AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053963


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053963.t1 MTR_5g049230 99.603 252 1 0 1 252 47 298 0.0 509
MS.gene053963.t1 MTR_5g049240 86.508 252 34 0 1 252 2 253 1.04e-160 449
MS.gene053963.t1 MTR_5g049240 86.508 252 34 0 1 252 47 298 1.47e-159 447
MS.gene053963.t1 MTR_8g069850 76.984 252 58 0 1 252 47 298 3.06e-147 414
MS.gene053963.t1 MTR_4g086150 44.017 234 124 2 19 252 61 287 2.54e-64 204
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053963.t1 AT1G13580 69.841 252 76 0 1 252 47 298 1.03e-130 372
MS.gene053963.t1 AT1G13580 69.841 252 76 0 1 252 47 298 1.03e-130 372
MS.gene053963.t1 AT3G25540 63.922 255 88 2 1 252 47 300 2.49e-118 340
MS.gene053963.t1 AT3G25540 63.922 255 88 2 1 252 47 300 2.49e-118 340
MS.gene053963.t1 AT1G26200 56.870 262 97 3 1 252 46 301 3.54e-104 305
MS.gene053963.t1 AT1G26200 54.444 270 102 3 1 252 46 312 2.67e-101 298
MS.gene053963.t1 AT1G13580 71.354 192 55 0 1 192 47 238 1.34e-99 290
MS.gene053963.t1 AT3G25540 64.615 195 66 1 1 192 47 241 2.03e-90 267
MS.gene053963.t1 AT1G26200 60.309 194 74 1 1 194 46 236 6.60e-82 245
MS.gene053963.t1 AT3G19260 45.528 246 127 2 7 252 51 289 9.46e-73 224

Find 37 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAAGATTAACAAATTTA+AGG 0.125028 5.2:+43127816 MS.gene053963:CDS
CCATACTTGCTTTAATATTC+TGG 0.136312 5.2:+43128123 MS.gene053963:CDS
TGCTTGTTCTTAACATTTAT+TGG 0.179322 5.2:+43129289 MS.gene053963:CDS
TGATGCTACTGATGTGTTTC+TGG 0.182167 5.2:+43128434 MS.gene053963:CDS
GTGTCGTTTACTACCCATTT+TGG 0.238501 5.2:+43128544 MS.gene053963:CDS
CCAGAATATTAAAGCAAGTA+TGG 0.250823 5.2:-43128123 None:intergenic
ACTGGTTGCCACCTTGAAAT+TGG 0.253838 5.2:+43129206 MS.gene053963:CDS
ACACTCAGGTTTGTTCGAAT+TGG 0.325304 5.2:+43128390 MS.gene053963:intron
GAAACAAGACGCTCTGACTT+TGG 0.337924 5.2:+43128146 MS.gene053963:CDS
GTACTTCGAAGAACCCAAAA+TGG 0.344972 5.2:-43128558 None:intergenic
CTGATTCTTCGGATGCTTGT+TGG 0.351437 5.2:+43129318 MS.gene053963:CDS
CCTTGAAATTGGAAAATCAT+TGG 0.362965 5.2:+43129217 MS.gene053963:CDS
AAACAAGACGCTCTGACTTT+GGG 0.369876 5.2:+43128147 MS.gene053963:CDS
CATACTTGCTTTAATATTCT+GGG 0.380439 5.2:+43128124 MS.gene053963:CDS
TTGGAAAATCATTGGGTGAA+TGG 0.396407 5.2:+43129225 MS.gene053963:CDS
ACTGATGTGTTTCTGGAGAT+AGG 0.414778 5.2:+43128441 MS.gene053963:CDS
