AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69416


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69416.t1 MTR_0189s0050 67.424 264 25 2 1 203 178 441 2.89e-118 345
MS.gene69416.t1 MTR_3g105990 66.540 263 27 2 2 203 181 443 3.34e-110 341
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69416.t1 AT3G18090 55.422 166 71 1 38 203 153 315 1.92e-60 202
MS.gene69416.t1 AT3G18090 55.422 166 71 1 38 203 153 315 2.06e-60 202
MS.gene69416.t1 AT3G18090 55.422 166 71 1 38 203 153 315 4.49e-60 202
MS.gene69416.t1 AT3G23780 54.217 166 73 1 38 203 271 433 1.34e-58 198
MS.gene69416.t1 AT3G23780 54.217 166 73 1 38 203 271 433 1.34e-58 198

Find 48 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTATGTCTTTCCGAACATTA+AGG 0.230507 3.3:-93089591 MS.gene69416:CDS
CATGGTGAAGGTTCTCTTAC+TGG 0.253238 3.3:-93089537 MS.gene69416:CDS
GAGAAGAGAGAAATAACTAT+TGG 0.324145 3.3:-93090560 MS.gene69416:CDS
ATTGTTGATCTCATCGATTA+TGG 0.355906 3.3:-93089779 MS.gene69416:CDS
GTTCTCTTACTGGCTTATAC+TGG 0.359333 3.3:-93089527 MS.gene69416:CDS
TATGTCTTTCCGAACATTAA+GGG 0.378939 3.3:-93089590 MS.gene69416:CDS
AGACCTGACTTGACCATAAC+AGG 0.387165 3.3:+93090530 None:intergenic
GGGATGACTTTCAAAATAAG+AGG 0.403829 3.3:-93089484 MS.gene69416:CDS
AACAATTTCTTTATCTGAAG+TGG 0.424244 3.3:+93089796 None:intergenic
TGGTCAAGTCAGGTCTCTGC+TGG 0.429579 3.3:-93090523 MS.gene69416:CDS
AAATGTATCACATTTGTTGT+CGG 0.435955 3.3:+93089706 None:intergenic
AGAAGAGAGAAATAACTATT+GGG 0.440381 3.3:-93090559 MS.gene69416:CDS
GCACATGCTCGGAAGCGAAT+GGG 0.446807 3.3:-93089413 MS.gene69416:CDS
CTGCCTGTTATGGTCAAGTC+AGG 0.458511 3.3:-93090533 MS.gene69416:CDS
TATTGGGAGACTGCCTGTTA+TGG 0.459953 3.3:-93090543 MS.gene69416:CDS
TCGGAAAGACATACAAGTTA+AGG 0.463583 3.3:+93089600 None:intergenic
TGGAGGCTACTTTCTGATCA+AGG 0.477024 3.3:-93090462 MS.gene69416:CDS
AATAAGAGGCTTGAGTTGAC+TGG 0.485554 3.3:-93089470 MS.gene69416:CDS
TTTGTTGTCGGCTTCACGAA+TGG 0.506428 3.3:+93089718 None:intergenic
GGCACGGTACCTGGCATACA+TGG 0.508318 3.3:-93089555 MS.gene69416:CDS
GCTCTGCAAAGAGACCTCTA+TGG 0.509833 3.3:-93089386 MS.gene69416:CDS
CAAATGTGATACATTTCGTA+GGG 0.514699 3.3:-93089699 MS.gene69416:CDS
TTTCTTAGAGGAACGTGTCA+AGG 0.521437 3.3:-93089660 MS.gene69416:CDS
TCTGATCAAGGGTGCTGAGA+AGG 0.528492 3.3:-93090450 MS.gene69416:intron
ATCGATTATGGAGAGGGAGA+TGG 0.529999 3.3:-93089767 MS.gene69416:CDS
TGCACATGCTCGGAAGCGAA+TGG 0.531358 3.3:-93089414 MS.gene69416:CDS
GAACCTTCACCATGTATGCC+AGG 0.538389 3.3:+93089546 None:intergenic
