+TGG + chr5.1:77175190-77175209 None:intergenic 30.0%
TACCAACGTTATGATGAAAT+CGG + chr5.1:77173796-77173815 None:intergenic 30.0%
TATATTCAAACATAGGTGAC+CGG + chr5.1:77174929-77174948 None:intergenic 30.0%
TATGTTTGCACAAGATTCTA+AGG - chr5.1:77174947-77174966 MS.gene38010:intron 30.0%
TGATTAAATGCACGTACATT+TGG + chr5.1:77174628-77174647 None:intergenic 30.0%
TTCTCTTAACATTCGAACAA+GGG + chr5.1:77174829-77174848 None:intergenic 30.0%
TTTCTCTTAACATTCGAACA+AGG + chr5.1:77174830-77174849 None:intergenic 30.0%
! TTTTCTTGCCTTCCTAAAAT+TGG - chr5.1:77175280-77175299 MS.gene38010:CDS 30.0%
!!! TTTTTTACTTCCCAACACAA+AGG - chr5.1:77173884-77173903 MS.gene38010:CDS 30.0%
AATGATATGTGCCTTTGTGT+TGG + chr5.1:77173898-77173917 None:intergenic 35.0%
ATATTCAAACATAGGTGACC+GGG + chr5.1:77174928-77174947 None:intergenic 35.0%
ATCCGATTTCATCATAACGT+TGG - chr5.1:77173791-77173810 MS.gene38010:CDS 35.0%
ATGAATGCTTGACAAACTTC+AGG + chr5.1:77175011-77175030 None:intergenic 35.0%
ATGATATGTGCCTTTGTGTT+GGG + chr5.1:77173897-77173916 None:intergenic 35.0%
CGAAACTGATGCATTTAACT+GGG - chr5.1:77174528-77174547 MS.gene38010:intron 35.0%
CGGAATTTGAAAGATGCAAT+TGG + chr5.1:77173988-77174007 None:intergenic 35.0%
CTTGACTCTATCGGAAAAAA+TGG - chr5.1:77174012-77174031 MS.gene38010:CDS 35.0%
GAATCATAGTTTCGAGCTAT+TGG - chr5.1:77175070-77175089 MS.gene38010:intron 35.0%
GCTCAATATCTAGTGGAATT+TGG - chr5.1:77175233-77175252 MS.gene38010:CDS 35.0%
TACAATCAAGCTCGTATCAT+CGG - chr5.1:77174866-77174885 MS.gene38010:CDS 35.0%
TAGGAATTCAACTTCAACAC+AGG + chr5.1:77174587-77174606 None:intergenic 35.0%
TATGAATAGGGACTATGAGT+TGG - chr5.1:77174337-77174356 MS.gene38010:CDS 35.0%
TTCCGATAGAGTCAAGAATA+CGG + chr5.1:77174008-77174027 None:intergenic 35.0%
TTCCGTATTCTTGACTCTAT+CGG - chr5.1:77174003-77174022 MS.gene38010:CDS 35.0%
! CATCATCATCTGCCAATTTT+AGG + chr5.1:77175295-77175314 None:intergenic 35.0%
! GTTTTACTCTCCATTCAAAG+TGG - chr5.1:77173553-77173572 MS.gene38010:CDS 35.0%
! TAATTTGATAGTAACCGGAC+TGG + chr5.1:77173938-77173957 None:intergenic 35.0%
!! ATCATCTGCCAATTTTAGGA+AGG + chr5.1:77175291-77175310 None:intergenic 35.0%
!! TGCAATTGGTGGATTATTTG+TGG + chr5.1:77173974-77173993 None:intergenic 35.0%
AAGGCACATATCATTCTCGA+GGG - chr5.1:77173903-77173922 MS.gene38010:CDS 40.0%
ACACAGGATGTTGTAACATC+AGG + chr5.1:77174571-77174590 None:intergenic 40.0%
AGCGCAACTAATCTTCAAGT+AGG + chr5.1:77175216-77175235 None:intergenic 40.0%
GATTTGCAGTCTTGAGATCT+AGG + chr5.1:77174606-77174625 None:intergenic 40.0%