CTTGAAATTGGAAAATCATT+GGG 0.421846 5.2:+43129218 MS.gene053963:CDS
ATTGGTGGGTGCTGATTCTT+CGG 0.444061 5.2:+43129307 MS.gene053963:CDS
TCTGGCCATCTCTGATTCCC+TGG 0.444917 5.2:-43127943 None:intergenic
TCTTTGTTGCAGCTATGAAC+TGG 0.456363 5.2:+43129188 MS.gene053963:intron
CTGTAACATACGACGAGCCT+TGG 0.465040 5.2:+43127890 MS.gene053963:CDS
CTGATGTGTTTCTGGAGATA+GGG 0.490323 5.2:+43128442 MS.gene053963:CDS
TTTGGGTTCTTCGAAGTACA+AGG 0.496763 5.2:+43128562 MS.gene053963:CDS
TTGTTCTTAACATTTATTGG+TGG 0.510641 5.2:+43129292 MS.gene053963:CDS
GTTAGTGAAGATATACGATC+TGG 0.513493 5.2:+43129363 MS.gene053963:CDS
GTAGTAAACGACACGTAGTA+TGG 0.517462 5.2:-43128535 None:intergenic
GGGCTGTATATGTATGGTGC+TGG 0.528738 5.2:+43128086 MS.gene053963:CDS
TGTTCTTAACATTTATTGGT+GGG 0.530572 5.2:+43129293 MS.gene053963:CDS
TTGAAAGGGCTGTATATGTA+TGG 0.545225 5.2:+43128080 MS.gene053963:CDS
TACTTCGAAGAACCCAAAAT+GGG 0.551224 5.2:-43128557 None:intergenic
TTGGGCCAGGGAATCAGAGA+TGG 0.559128 5.2:+43127938 MS.gene053963:CDS
GTTGGTCAAATTCGAGCAAG+AGG 0.587622 5.2:+43129336 MS.gene053963:CDS
TTGGTCAAATTCGAGCAAGA+GGG 0.591303 5.2:+43129337 MS.gene053963:CDS
ATGTGTAGAAATTGGCCAGA+CGG 0.612314 5.2:+43127740 None:intergenic
AAATGTAGGATAACACAATG+AGG 0.666787 5.2:-43128202 None:intergenic
GGGAAAATGTCCAAATACAG+CGG 0.695232 5.2:+43128462 MS.gene053963:CDS
ACAAATTTAAGGAATCAGCG+TGG 0.724000 5.2:+43127827 MS.gene053963:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGAAGATTAACAAATTTA+AGG + chr5.2:43127816-43127835 MS.gene053963:CDS 15.0%
!! AATAAATTACTCAGTTTATA+CGG + chr5.2:43129130-43129149 MS.gene053963:intron 15.0%
!! ATATCCTTTAAATTTACATT+TGG - chr5.2:43128699-43128718 None:intergenic 15.0%
!! ATTGAAAAGTTAAGTAAAAT+AGG - chr5.2:43128370-43128389 None:intergenic 15.0%
!! TATCCTTTAAATTTACATTT+GGG - chr5.2:43128698-43128717 None:intergenic 15.0%
!!! TACTGATACAAAATATTTTT+GGG + chr5.2:43127915-43127934 MS.gene053963:CDS 15.0%
!!! TTACTGATACAAAATATTTT+TGG + chr5.2:43127914-43127933 MS.gene053963:CDS 15.0%
!! AATCCCAAATGTAAATTTAA+AGG + chr5.2:43128692-43128711 MS.gene053963:intron 20.0%
!! TATATGAGTAAAGTATAAAG+TGG + chr5.2:43128997-43129016 MS.gene053963:intron 20.0%
!! TCTTGTAAAAAAGTAATCAT+TGG + chr5.2:43128742-43128761 MS.gene053963:intron 20.0%
!! TTCAATCTGAAAATTGTAAA+TGG - chr5.2:43128059-43128078 None:intergenic 20.0%