TTTATCTGAAGTGGCACCAA+GGG 0.546561 3.3:+93089805 None:intergenic
TGCTCGGAAGCGAATGGGGA+AGG 0.548332 3.3:-93089408 MS.gene69416:CDS
AAGTGCACTTTGCACATGCT+CGG 0.551400 3.3:-93089424 MS.gene69416:CDS
ACAAATGTGATACATTTCGT+AGG 0.562166 3.3:-93089700 MS.gene69416:CDS
GCACTCGTCAATAGATTCTG+AGG 0.566118 3.3:+93089622 None:intergenic
TGATCAGAAAGTAGCCTCCA+TGG 0.573050 3.3:+93090465 None:intergenic
GATCTCATCGATTATGGAGA+GGG 0.573846 3.3:-93089773 MS.gene69416:CDS
GCATAAAATAGTATCCATAC+CGG 0.577092 3.3:+93089827 None:intergenic
TTCTTAGAGGAACGTGTCAA+GGG 0.577874 3.3:-93089659 MS.gene69416:CDS
GGAGGCTACTTTCTGATCAA+GGG 0.578986 3.3:-93090461 MS.gene69416:CDS
CACATGCTCGGAAGCGAATG+GGG 0.584920 3.3:-93089412 MS.gene69416:CDS
AAACATCTCAATCTCCATAG+AGG 0.600669 3.3:+93089372 None:intergenic
TGTCTGTTGAGATTCCGGTA+TGG 0.606023 3.3:-93089841 MS.gene69416:intron
CTTTATCTGAAGTGGCACCA+AGG 0.607323 3.3:+93089804 None:intergenic
CACTCGTCAATAGATTCTGA+GGG 0.638441 3.3:+93089623 None:intergenic
TGATCTCATCGATTATGGAG+AGG 0.644956 3.3:-93089774 MS.gene69416:CDS
AGTGATTGTGAATTTGACCA+TGG 0.651979 3.3:-93090482 MS.gene69416:CDS
GTACCTGGCATACATGGTGA+AGG 0.671158 3.3:-93089549 MS.gene69416:CDS
TCGTCAATAGATTCTGAGGG+CGG 0.676515 3.3:+93089626 None:intergenic
AAATGTGATACATTTCGTAG+GGG 0.702228 3.3:-93089698 MS.gene69416:CDS
GATTGTGAATTTGACCATGG+AGG 0.783133 3.3:-93090479 MS.gene69416:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACAAAATCCTATTTTTATA+GGG - chr3.3:93089758-93089777 MS.gene69416:CDS 15.0%
!!! TACATATTTTATACATCTTA+TGG - chr3.3:93089572-93089591 MS.gene69416:CDS 15.0%
!!! TTACAAAATCCTATTTTTAT+AGG - chr3.3:93089757-93089776 MS.gene69416:CDS 15.0%
!!! TTTTTAATCCCTATAAAAAT+AGG + chr3.3:93089769-93089788 None:intergenic 15.0%
!! AGTTTAACAAAATTTATGCA+CGG + chr3.3:93089637-93089656 None:intergenic 20.0%
!! ATTTGAGTAAAATTTATCCA+CGG - chr3.3:93089727-93089746 MS.gene69416:CDS 20.0%
!!! AAATACTCATTTTTTGTATG+AGG - chr3.3:93089685-93089704 MS.gene69416:CDS 20.0%
! AAATAGGATGGTTGTTAAAT+TGG - chr3.3:93090022-93090041 MS.gene69416:intron 25.0%
! AACAAAAGCAATTTACAAAC+AGG + chr3.3:93089906-93089925 None:intergenic 25.0%
! AACAATTTCTTTATCTGAAG+TGG + chr3.3:93090152-93090171 None:intergenic 25.0%
! AGAAGAGAGAAATAACTATT+GGG - chr3.3:93089386-93089405 MS.gene69416:CDS 25.0%
! CATTAAGGGATTAAAAAGAA+AGG - chr3.3:93090369-93090388 MS.gene69416:intron 25.0%
! GTTTAACAAAATTTATGCAC+GGG + chr3.3:93089636-93089655 None:intergenic 25.0%
! TTAGTTCCTAATGCAAAATA+GGG + chr3.3:93089665-93089684 None:intergenic 25.0%
