AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene34477

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34477.t1 MTR_1g100697 99.344 305 2 0 1 305 1 305 0.0 619
MS.gene34477.t1 MTR_1g100707 91.475 305 26 0 1 305 1 305 0.0 572
MS.gene34477.t1 MTR_1g100713 55.705 298 128 1 12 305 21 318 2.12e-112 328
MS.gene34477.t1 MTR_0013s0100 53.265 291 134 2 17 305 25 315 1.03e-105 311
MS.gene34477.t1 MTR_4g099030 48.136 295 140 2 12 305 21 303 2.18e-97 289
MS.gene34477.t1 MTR_7g074410 34.812 293 186 2 12 304 13 300 2.06e-53 177
MS.gene34477.t1 MTR_7g074430 32.441 299 197 2 6 304 7 300 9.37e-51 170
MS.gene34477.t1 MTR_7g075970 34.122 296 174 5 17 304 13 295 6.02e-44 152
MS.gene34477.t1 MTR_1g029330 32.313 294 193 4 12 304 13 301 1.09e-40 144
MS.gene34477.t1 MTR_2g018940 29.289 239 143 7 4 233 18 239 8.68e-17 79.7
MS.gene34477.t1 MTR_2g018910 28.151 238 143 7 6 233 23 242 1.98e-16 79.0
MS.gene34477.t1 MTR_8g091730 26.050 238 157 5 3 232 15 241 4.06e-16 77.8
MS.gene34477.t1 MTR_2g018950 27.530 247 145 6 4 233 17 246 1.17e-13 70.9
MS.gene34477.t1 MTR_3g080330 27.193 228 144 5 11 232 13 224 5.30e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34477.t1 AT3G48880 68.562 299 92 2 9 305 11 309 1.34e-152 429
MS.gene34477.t1 AT3G48880 68.562 299 92 2 9 305 11 309 1.34e-152 429
MS.gene34477.t1 AT3G48880 68.562 299 92 2 9 305 11 309 1.34e-152 429
MS.gene34477.t1 AT4G11580 29.532 342 188 11 1 303 4 331 8.73e-33 124

Find 56 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGCTCAAGACTCTCAATTT+TGG 0.223803 1.2:-75491355 None:intergenic
ACAAGTATGAGGAAGGATTT+TGG 0.237709 1.2:+75491629 MS.gene34477:CDS
GCAATTTCCTCTAGAAAATA+TGG 0.237803 1.2:-75491250 None:intergenic
CTTGCTGTGATCCACTTCTT+TGG 0.265127 1.2:+75490502 MS.gene34477:CDS
CTTCAGTGAACTCAAGATTA+TGG 0.275898 1.2:+75491288 MS.gene34477:CDS
TCAAGGAAATCTTCAATAAT+CGG 0.286560 1.2:-75490620 None:intergenic
CGCGCAATCGAGAAGCCTTC+TGG 0.341689 1.2:-75491531 None:intergenic
ACGTAAACAAAAGGCTCTAA+TGG 0.360702 1.2:-75490570 None:intergenic
GACATATTCGAGTTAACTTC+TGG 0.361591 1.2:+75490447 MS.gene34477:CDS
TATATCACATTGCATTCTAA+TGG 0.362218 1.2:+75491450 MS.gene34477:CDS
CACTCACGTACAAGTTGAAA+TGG 0.379756 1.2:-75490677 None:intergenic
TTCGGTGTTCAACGCTATAT+AGG 0.386217 1.2:+75491377 MS.gene34477:CDS
CACGAGGAGATGGGAGGATC+TGG 0.389695 1.2:+75490389 MS.gene34477:CDS