!! TTTATACTTTACTCATATAG+AGG - chr5.2:43128996-43129015 None:intergenic 20.0%
!! TTTGTTAAAATTTCAACTCT+TGG - chr5.2:43129028-43129047 None:intergenic 20.0%
!!! ATACAAAATATTTTTGGGTT+GGG + chr5.2:43127920-43127939 MS.gene053963:CDS 20.0%
!!! ATTTTCAGATTGAAATTGAA+AGG + chr5.2:43128065-43128084 MS.gene053963:intron 20.0%
!!! GAAATGTGTTTATTTTCTAT+CGG + chr5.2:43127849-43127868 MS.gene053963:CDS 20.0%
!!! TTTTCAGATTGAAATTGAAA+GGG + chr5.2:43128066-43128085 MS.gene053963:intron 20.0%
!!! TTTTTTTAACTTCCACTAAA+TGG - chr5.2:43128674-43128693 None:intergenic 20.0%
! AAAAAGTAATCATTGGTGAA+TGG + chr5.2:43128749-43128768 MS.gene053963:intron 25.0%
! AAAATAGGAAATTGAACTAG+TGG - chr5.2:43128355-43128374 None:intergenic 25.0%
! ACAACTGACAAATAACAATT+GGG - chr5.2:43128001-43128020 None:intergenic 25.0%
! CATACTTGCTTTAATATTCT+GGG + chr5.2:43128124-43128143 MS.gene053963:CDS 25.0%
! CTAGGTGAATTATATAATGT+CGG + chr5.2:43128642-43128661 MS.gene053963:intron 25.0%
! CTTGAAATTGGAAAATCATT+GGG + chr5.2:43129218-43129237 MS.gene053963:CDS 25.0%
! TGCTTGTTCTTAACATTTAT+TGG + chr5.2:43129289-43129308 MS.gene053963:CDS 25.0%
! TGTTCTTAACATTTATTGGT+GGG + chr5.2:43129293-43129312 MS.gene053963:CDS 25.0%
! TTGTTCTTAACATTTATTGG+TGG + chr5.2:43129292-43129311 MS.gene053963:CDS 25.0%
!! TATTTTGTATCAGTAAACCA+AGG - chr5.2:43127910-43127929 None:intergenic 25.0%
!! TCTTACTTAATCTTTTGATC+TGG - chr5.2:43127964-43127983 None:intergenic 25.0%
!! TTGTGTTATCCTACATTTTT+AGG + chr5.2:43128207-43128226 MS.gene053963:CDS 25.0%
!!! GATACAAAATATTTTTGGGT+TGG + chr5.2:43127919-43127938 MS.gene053963:CDS 25.0%
AAATGTAGGATAACACAATG+AGG - chr5.2:43128205-43128224 None:intergenic 30.0%
CCAGAATATTAAAGCAAGTA+TGG - chr5.2:43128126-43128145 None:intergenic 30.0%
CCATACTTGCTTTAATATTC+TGG + chr5.2:43128123-43128142 MS.gene053963:CDS 30.0%
CCTTGAAATTGGAAAATCAT+TGG + chr5.2:43129217-43129236 MS.gene053963:CDS 30.0%
CTAAACTCTTAACAAAACAG+AGG + chr5.2:43128799-43128818 MS.gene053963:intron 30.0%
GAAATCACACCTAAAAATGT+AGG - chr5.2:43128219-43128238 None:intergenic 30.0%
GACAACTGACAAATAACAAT+TGG - chr5.2:43128002-43128021 None:intergenic 30.0%
! ATGATTTTCCAATTTCAAGG+TGG - chr5.2:43129217-43129236 None:intergenic 30.0%
! CCAATGATTTTCCAATTTCA+AGG - chr5.2:43129220-43129239 None:intergenic 30.0%
! CTTAACTTTTCAATACACTC+AGG + chr5.2:43128376-43128395 MS.gene053963:intron 30.0%
