AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010060.t1 MTR_5g080150 50.186 269 77 5 20 233 113 379 2.35e-76 238
MS.gene010060.t1 MTR_2g048140 29.683 347 154 8 20 281 114 455 9.47e-36 133
MS.gene010060.t1 MTR_1g090907 29.683 347 153 9 20 281 114 454 2.16e-32 124
MS.gene010060.t1 MTR_5g080160 53.846 104 43 1 183 281 56 159 6.54e-32 116
MS.gene010060.t1 MTR_3g448340 32.367 207 112 4 20 199 110 315 2.97e-26 107
MS.gene010060.t1 MTR_3g049530 33.168 202 92 8 13 186 52 238 2.03e-20 90.5
MS.gene010060.t1 MTR_7g029260 48.352 91 47 0 163 253 69 159 3.50e-20 87.0
MS.gene010060.t1 MTR_1g090903 25.316 316 165 9 20 281 112 410 4.70e-19 86.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010060.t1 AT1G56400 29.060 234 129 6 23 223 81 310 6.47e-17 80.5
MS.gene010060.t1 AT1G56400 30.348 201 105 5 23 190 122 320 7.21e-17 80.5
MS.gene010060.t1 AT3G29830 32.843 204 96 8 23 190 117 315 2.46e-16 79.0
MS.gene010060.t1 AT3G29830 32.843 204 96 8 23 190 117 315 2.62e-16 79.0
MS.gene010060.t1 AT3G62230 21.965 346 181 9 23 282 119 461 1.70e-13 70.5
MS.gene010060.t1 AT5G54820 27.670 206 109 6 23 197 120 316 8.93e-13 68.6

Find 40 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCAAAAGCTTCAACTAATT+TGG 0.112130 5.2:-56858698 MS.gene010060:CDS
TTTGACCAATTGTGAAAATT+TGG 0.130183 5.2:-56860210 MS.gene010060:CDS
CATCCCATCTATCATCTTTA+AGG 0.131556 5.2:+56858761 None:intergenic
AATCGAGATTAAGGGCTTTA+AGG 0.171731 5.2:-56858860 MS.gene010060:CDS
TTTGAAGGAAATCGAGATTA+AGG 0.240544 5.2:-56858869 MS.gene010060:CDS
TCCAAATTAGTTGAAGCTTT+TGG 0.251791 5.2:+56858697 None:intergenic
CTTTGGGTTACATGAGAATA+AGG 0.261302 5.2:-56860253 MS.gene010060:CDS
TTCACTCAAAGATATTTCTT+TGG 0.270492 5.2:-56860270 MS.gene010060:CDS
ATGTTATCCCAGAGAGATAT+TGG 0.293798 5.2:-56858930 MS.gene010060:CDS
GAAAATGTTCTACTGCTTTA+CGG 0.302378 5.2:+56858728 None:intergenic
AATAAGGCACTGTGCTATTA+AGG 0.308091 5.2:-56860237 MS.gene010060:CDS
ATCGAGATTAAGGGCTTTAA+GGG 0.315026 5.2:-56858859 MS.gene010060:CDS
TCATGGATATATGACACTTT+TGG 0.319471 5.2:-56860099 MS.gene010060:CDS
ATTTCCTTAAAGATGATAGA+TGG 0.323682 5.2:-56858765 MS.gene010060:CDS
AAGAAATGGAGTCAAGGATT+TGG 0.324683 5.2:-56860429 MS.gene010060:CDS
TATCCTTGACAACGATGTTC+AGG 0.352908 5.2:+56860026 None:intergenic
TCACTCAAAGATATTTCTTT+GGG 0.355275 5.2:-56860269 MS.gene010060:CDS
CTTCTTTGAAAGCAATGATT+CGG 0.356973 5.2:+56860705 None:intergenic
GAACATCGTTGTCAAGGATA+TGG 0.362197 5.2:-56860023 MS.gene010060:CDS
TTCTTTGAAAGCAATGATTC+GGG 0.385459 5.2:+56860706 None:intergenic
GAGTCGACCCAATATCTCTC+TGG 0.421480 5.2:+56858922 None:intergenic
TTGAAGGAAATCGAGATTAA+GGG 0.425132 5.2:-56858868 MS.gene010060:CDS
ATTACTTACTTTCTCACTCA+TGG 0.430107 5.2:-56858814 MS.gene010060:CDS
TGTATGCAGCTACTTACTTC+AGG 0.442006 5.2:-56859949 MS.gene010060:intron
AGTAAATGCGCCAAATCTAA+AGG 0.461768 5.2:-56860132 MS.gene010060:CDS