!! CTTTTTAATCCCTTAATGTT+CGG + chr3.3:93090367-93090386 None:intergenic 25.0%
!! TTTAGTTCCTAATGCAAAAT+AGG + chr3.3:93089666-93089685 None:intergenic 25.0%
!!! AAATGTATCACATTTGTTGT+CGG + chr3.3:93090242-93090261 None:intergenic 25.0%
!!! ATTTTTAATTCCTTCAATGC+TGG + chr3.3:93090057-93090076 None:intergenic 25.0%
AAATGTGATACATTTCGTAG+GGG - chr3.3:93090247-93090266 MS.gene69416:intron 30.0%
ACAAATGTGATACATTTCGT+AGG - chr3.3:93090245-93090264 MS.gene69416:intron 30.0%
CAAATGTGATACATTTCGTA+GGG - chr3.3:93090246-93090265 MS.gene69416:intron 30.0%
GAGAAGAGAGAAATAACTAT+TGG - chr3.3:93089385-93089404 MS.gene69416:CDS 30.0%
GCATAAAATAGTATCCATAC+CGG + chr3.3:93090121-93090140 None:intergenic 30.0%
TATGTCTTTCCGAACATTAA+GGG - chr3.3:93090355-93090374 MS.gene69416:intron 30.0%
! AAATATTTCTGAAGAGGCTT+TGG - chr3.3:93089949-93089968 MS.gene69416:intron 30.0%
! AAGAGCAAATATTTCTGAAG+AGG - chr3.3:93089943-93089962 MS.gene69416:intron 30.0%
! AATATTTCTGAAGAGGCTTT+GGG - chr3.3:93089950-93089969 MS.gene69416:intron 30.0%
! ATTGTTGATCTCATCGATTA+TGG - chr3.3:93090166-93090185 MS.gene69416:intron 30.0%
! GATTTTGTAAGTTTAATCCG+TGG + chr3.3:93089747-93089766 None:intergenic 30.0%
! TTTAGTCCCTATTTTGCATT+AGG - chr3.3:93089656-93089675 MS.gene69416:CDS 30.0%
!!! TTTTTTGTCTGTTGAGATTC+CGG - chr3.3:93090099-93090118 MS.gene69416:intron 30.0%
AAATGAAGAGAAGTTGCTCA+CGG - chr3.3:93090073-93090092 MS.gene69416:intron 35.0%
ACAAAATTTATGCACGGGAA+CGG + chr3.3:93089631-93089650 None:intergenic 35.0%
ACAGATGAAGAGAAATAGGA+TGG - chr3.3:93090010-93090029 MS.gene69416:intron 35.0%
AGGGATTAAAAAGAAAGGCA+CGG - chr3.3:93090374-93090393 MS.gene69416:intron 35.0%
AGTGACAGATGAAGAGAAAT+AGG - chr3.3:93090006-93090025 MS.gene69416:intron 35.0%
AGTGATTGTGAATTTGACCA+TGG - chr3.3:93089463-93089482 MS.gene69416:CDS 35.0%
GGGATGACTTTCAAAATAAG+AGG - chr3.3:93090461-93090480 MS.gene69416:CDS 35.0%
GGGTTTCAAATATTCCGTAT+TGG - chr3.3:93089970-93089989 MS.gene69416:intron 35.0%
GTATGTCTTTCCGAACATTA+AGG - chr3.3:93090354-93090373 MS.gene69416:intron 35.0%
TAGGATGGTTGTTAAATTGG+TGG - chr3.3:93090025-93090044 MS.gene69416:intron 35.0%
TCGGAAAGACATACAAGTTA+AGG + chr3.3:93090348-93090367 None:intergenic 35.0%
TTATACTGGACGCCAAAAAA+CGG - chr3.3:93090432-93090451 MS.gene69416:intron 35.0%
TTGTATGCAACTGTCCAATA+CGG + chr3.3:93089987-93090006 None:intergenic 35.0%
! GAATGCTGTTCTTTTCTTAG+AGG - chr3.3:93090273-93090292 MS.gene69416:intron 35.0%
! TGGATACTATTTTATGCCCT+TGG - chr3.3:93090124-93090143 MS.gene69416:intron 35.0%