! CTTTACCTTTAGGAAATTGT+CGG + chr5.2:43128252-43128271 MS.gene053963:intron 30.0%
!! CTCTGTTTTGTTAAGAGTTT+AGG - chr5.2:43128801-43128820 None:intergenic 30.0%
!!! ATATGTTAGCTTTTCAACAG+TGG + chr5.2:43128948-43128967 MS.gene053963:intron 30.0%
!!! GGCTGTGCAATTTAATTTTT+TGG + chr5.2:43128820-43128839 MS.gene053963:intron 30.0%
AATCATTGGTGAATGGTGAT+AGG + chr5.2:43128756-43128775 MS.gene053963:intron 35.0%
ACAAATTTAAGGAATCAGCG+TGG + chr5.2:43127827-43127846 MS.gene053963:CDS 35.0%
ACCTAGATTAGCAACTACAA+TGG - chr5.2:43128628-43128647 None:intergenic 35.0%
CAGTTGTTTAATCCATCATG+AGG - chr5.2:43128894-43128913 None:intergenic 35.0%
CGACAATTTCCTAAAGGTAA+AGG - chr5.2:43128254-43128273 None:intergenic 35.0%
GGTGAATTATATAATGTCGG+CGG + chr5.2:43128645-43128664 MS.gene053963:intron 35.0%
GTCTAAATGCCTTTACCTTT+AGG + chr5.2:43128242-43128261 MS.gene053963:intron 35.0%
TACAAAAAGTGACCTCATGA+TGG + chr5.2:43128879-43128898 MS.gene053963:intron 35.0%
TACTTCGAAGAACCCAAAAT+GGG - chr5.2:43128560-43128579 None:intergenic 35.0%
TTGAAAGGGCTGTATATGTA+TGG + chr5.2:43128080-43128099 MS.gene053963:CDS 35.0%
TTGGAAAATCATTGGGTGAA+TGG + chr5.2:43129225-43129244 MS.gene053963:CDS 35.0%
!! AGACGGTTCATTTTTGGAAA+GGG + chr5.2:43127757-43127776 MS.gene053963:CDS 35.0%
!! GCAACTGAGGGAATTTTAAT+AGG - chr5.2:43128606-43128625 None:intergenic 35.0%
!! TGTCGTTTACTACCCATTTT+GGG + chr5.2:43128545-43128564 MS.gene053963:CDS 35.0%
AAACAAGACGCTCTGACTTT+GGG + chr5.2:43128147-43128166 MS.gene053963:CDS 40.0%
AGACACCGACAATTTCCTAA+AGG - chr5.2:43128260-43128279 None:intergenic 40.0%
CTTTCCAAAAATGAACCGTC+TGG - chr5.2:43127758-43127777 None:intergenic 40.0%
GCCATTGTAGTTGCTAATCT+AGG + chr5.2:43128624-43128643 MS.gene053963:intron 40.0%
GGGAAAATGTCCAAATACAG+CGG + chr5.2:43128462-43128481 MS.gene053963:CDS 40.0%
GTACTTCGAAGAACCCAAAA+TGG - chr5.2:43128561-43128580 None:intergenic 40.0%
GTAGTAAACGACACGTAGTA+TGG - chr5.2:43128538-43128557 None:intergenic 40.0%
TCTTTGTTGCAGCTATGAAC+TGG + chr5.2:43129188-43129207 MS.gene053963:intron 40.0%
TGATGCTACTGATGTGTTTC+TGG + chr5.2:43128434-43128453 MS.gene053963:CDS 40.0%
TTGGTCAAATTCGAGCAAGA+GGG + chr5.2:43129337-43129356 MS.gene053963:CDS 40.0%
TTGGTGAATGGTGATAGGAT+AGG + chr5.2:43128761-43128780 MS.gene053963:intron 40.0%
! ACACTCAGGTTTGTTCGAAT+TGG + chr5.2:43128390-43128409 MS.gene053963:intron 40.0%