GGATCTGGACACAGATATAT+TGG 0.398991 1.2:+75490404 MS.gene34477:CDS
TTCAGTGAACTCAAGATTAT+GGG 0.400982 1.2:+75491289 MS.gene34477:CDS
TGTGCAAGGCAATCCGTTGC+TGG 0.424432 1.2:+75491185 MS.gene34477:CDS
ACTCATTCTGCTCAGATTCA+AGG 0.426417 1.2:-75490637 None:intergenic
AATTGAGAGTCTTGAGCCTT+CGG 0.435748 1.2:+75491359 MS.gene34477:CDS
CAAGGAAATCTTCAATAATC+GGG 0.435917 1.2:-75490619 None:intergenic
GAACTGATGAAGGGATAGTT+AGG 0.442152 1.2:+75491602 MS.gene34477:CDS
AACGACTGGTTCTTCCGGCT+TGG 0.442940 1.2:+75491140 MS.gene34477:CDS
TTGTTTCGAACACGAGGAGA+TGG 0.448455 1.2:+75490379 MS.gene34477:CDS
GCTCAAACGACTGGTTCTTC+CGG 0.448751 1.2:+75491135 MS.gene34477:CDS
AGTTAGGTGGTACAAGTATG+AGG 0.451024 1.2:+75491618 MS.gene34477:CDS
TGGAACAGAATTAAAAGAAC+AGG 0.456792 1.2:+75491160 MS.gene34477:CDS
TTGCTCATGTTTGTAGCGCA+TGG 0.458078 1.2:+75490472 MS.gene34477:CDS
TCGGTGTTCAACGCTATATA+GGG 0.478065 1.2:+75491378 MS.gene34477:CDS
TATTCTCTGTTTAAAGTGCA+AGG 0.494057 1.2:-75491672 None:intergenic
CTTCATCAGTTCTTGTACGT+TGG 0.501934 1.2:-75491591 None:intergenic
CTAAATGTTCTAAGCTGTCT+AGG 0.503752 1.2:-75491417 None:intergenic
CGTTCATCAACGTAAACAAA+AGG 0.517545 1.2:-75490579 None:intergenic
GAACCAGTCGTTTGAGCTGT+GGG 0.524995 1.2:-75491129 None:intergenic
TGTTTCGAACACGAGGAGAT+GGG 0.527745 1.2:+75490380 MS.gene34477:CDS
TGTTTGTAGCGCATGGCGCA+TGG 0.531694 1.2:+75490479 MS.gene34477:CDS
ATTCTCTGTTTAAAGTGCAA+GGG 0.539339 1.2:-75491671 None:intergenic
TGATTCTACTATTCGCCAGA+AGG 0.543301 1.2:+75491516 MS.gene34477:CDS
AGGTGGTACAAGTATGAGGA+AGG 0.544931 1.2:+75491622 MS.gene34477:CDS
AATCCGTTGCTGGAAAGAGC+TGG 0.549877 1.2:+75491195 MS.gene34477:CDS
CAACGTACAAGAACTGATGA+AGG 0.552652 1.2:+75491592 MS.gene34477:CDS
AGAACCAGTCGTTTGAGCTG+TGG 0.570755 1.2:-75491130 None:intergenic
GCGCGAATTTATCACATGCA+TGG 0.572175 1.2:+75491549 MS.gene34477:CDS
ACTCCAGCTCTTTCCAGCAA+CGG 0.573617 1.2:-75491198 None:intergenic
TCAAGCGTCTTCCAAAGAAG+TGG 0.580522 1.2:-75490513 None:intergenic
TTTCCTCTAGAAAATATGGC+GGG 0.587537 1.2:-75491246 None:intergenic
TATGGCGGGTTTGCTATACT+AGG 0.604329 1.2:-75491232 None:intergenic
GTGCCCACAGCTCAAACGAC+TGG 0.606234 1.2:+75491126 MS.gene34477:CDS
TATATAGCGTTGAACACCGA+AGG 0.621770 1.2:-75491375 None:intergenic
TAAAAGAACAGGAATGTGCA+AGG 0.624054 1.2:+75491171 MS.gene34477:CDS
AGTTGACATACACTGCTGAA+AGG 0.630322 1.2:+75490706 MS.gene34477:CDS