GCGAAACTGATGCATTTAAC+TGG - chr5.1:77174527-77174546 MS.gene38010:intron 40.0%
GCGCAACTAATCTTCAAGTA+GGG + chr5.1:77175215-77175234 None:intergenic 40.0%
GTTAAATGCATCAGTTTCGC+TGG + chr5.1:77174527-77174546 None:intergenic 40.0%
TAGTTGCGCTCAATATCTAG+TGG - chr5.1:77175226-77175245 MS.gene38010:CDS 40.0%
TTGGTTGCTGCTGAGAAATA+CGG - chr5.1:77175089-77175108 MS.gene38010:intron 40.0%
! AAAGGCACATATCATTCTCG+AGG - chr5.1:77173902-77173921 MS.gene38010:CDS 40.0%
! CTTTTTCTTCTGCATCGTTG+TGG + chr5.1:77174492-77174511 None:intergenic 40.0%
CCATTCAAAGTGGAATCCGT+GGG - chr5.1:77173563-77173582 MS.gene38010:CDS 45.0%
CGGCGTTAATGATTTGAGAG+AGG - chr5.1:77175109-77175128 MS.gene38010:intron 45.0%
GATGTGTGGATAAAGCTGTG+GGG + chr5.1:77173635-77173654 None:intergenic 45.0%
GGATGTGTGGATAAAGCTGT+GGG + chr5.1:77173636-77173655 None:intergenic 45.0%
TCCATTCAAAGTGGAATCCG+TGG - chr5.1:77173562-77173581 MS.gene38010:CDS 45.0%
TCTGCATCGTTGTGGAAAAG+AGG + chr5.1:77174484-77174503 None:intergenic 45.0%
TCTTGAAAGCTTCGGATGTG+TGG + chr5.1:77173649-77173668 None:intergenic 45.0%
TGGAATAACCTTCGCAGAGA+CGG - chr5.1:77174032-77174051 MS.gene38010:CDS 45.0%
! GATAGTAACCGGACTGGAAA+GGG + chr5.1:77173932-77173951 None:intergenic 45.0%
! TGATAGTAACCGGACTGGAA+AGG + chr5.1:77173933-77173952 None:intergenic 45.0%
!!! TTTTTTACCCGTCTCTGCGA+AGG + chr5.1:77174043-77174062 None:intergenic 45.0%
ATCTAGCTGTTCTTGCTGCC+CGG - chr5.1:77174907-77174926 MS.gene38010:CDS 50.0%
CCCACGGATTCCACTTTGAA+TGG + chr5.1:77173566-77173585 None:intergenic 50.0%
CGGATGTGTGGATAAAGCTG+TGG + chr5.1:77173637-77173656 None:intergenic 50.0%
GCTTGATTGTAGCGTCTGTG+TGG + chr5.1:77174857-77174876 None:intergenic 50.0%
GGAATAACCTTCGCAGAGAC+GGG - chr5.1:77174033-77174052 MS.gene38010:CDS 50.0%
CCATTGAGCGACGTAACCCA+CGG + chr5.1:77173582-77173601 None:intergenic 55.0%
GAGGGATTCCCTTTCCAGTC+CGG - chr5.1:77173921-77173940 MS.gene38010:CDS 55.0%
! CCGTGGGTTACGTCGCTCAA+TGG - chr5.1:77173579-77173598 MS.gene38010:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 77173551 77175349 77173551 ID=MS.gene38010
chr5.1 mRNA 77173551 77175349 77173551 ID=MS.gene38010.t1;Parent=MS.gene38010
chr5.1 exon 77175216 77175349 77175216 ID=MS.gene38010.t1.exon1;Parent=MS.gene38010.t1
chr5.1 CDS 77175216 77175349 77175216 ID=cds.MS.gene38010.t1;Parent=MS.gene38010.t1
chr5.1 exon 77174846 77174961 77174846 ID=MS.gene38010.t1.exon2;Parent=MS.gene38010.t1
chr5.1 CDS 77174846 77174961 77174846 ID=cds.MS.gene38010.t1;Parent=MS.gene38010.t1
chr5.1 exon 77174270 77174445 77174270 ID=MS.gene38010.t1.exon3;Parent=MS.gene38010.t1