! TTTGGGTTCTTCGAAGTACA+AGG + chr5.2:43128562-43128581 MS.gene053963:CDS 40.0%
!! ACTGATGTGTTTCTGGAGAT+AGG + chr5.2:43128441-43128460 MS.gene053963:CDS 40.0%
!! CAGACGGTTCATTTTTGGAA+AGG + chr5.2:43127756-43127775 MS.gene053963:CDS 40.0%
!! CTGATGTGTTTCTGGAGATA+GGG + chr5.2:43128442-43128461 MS.gene053963:CDS 40.0%
!! TTTTTCAGCACCGCTGTATT+TGG - chr5.2:43128475-43128494 None:intergenic 40.0%
!!! AAATATTTTTGGGTTGGGCC+AGG + chr5.2:43127925-43127944 MS.gene053963:CDS 40.0%
!!! AATATTTTTGGGTTGGGCCA+GGG + chr5.2:43127926-43127945 MS.gene053963:CDS 40.0%
!!! GTGTCGTTTACTACCCATTT+TGG + chr5.2:43128544-43128563 MS.gene053963:CDS 40.0%
ACTGGTTGCCACCTTGAAAT+TGG + chr5.2:43129206-43129225 MS.gene053963:CDS 45.0%
AGCAACTACAATGGCAACTG+AGG - chr5.2:43128619-43128638 None:intergenic 45.0%
CTGATTCTTCGGATGCTTGT+TGG + chr5.2:43129318-43129337 MS.gene053963:CDS 45.0%
GAAACAAGACGCTCTGACTT+TGG + chr5.2:43128146-43128165 MS.gene053963:CDS 45.0%
GCAACTACAATGGCAACTGA+GGG - chr5.2:43128618-43128637 None:intergenic 45.0%
GTTGGTCAAATTCGAGCAAG+AGG + chr5.2:43129336-43129355 MS.gene053963:CDS 45.0%
! GGAAATTGTCGGTGTCTCTA+CGG + chr5.2:43128263-43128282 MS.gene053963:intron 45.0%
! TTGGCCAGACGGTTCATTTT+TGG + chr5.2:43127751-43127770 MS.gene053963:CDS 45.0%
!! ATTGGTGGGTGCTGATTCTT+CGG + chr5.2:43129307-43129326 MS.gene053963:CDS 45.0%
CTGTAACATACGACGAGCCT+TGG + chr5.2:43127890-43127909 MS.gene053963:CDS 50.0%
GGGCTGTATATGTATGGTGC+TGG + chr5.2:43128086-43128105 MS.gene053963:CDS 50.0%
TGTCGGCGGTAACCATTTAG+TGG + chr5.2:43128659-43128678 MS.gene053963:intron 50.0%
! GTCGGTGTCTCTACGGAAAT+TGG + chr5.2:43128270-43128289 MS.gene053963:intron 50.0%
TCTGGCCATCTCTGATTCCC+TGG - chr5.2:43127946-43127965 None:intergenic 55.0%
TTGGGCCAGGGAATCAGAGA+TGG + chr5.2:43127938-43127957 MS.gene053963:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 43127748 43129384 43127748 ID=MS.gene053963
chr5.2 mRNA 43127748 43129384 43127748 ID=MS.gene053963.t1;Parent=MS.gene053963
chr5.2 exon 43127748 43127977 43127748 ID=MS.gene053963.t1.exon1;Parent=MS.gene053963.t1
chr5.2 CDS 43127748 43127977 43127748 ID=cds.MS.gene053963.t1;Parent=MS.gene053963.t1
chr5.2 exon 43128073 43128228 43128073 ID=MS.gene053963.t1.exon2;Parent=MS.gene053963.t1
chr5.2 CDS 43128073 43128228 43128073 ID=cds.MS.gene053963.t1;Parent=MS.gene053963.t1