AAGACGTTGTTTCGAACACG+AGG 0.632817 1.2:+75490373 MS.gene34477:CDS
TCAGTGAACTCAAGATTATG+GGG 0.652634 1.2:+75491290 MS.gene34477:CDS
TTCGAACACGAGGAGATGGG+AGG 0.657865 1.2:+75490383 MS.gene34477:CDS
AACGTACAAGAACTGATGAA+GGG 0.659917 1.2:+75491593 MS.gene34477:CDS
CTGATGAAGGGATAGTTAGG+TGG 0.665188 1.2:+75491605 MS.gene34477:CDS
ATTTCCTCTAGAAAATATGG+CGG 0.666839 1.2:-75491247 None:intergenic
GAAGCAAAGAAGATGTCACA+TGG 0.687775 1.2:-75491313 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATTTAGAGAGATTAA+TGG + chr1.2:75490744-75490763 MS.gene34477:intron 15.0%
!!! CTCTAAATATATTTTAAAGT+TGG - chr1.2:75490737-75490756 None:intergenic 15.0%
!!! TTATTTTTGAAAAGATAATG+CGG + chr1.2:75491018-75491037 MS.gene34477:intron 15.0%
!!! TTGATAATTTTTTTATGTTG+AGG - chr1.2:75491490-75491509 None:intergenic 15.0%
!!! ATAATTTTTTTATGTTGAGG+AGG - chr1.2:75491487-75491506 None:intergenic 20.0%
!!! TAATTTTTTTATGTTGAGGA+GGG - chr1.2:75491486-75491505 None:intergenic 20.0%
!!! TTTGACGGTTTTTAAATAAA+AGG - chr1.2:75490849-75490868 None:intergenic 20.0%
! TATATCACATTGCATTCTAA+TGG + chr1.2:75491450-75491469 MS.gene34477:CDS 25.0%
! TCAAGGAAATCTTCAATAAT+CGG - chr1.2:75490623-75490642 None:intergenic 25.0%
!!! AATTTTTTTATGTTGAGGAG+GGG - chr1.2:75491485-75491504 None:intergenic 25.0%
!!! TATGCAGTTATTTGTTATGT+TGG - chr1.2:75490822-75490841 None:intergenic 25.0%
CAAGGAAATCTTCAATAATC+GGG - chr1.2:75490622-75490641 None:intergenic 30.0%
CTAGATTGAAGAATTGTGAT+CGG + chr1.2:75490878-75490897 MS.gene34477:intron 30.0%
TGGAACAGAATTAAAAGAAC+AGG + chr1.2:75491160-75491179 MS.gene34477:CDS 30.0%
TTATTAGCACTCCTTCAAAA+TGG + chr1.2:75491054-75491073 MS.gene34477:intron 30.0%
TTCAGTGAACTCAAGATTAT+GGG + chr1.2:75491289-75491308 MS.gene34477:CDS 30.0%
! ATTTCCTCTAGAAAATATGG+CGG - chr1.2:75491250-75491269 None:intergenic 30.0%
! CATTGTACTATCCATTTTGA+AGG - chr1.2:75491068-75491087 None:intergenic 30.0%
! GACGGTTTTTAAATAAAAGG+CGG - chr1.2:75490846-75490865 None:intergenic 30.0%
! GATTCAAGTTATGAGATTGA+CGG - chr1.2:75490951-75490970 None:intergenic 30.0%
! GCAATTTCCTCTAGAAAATA+TGG - chr1.2:75491253-75491272 None:intergenic 30.0%
! TTATGTTGGTGAGTTCTAAT+TGG - chr1.2:75490808-75490827 None:intergenic 30.0%
!!! ATTTTTTTATGTTGAGGAGG+GGG - chr1.2:75491484-75491503 None:intergenic 30.0%
AACGTACAAGAACTGATGAA+GGG + chr1.2:75491593-75491612 MS.gene34477:CDS 35.0%