chr5.1 CDS 77174270 77174445 77174270 ID=cds.MS.gene38010.t1;Parent=MS.gene38010.t1
chr5.1 exon 77173551 77174111 77173551 ID=MS.gene38010.t1.exon4;Parent=MS.gene38010.t1
chr5.1 CDS 77173551 77174111 77173551 ID=cds.MS.gene38010.t1;Parent=MS.gene38010.t1
Gene Sequence

>MS.gene38010

ATGTTTTACTCTCCATTCAAAGTGGAATCCGTGGGTTACGTCGCTCAATGGAGACTCAGCTTTAAGAGCATGAATATGATTCCCCACAGCTTTATCCACACATCCGAAGCTTTCAAGATATCTAAATGGAATTGGTAATTTTTTTCTTTTTCTCTTCTATAGTTCGACAATACATTATTTTATTTTAATTTTGACAATAATTCATATATGACTCTAATCATAAAAATCATATGGTCTGGTATCCGATTTCATCATAACGTTGGTAATAGTTAAAGTTTATATTTTATTTACGTGTAAATTTGTGAAAATATAAATTGCTAAGTTTTTCATTTTTTTTTTACTTCCCAACACAAAGGCACATATCATTCTCGAGGGATTCCCTTTCCAGTCCGGTTACTATCAAATTATATGCAGAAGAGTCCACAAATAATCCACCAATTGCATCTTTCAAATTCCGTATTCTTGACTCTATCGGAAAAAATGGAATAACCTTCGCAGAGACGGGTAAAAAAATCGACTCTCTCTTTTTAGCATGCTTTACTTATAGAACTATGAGTTGGATTCTTTTATTATTTCAATTATATCATTAAGGTTTAAACAAATTTACTTATAAAATGCTATATTTTTTGTGTTATTGAAAAGATGATAATTTATATTTGATTTGTTATATCGTTATTAAAAGATTAACCTAATTTGTTACATTCTGAAAGCCACAAACATATATACTTATAATTTTAATCAAAATAAATATTTTTTAAATTTTTTTTAAAAAAATGCTTATATCTATATGAATAGGGACTATGAGTTGGACTTGTCATTATTTCAATTATATACCTAAAAAATTTTGTCTATGAAAATGTTGTTTTTGGTGTTATTGAATAAAACAAGACATATGGTTAAATAGGTATATATAAGTTTATAATTTGTCTTCCTCTTTTCCACAACGATGCAGAAGAAAAAGACAAGCTTTTCACCAGCGAAACTGATGCATTTAACTGGGAGTTTGATGTTCGACTACCTGATGTTACAACATCCTGTGTTGAAGTTGAATTCCTAGATCTCAAGACTGCAAATCCAAATGTACGTGCATTTAATCAATTTATTTGTTCAAGTATCTTACTAATATTGATATAATCATGAAGTATGTATGTTGCACTTTTATAATTTTAGTATTGATATTAGGTTACTATTAATTTACTTCATGTTATTCACTATTTGTTTAAATTTTTTGAATGAAGGATAGAGAAACTAACTCAACTAGGAAAAGATCAACAACCCTTGTTCGAATGTTAAGAGAAAGTATCCACACAGACGCTACAATCAAGCTCGTATCATCGGATAAAATCATAAGAGTTCATCTAGCTGTTCTTGCTGCCCGGTCACCTATGTTTGAATATATGTTTGCACAAGATTCTAAGGAGAATAACATGTCTGTTATTAACATCTCAGATATGTCACCTGAAGTTTGTCAAGCATTCATAGATTATCTATATGACAACATCGACGATGAAGAACTTGCGAATCATAGTTTCGAGCTATTGGTTGCTGCTGAGAAATACGGCGTTAATGATTTGAGAGAGGAGTGTGAAAAGAGTCTTCAAGAAGATATCAACAGAAAAAATATACTTGAGTGGCTCCATGCTGCATATTTCTATCAATTGCCCTACTTGAAGATTAGTTGCGCTCAATATCTAGTGGAATTTGGTAAAATACATGAAATCTGGGATGATTTTCTTGCCTTCCTAAAATTGGCAGATGATGATGTAATTTGCGAAATTTTCCGTGAATTTCTTCCTTAG
Protein sequence

>MS.gene38010.t1

MFYSPFKVESVGYVAQWRLSFKSMNMIPHSFIHTSEAFKISKWNCPVTIKLYAEESTNNPPIASFKFRILDSIGKNGITFAETGIYKFIICLPLFHNDAEEKDKLFTSETDAFNWEFDVRLPDVTTSCVEVEFLDLKTANPNDRETNSTRKRSTTLVRMLRESIHTDATIKLVSSDKIIRVHLAVLAARSPMFEYMFAQDSKENNMSVINISDMSPEVCQAFIDYLYDNIDDEELANHSFELLVAAEKYGVNDLREECEKSLQEDINRKNILEWLHAAYFYQLPYLKISCAQYLVEFGKIHEIWDDFLAFLKLADDDVICEIFREFLP