chr5.2 exon 43128398 43128583 43128398 ID=MS.gene053963.t1.exon3;Parent=MS.gene053963.t1
chr5.2 CDS 43128398 43128583 43128398 ID=cds.MS.gene053963.t1;Parent=MS.gene053963.t1
chr5.2 exon 43129200 43129384 43129200 ID=MS.gene053963.t1.exon4;Parent=MS.gene053963.t1
chr5.2 CDS 43129200 43129384 43129200 ID=cds.MS.gene053963.t1;Parent=MS.gene053963.t1
Gene Sequence

>MS.gene053963

AAATTGGCCAGACGGTTCATTTTTGGAAAGGGACATGAAGTGCTTGATTTTCATACAGATGATAGTAGAAAGAAGATTAACAAATTTAAGGAATCAGCGTGGAAATGTGTTTATTTTCTATCGGCAGAAATTTTTGCGTTGTCTGTAACATACGACGAGCCTTGGTTTACTGATACAAAATATTTTTGGGTTGGGCCAGGGAATCAGAGATGGCCAGATCAAAAGATTAAGTAAGATTTTTATTTACATGCCCAATTGTTATTTGTCAGTTGTCATTTCAAGTTAGTAGTTAACTATCGATTGAGTAACCATTTACAATTTTCAGATTGAAATTGAAAGGGCTGTATATGTATGGTGCTGGATTTTATTCATACTCCATACTTGCTTTAATATTCTGGGAAACAAGACGCTCTGACTTTGGGATTTCTATGACACATCATGTTGCTTCTCTCAGCCTCATTGTGTTATCCTACATTTTTAGGTGTGATTTCATTGTCTAAATGCCTTTACCTTTAGGAAATTGTCGGTGTCTCTACGGAAATTGGTTTTAAGAGCACATTTTGTACTTAATGTCTGCACTAATTCTATTTTATTTAAATTTACTCCACTAGTTCAATTTCCTATTTTACTTAACTTTTCAATACACTCAGGTTTGTTCGAATTGGATCAGTTGTTTTAGCTCTTCATGATGCTACTGATGTGTTTCTGGAGATAGGGAAAATGTCCAAATACAGCGGTGCTGAAAAAATCGCTAGCTTTGCATTTGTTCTGTTTGTTTTATCTTTCACCATACTACGTGTCGTTTACTACCCATTTTGGGTTCTTCGAAGTACAAGGTTTGTTTTCTTTCTTTCACCTATTAAAATTCCCTCAGTTGCCATTGTAGTTGCTAATCTAGGTGAATTATATAATGTCGGCGGTAACCATTTAGTGGAAGTTAAAAAAATCCCAAATGTAAATTTAAAGGATATGATCAGTTTGCTGCTCTTCTTAATCTTGTAAAAAAGTAATCATTGGTGAATGGTGATAGGATAGGTACACTTTTTTTCTCCTAAACTCTTAACAAAACAGAGGCTGTGCAATTTAATTTTTTGGATTTTACTTCTAAAGTGAGCAATTCTCTTCAGACGATACAAAAAGTGACCTCATGATGGATTAAACAACTGTTTATATTGCGTTTATATGCATAACAAATCATATATATGTTAGCTTTTCAACAGTGGATTTTCTCATCAATAGCTGACACCTCTATATGAGTAAAGTATAAAGTGGAAAAACCAAGAGTTGAAATTTTAACAAACTTGTAATTTGTCATGATTTATCTAGAATATTCATCTTTGACTTGTTAATTAATAATTGATAATACTCATCACATAGTCTAAAATAAATTACTCAGTTTATACGGACATATACTTTTATTTCTCTATTTAATTGTTTTATTCTTTGTTGCAGCTATGAACTGGTTGCCACCTTGAAATTGGAAAATCATTGGGTGAATGGTTCTATACATTATTATGTATTCAATAGTCTTCTATTCTGCTTGCTTGTTCTTAACATTTATTGGTGGGTGCTGATTCTTCGGATGCTTGTTGGTCAAATTCGAGCAAGAGGGAAAGTTAGTGAAGATATACGATCTG

Protein sequence

>MS.gene053963.t1

KLARRFIFGKGHEVLDFHTDDSRKKINKFKESAWKCVYFLSAEIFALSVTYDEPWFTDTKYFWVGPGNQRWPDQKIKLKLKGLYMYGAGFYSYSILALIFWETRRSDFGISMTHHVASLSLIVLSYIFRFVRIGSVVLALHDATDVFLEIGKMSKYSGAEKIASFAFVLFVLSFTILRVVYYPFWVLRSTSYELVATLKLENHWVNGSIHYYVFNSLLFCLLVLNIYWWVLILRMLVGQIRARGKVSEDIRS