AGTGTAAAACAACTTTCCAC+TGG - chr1.2:75490780-75490799 None:intergenic 35.0%
ATCTAGCGAATCATGTTTGA+CGG - chr1.2:75490864-75490883 None:intergenic 35.0%
CGTTCATCAACGTAAACAAA+AGG - chr1.2:75490582-75490601 None:intergenic 35.0%
CTTCAGTGAACTCAAGATTA+TGG + chr1.2:75491288-75491307 MS.gene34477:CDS 35.0%
TAAAAGAACAGGAATGTGCA+AGG + chr1.2:75491171-75491190 MS.gene34477:CDS 35.0%
TCAGTGAACTCAAGATTATG+GGG + chr1.2:75491290-75491309 MS.gene34477:CDS 35.0%
! AAGAATTGTGATCGGTTCAT+CGG + chr1.2:75490886-75490905 MS.gene34477:intron 35.0%
! ACAAGTATGAGGAAGGATTT+TGG + chr1.2:75491629-75491648 MS.gene34477:CDS 35.0%
! ACGTAAACAAAAGGCTCTAA+TGG - chr1.2:75490573-75490592 None:intergenic 35.0%
! AGGGGTGAGATTAGTTATTT+AGG - chr1.2:75491098-75491117 None:intergenic 35.0%
! CTAAATGTTCTAAGCTGTCT+AGG - chr1.2:75491420-75491439 None:intergenic 35.0%
! GACATATTCGAGTTAACTTC+TGG + chr1.2:75490447-75490466 MS.gene34477:CDS 35.0%
! TTTCCTCTAGAAAATATGGC+GGG - chr1.2:75491249-75491268 None:intergenic 35.0%
!! AGGATTTTGGAAAGAAGATG+AGG + chr1.2:75491642-75491661 MS.gene34477:CDS 35.0%
!! CTTTTAATTCTGTTCCAAGC+CGG - chr1.2:75491157-75491176 None:intergenic 35.0%
!!! TTTTTTTATGTTGAGGAGGG+GGG - chr1.2:75491483-75491502 None:intergenic 35.0%
AATTGAGAGTCTTGAGCCTT+CGG + chr1.2:75491359-75491378 MS.gene34477:CDS 40.0%
ACTCATTCTGCTCAGATTCA+AGG - chr1.2:75490640-75490659 None:intergenic 40.0%
AGTTAGGTGGTACAAGTATG+AGG + chr1.2:75491618-75491637 MS.gene34477:CDS 40.0%
AGTTGACATACACTGCTGAA+AGG + chr1.2:75490706-75490725 MS.gene34477:CDS 40.0%
CAACGTACAAGAACTGATGA+AGG + chr1.2:75491592-75491611 MS.gene34477:CDS 40.0%
CTACGAAACATCGTACGAAA+AGG - chr1.2:75490980-75490999 None:intergenic 40.0%
CTTCATCAGTTCTTGTACGT+TGG - chr1.2:75491594-75491613 None:intergenic 40.0%
GAACTGATGAAGGGATAGTT+AGG + chr1.2:75491602-75491621 MS.gene34477:CDS 40.0%
GAAGCAAAGAAGATGTCACA+TGG - chr1.2:75491316-75491335 None:intergenic 40.0%
GGATCTGGACACAGATATAT+TGG + chr1.2:75490404-75490423 MS.gene34477:CDS 40.0%
TGATTCTACTATTCGCCAGA+AGG + chr1.2:75491516-75491535 MS.gene34477:CDS 40.0%
! AAACCCGCCATATTTTCTAG+AGG + chr1.2:75491243-75491262 MS.gene34477:CDS 40.0%
! AGGCTCAAGACTCTCAATTT+TGG - chr1.2:75491358-75491377 None:intergenic 40.0%
! CACTCACGTACAAGTTGAAA+TGG - chr1.2:75490680-75490699 None:intergenic 40.0%
! CTTTTCGTACGATGTTTCGT+AGG + chr1.2:75490978-75490997 MS.gene34477:intron 40.0%