ACGCCAAAAAACGGATAACA+GGG - chr3.3:93090441-93090460 MS.gene69416:intron 40.0%
CACTCGTCAATAGATTCTGA+GGG + chr3.3:93090325-93090344 None:intergenic 40.0%
GATTGTGAATTTGACCATGG+AGG - chr3.3:93089466-93089485 MS.gene69416:CDS 40.0%
TTCTTAGAGGAACGTGTCAA+GGG - chr3.3:93090286-93090305 MS.gene69416:intron 40.0%
TTTCTTAGAGGAACGTGTCA+AGG - chr3.3:93090285-93090304 MS.gene69416:intron 40.0%
! GATCTCATCGATTATGGAGA+GGG - chr3.3:93090172-93090191 MS.gene69416:intron 40.0%
! TGATCTCATCGATTATGGAG+AGG - chr3.3:93090171-93090190 MS.gene69416:intron 40.0%
! TTTATCTGAAGTGGCACCAA+GGG + chr3.3:93090143-93090162 None:intergenic 40.0%
!! AATAAGAGGCTTGAGTTGAC+TGG - chr3.3:93090475-93090494 MS.gene69416:CDS 40.0%
!! GTTCTCTTACTGGCTTATAC+TGG - chr3.3:93090418-93090437 MS.gene69416:intron 40.0%
!!! CATCCCTGTTATCCGTTTTT+TGG + chr3.3:93090447-93090466 None:intergenic 40.0%
AAGTGCACTTTGCACATGCT+CGG - chr3.3:93090521-93090540 MS.gene69416:CDS 45.0%
ATCGATTATGGAGAGGGAGA+TGG - chr3.3:93090178-93090197 MS.gene69416:intron 45.0%
CATGGTGAAGGTTCTCTTAC+TGG - chr3.3:93090408-93090427 MS.gene69416:intron 45.0%
GACGCCAAAAAACGGATAAC+AGG - chr3.3:93090440-93090459 MS.gene69416:intron 45.0%
GCACTCGTCAATAGATTCTG+AGG + chr3.3:93090326-93090345 None:intergenic 45.0%
GGAACGGCTGTGAATTGTAT+AGG + chr3.3:93089615-93089634 None:intergenic 45.0%
TATTGGGAGACTGCCTGTTA+TGG - chr3.3:93089402-93089421 MS.gene69416:CDS 45.0%
TGATCAGAAAGTAGCCTCCA+TGG + chr3.3:93089483-93089502 None:intergenic 45.0%
TGTCTGTTGAGATTCCGGTA+TGG - chr3.3:93090104-93090123 MS.gene69416:intron 45.0%
! AAAAAGAAAGGCACGGTACC+TGG - chr3.3:93090381-93090400 MS.gene69416:intron 45.0%
! AGACCTGACTTGACCATAAC+AGG + chr3.3:93089418-93089437 None:intergenic 45.0%
! CTTTATCTGAAGTGGCACCA+AGG + chr3.3:93090144-93090163 None:intergenic 45.0%
! GGAGGCTACTTTCTGATCAA+GGG - chr3.3:93089484-93089503 MS.gene69416:CDS 45.0%
! GTGGAGAATTCCAGCATTGA+AGG - chr3.3:93090044-93090063 MS.gene69416:intron 45.0%
! TCGTCAATAGATTCTGAGGG+CGG + chr3.3:93090322-93090341 None:intergenic 45.0%
! TGGAGGCTACTTTCTGATCA+AGG - chr3.3:93089483-93089502 MS.gene69416:CDS 45.0%
!! TTTGTTGTCGGCTTCACGAA+TGG + chr3.3:93090230-93090249 None:intergenic 45.0%
CTGCCTGTTATGGTCAAGTC+AGG - chr3.3:93089412-93089431 MS.gene69416:CDS 50.0%
GAACCTTCACCATGTATGCC+AGG + chr3.3:93090402-93090421 None:intergenic 50.0%
GCTCTGCAAAGAGACCTCTA+TGG - chr3.3:93090559-93090578 MS.gene69416:CDS 50.0%
GTACCTGGCATACATGGTGA+AGG - chr3.3:93090396-93090415 MS.gene69416:intron 50.0%