! TATATAGCGTTGAACACCGA+AGG - chr1.2:75491378-75491397 None:intergenic 40.0%
! TCGGTGTTCAACGCTATATA+GGG + chr1.2:75491378-75491397 MS.gene34477:CDS 40.0%
!! AGGAGTGCTAATAACTAGCA+AGG - chr1.2:75491048-75491067 None:intergenic 40.0%
!! TTCGGTGTTCAACGCTATAT+AGG + chr1.2:75491377-75491396 MS.gene34477:CDS 40.0%
AGGTGGTACAAGTATGAGGA+AGG + chr1.2:75491622-75491641 MS.gene34477:CDS 45.0%
CGAAACATCGTACGAAAAGG+TGG - chr1.2:75490977-75490996 None:intergenic 45.0%
CTGATGAAGGGATAGTTAGG+TGG + chr1.2:75491605-75491624 MS.gene34477:CDS 45.0%
GCGCGAATTTATCACATGCA+TGG + chr1.2:75491549-75491568 MS.gene34477:CDS 45.0%
TCAAGCGTCTTCCAAAGAAG+TGG - chr1.2:75490516-75490535 None:intergenic 45.0%
TGTTTCGAACACGAGGAGAT+GGG + chr1.2:75490380-75490399 MS.gene34477:CDS 45.0%
TTGCTCATGTTTGTAGCGCA+TGG + chr1.2:75490472-75490491 MS.gene34477:CDS 45.0%
TTGTTTCGAACACGAGGAGA+TGG + chr1.2:75490379-75490398 MS.gene34477:CDS 45.0%
! AAGACGTTGTTTCGAACACG+AGG + chr1.2:75490373-75490392 MS.gene34477:CDS 45.0%
! CTTGCTGTGATCCACTTCTT+TGG + chr1.2:75490502-75490521 MS.gene34477:CDS 45.0%
! TAATGGATATGCACTGCCAG+TGG + chr1.2:75490761-75490780 MS.gene34477:intron 45.0%
!! TATGGCGGGTTTGCTATACT+AGG - chr1.2:75491235-75491254 None:intergenic 45.0%
AATCCGTTGCTGGAAAGAGC+TGG + chr1.2:75491195-75491214 MS.gene34477:CDS 50.0%
ACTCCAGCTCTTTCCAGCAA+CGG - chr1.2:75491201-75491220 None:intergenic 50.0%
AGAACCAGTCGTTTGAGCTG+TGG - chr1.2:75491133-75491152 None:intergenic 50.0%
CTAATCTCACCCCTTGTTGC+AGG + chr1.2:75491104-75491123 MS.gene34477:intron 50.0%
GAACCAGTCGTTTGAGCTGT+GGG - chr1.2:75491132-75491151 None:intergenic 50.0%
! GCTCAAACGACTGGTTCTTC+CGG + chr1.2:75491135-75491154 MS.gene34477:CDS 50.0%
TGTGCAAGGCAATCCGTTGC+TGG + chr1.2:75491185-75491204 MS.gene34477:CDS 55.0%
TGTTTGTAGCGCATGGCGCA+TGG + chr1.2:75490479-75490498 MS.gene34477:CDS 55.0%
TTCGAACACGAGGAGATGGG+AGG + chr1.2:75490383-75490402 MS.gene34477:CDS 55.0%
! AACGACTGGTTCTTCCGGCT+TGG + chr1.2:75491140-75491159 MS.gene34477:CDS 55.0%
AGCTGTGGGCACCTGCAACA+AGG - chr1.2:75491118-75491137 None:intergenic 60.0%
CACGAGGAGATGGGAGGATC+TGG + chr1.2:75490389-75490408 MS.gene34477:CDS 60.0%
CGCGCAATCGAGAAGCCTTC+TGG - chr1.2:75491534-75491553 None:intergenic 60.0%
CTGTGGGCACCTGCAACAAG+GGG - chr1.2:75491116-75491135 None:intergenic 60.0%
GCTGTGGGCACCTGCAACAA+GGG - chr1.2:75491117-75491136 None:intergenic 60.0%
GTGCCCACAGCTCAAACGAC+TGG + chr1.2:75491126-75491145 MS.gene34477:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 75490369 75491684 75490369 ID=MS.gene34477
chr1.2 mRNA 75490369 75491684 75490369 ID=MS.gene34477.t1;Parent=MS.gene34477
chr1.2 exon 75490369 75490727 75490369 ID=MS.gene34477.t1.exon1;Parent=MS.gene34477.t1
chr1.2 CDS 75490369 75490727 75490369 ID=cds.MS.gene34477.t1;Parent=MS.gene34477.t1
chr1.2 exon 75491126 75491684 75491126 ID=MS.gene34477.t1.exon2;Parent=MS.gene34477.t1
chr1.2 CDS 75491126 75491684 75491126 ID=cds.MS.gene34477.t1;Parent=MS.gene34477.t1
Gene Sequence

>MS.gene34477

ATGGAAGACGTTGTTTCGAACACGAGGAGATGGGAGGATCTGGACACAGATATATTGGTGAAGATTTTTCAGTTGCTTGACATATTCGAGTTAACTTCTGGCATTGCTCATGTTTGTAGCGCATGGCGCATGGCTTGCTGTGATCCACTTCTTTGGAAGACGCTTGATTTGTCAATGTTGAGAAGTAACTTCATCAAGATTCCATTAGAGCCTTTTGTTTACGTTGATGAACGATCTGATAAGAAATTAACCCGATTATTGAAGATTTCCTTGAATCTGAGCAGAATGAGTATAGTGACATTAATCTTCCATTTCAACTTGTACGTGAGTGATGATCAGTTGACATACACTGCTGAAAGGTAATTCCAACTTTAAAATATATTTAGAGAGATTAATGGATATGCACTGCCAGTGGAAAGTTGTTTTACACTGACAACCAATTAGAACTCACCAACATAACAAATAACTGCATAACCGCCTTTTATTTAAAAACCGTCAAACATGATTCGCTAGATTGAAGAATTGTGATCGGTTCATCGGATGTCAGTGTAAAATAACTTTACACTTACAATACATATTCCGTCAATCTCATAACTTGAATCGAACCACCTTTTCGTACGATGTTTCGTAGGATAAGTTGCTTGTATTTTTATTTTTGAAAAGATAATGCGGCACTCCTTGCTAGTTATTAGCACTCCTTCAAAATGGATAGTACAATGTGAATTGCCTAAATAACTAATCTCACCCCTTGTTGCAGGTGCCCACAGCTCAAACGACTGGTTCTTCCGGCTTGGAACAGAATTAAAAGAACAGGAATGTGCAAGGCAATCCGTTGCTGGAAAGAGCTGGAGTCTCTTACAATGCCTAGTATAGCAAACCCGCCATATTTTCTAGAGGAAATTGCAACAAACTGCAAGAACTTCAGTGAACTCAAGATTATGGGGCCATGTGACATCTTCTTTGCTTCAACTCTTGCTGCATTTGTTCCAAAATTGAGAGTCTTGAGCCTTCGGTGTTCAACGCTATATAGGGATGTTCTCATTCTCATCCTAGACAGCTTAGAACATTTAGAAGTGCTCAATATATCACATTGCATTCTAATGGAATGTCTCCCCCCTCCTCAACATAAAAAAATTATCAATGAAATTGATTCTACTATTCGCCAGAAGGCTTCTCGATTGCGCGAATTTATCACATGCATGGATGACTCGTGTATCATGTGCCAACGTACAAGAACTGATGAAGGGATAGTTAGGTGGTACAAGTATGAGGAAGGATTTTGGAAAGAAGATGAGGTGAAGTCCCTTGCACTTTAA
Protein sequence

>MS.gene34477.t1

MEDVVSNTRRWEDLDTDILVKIFQLLDIFELTSGIAHVCSAWRMACCDPLLWKTLDLSMLRSNFIKIPLEPFVYVDERSDKKLTRLLKISLNLSRMSIVTLIFHFNLYVSDDQLTYTAERCPQLKRLVLPAWNRIKRTGMCKAIRCWKELESLTMPSIANPPYFLEEIATNCKNFSELKIMGPCDIFFASTLAAFVPKLRVLSLRCSTLYRDVLILILDSLEHLEVLNISHCILMECLPPPQHKKIINEIDSTIRQKASRLREFITCMDDSCIMCQRTRTDEGIVRWYKYEEGFWKEDEVKSLAL