!! TCTGATCAAGGGTGCTGAGA+AGG - chr3.3:93089495-93089514 MS.gene69416:CDS 50.0%
CACATGCTCGGAAGCGAATG+GGG - chr3.3:93090533-93090552 MS.gene69416:CDS 55.0%
GCACATGCTCGGAAGCGAAT+GGG - chr3.3:93090532-93090551 MS.gene69416:CDS 55.0%
TGCACATGCTCGGAAGCGAA+TGG - chr3.3:93090531-93090550 MS.gene69416:CDS 55.0%
TGGTCAAGTCAGGTCTCTGC+TGG - chr3.3:93089422-93089441 MS.gene69416:CDS 55.0%
GGCACGGTACCTGGCATACA+TGG - chr3.3:93090390-93090409 MS.gene69416:intron 60.0%
TGCTCGGAAGCGAATGGGGA+AGG - chr3.3:93090537-93090556 MS.gene69416:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 93089379 93090588 93089379 ID=MS.gene69416
chr3.3 mRNA 93089379 93090588 93089379 ID=MS.gene69416.t1;Parent=MS.gene69416
chr3.3 exon 93090451 93090588 93090451 ID=MS.gene69416.t1.exon1;Parent=MS.gene69416.t1
chr3.3 CDS 93090451 93090588 93090451 ID=cds.MS.gene69416.t1;Parent=MS.gene69416.t1
chr3.3 exon 93089379 93089852 93089379 ID=MS.gene69416.t1.exon2;Parent=MS.gene69416.t1
chr3.3 CDS 93089379 93089852 93089379 ID=cds.MS.gene69416.t1;Parent=MS.gene69416.t1
Gene Sequence

>MS.gene69416

ATGGAGGAGAAGAGAGAAATAACTATTGGGAGACTGCCTGTTATGGTCAAGTCAGGTCTCTGCTGGATGAGTGATGTTGAAAAAAGTGATTGTGAATTTGACCATGGAGGCTACTTTCTGATCAAGGGTGCTGAGAAGGTTAGCTATAATTATGATTTCTTTATTTACTTACATGAATTTCTGTCTTGTTTGCTACATATTTTATACATCTTATGGTTGCATATATTTTTAGTCCTATACAATTCACAGCCGTTCCCGTGCATAAATTTTGTTAAACTTTAGTCCCTATTTTGCATTAGGAACTAAAAATACTCATTTTTTGTATGAGGTTTTCAAAATACAGACTAAATTTGAGTAAAATTTATCCACGGATTAAACTTACAAAATCCTATTTTTATAGGGATTAAAAACATGCATCTCTAGTCTACATTTTAATTCAGTGCATTAATGTTGTATTTATATTATTGTGCTTTGTTTTTGTATGTCTATATTATTATTATATCTTCACAATGTCTTTCTTTGCTCCTGTTTGTAAATTGCTTTTGTTGCAGATTTTTATTGCACAAGAGCAAATATTTCTGAAGAGGCTTTGGGTTTCAAATATTCCGTATTGGACAGTTGCATACAAGTGACAGATGAAGAGAAATAGGATGGTTGTTAAATTGGTGGAGAATTCCAGCATTGAAGGAATTAAAAATGAAGAGAAGTTGCTCACGGTTTTTTTTTGTCTGTTGAGATTCCGGTATGGATACTATTTTATGCCCTTGGTGCCACTTCAGATAAAGAAATTGTTGATCTCATCGATTATGGAGAGGGAGATGGAAGAATTCATAACATTCTCTTTGCATCCATTCGTGAAGCCGACAACAAATGTGATACATTTCGTAGGGGAAAGAATGCTGTTCTTTTCTTAGAGGAACGTGTCAAGGGTGTTCAATATCCGCCCTCAGAATCTATTGACGAGTGCCTTAACTTGTATGTCTTTCCGAACATTAAGGGATTAAAAAGAAAGGCACGGTACCTGGCATACATGGTGAAGGTTCTCTTACTGGCTTATACTGGACGCCAAAAAACGGATAACAGGGATGACTTTCAAAATAAGAGGCTTGAGTTGACTGGTGAGCTGCGCGAGCACGAGATCAAAGTGCACTTTGCACATGCTCGGAAGCGAATGGGGAAGGCTCTGCAAAGAGACCTCTATGGAGATTGA

Protein sequence

>MS.gene69416.t1

MEEKREITIGRLPVMVKSGLCWMSDVEKSDCEFDHGGYFLIKGAEKIPVWILFYALGATSDKEIVDLIDYGEGDGRIHNILFASIREADNKCDTFRRGKNAVLFLEERVKGVQYPPSESIDECLNLYVFPNIKGLKRKARYLAYMVKVLLLAYTGRQKTDNRDDFQNKRLELTGELREHEIKVHFAHARKRMGKALQRDLYGD