TGATATTCAATCACCTGCAT+TGG 0.483970 5.2:-56860072 MS.gene010060:CDS
TGTTATCCCAGAGAGATATT+GGG 0.495539 5.2:-56858929 MS.gene010060:CDS
ACAACATCAACAATATCATA+AGG 0.501868 5.2:+56860389 None:intergenic
TCCCCTGAACATCGTTGTCA+AGG 0.512754 5.2:-56860029 MS.gene010060:CDS
TTACTTACTTTCTCACTCAT+GGG 0.518448 5.2:-56858813 MS.gene010060:CDS
TCAATCACCTGCATTGGATG+AGG 0.524045 5.2:-56860066 MS.gene010060:CDS
TTTCCTTAAAGATGATAGAT+GGG 0.525028 5.2:-56858764 MS.gene010060:CDS
ATCCTTGACAACGATGTTCA+GGG 0.531060 5.2:+56860027 None:intergenic
TGCTTTAAGAAATGGAGTCA+AGG 0.551610 5.2:-56860435 MS.gene010060:intron
AGTCGACCCAATATCTCTCT+GGG 0.553459 5.2:+56858923 None:intergenic
TATGTCATTGCTCACTCCCA+TGG 0.561333 5.2:+56860741 None:intergenic
AATCATTGCTTTCAAAGAAG+CGG 0.565567 5.2:-56860702 MS.gene010060:intron
TGCAGGTGATTGAATATCAA+CGG 0.579848 5.2:+56860076 None:intergenic
AGATTAACCTCATCCAATGC+AGG 0.587470 5.2:+56860059 None:intergenic
TCCTTGACAACGATGTTCAG+GGG 0.668282 5.2:+56860028 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAAATAAAATTAGTGAA+AGG + chr5.2:56859958-56859977 None:intergenic 10.0%
!!! AAAAAGTATATATTTTTCTT+AGG - chr5.2:56859739-56859758 MS.gene010060:intron 10.0%
!! TAATTAAAAACCTTTAGATT+TGG + chr5.2:56859301-56859320 None:intergenic 15.0%
!! TATATATTATGCATCTAATT+TGG - chr5.2:56860177-56860196 MS.gene010060:CDS 15.0%
!! TTGATGTAAAATTAAAAACA+TGG - chr5.2:56860418-56860437 MS.gene010060:CDS 15.0%
!!! AAAATTTAATTTATATGCAC+CGG + chr5.2:56860382-56860401 None:intergenic 15.0%
!!! TCTTTACAAATTTTTAAAAG+AGG - chr5.2:56859426-56859445 MS.gene010060:intron 15.0%
!! AAAAGACAAAAGGTAAAAAA+TGG + chr5.2:56859499-56859518 None:intergenic 20.0%
!! AAAATTTCACACAAAGTTAA+TGG + chr5.2:56859838-56859857 None:intergenic 20.0%
!! CTATAACCATAAAAATAAGT+AGG + chr5.2:56859067-56859086 None:intergenic 20.0%
!! CTCTATATATGTATTCATTT+GGG - chr5.2:56859662-56859681 MS.gene010060:intron 20.0%
!! TCTATATATGTATTCATTTG+GGG - chr5.2:56859663-56859682 MS.gene010060:intron 20.0%
!! TCTCTATATATGTATTCATT+TGG - chr5.2:56859661-56859680 MS.gene010060:intron 20.0%
!!! ACTTATTTTTATGGTTATAG+TGG - chr5.2:56859067-56859086 MS.gene010060:intron 20.0%
!!! ACTTTAAGAAAAAAGACAAA+AGG + chr5.2:56859509-56859528 None:intergenic 20.0%
!!! CTAAAGGTTTTTAATTATCA+TGG - chr5.2:56859304-56859323 MS.gene010060:intron 20.0%
!!! CTTATTTTTATGGTTATAGT+GGG - chr5.2:56859068-56859087 MS.gene010060:intron 20.0%
!!! TAATTGTGAATTTTTGTAGT+AGG - chr5.2:56860285-56860304 MS.gene010060:CDS 20.0%
!!! TTCTATTTTCTCTAAAGATT+GGG - chr5.2:56858748-56858767 MS.gene010060:CDS 20.0%
!!! TTGTTGTTGTTTATATTGTA+GGG - chr5.2:56860450-56860469 MS.gene010060:intron 20.0%
! ACAACATCAACAATATCATA+AGG + chr5.2:56859034-56859053 None:intergenic 25.0%
! ATTTCCTTAAAGATGATAGA+TGG - chr5.2:56860655-56860674 MS.gene010060:intron 25.0%
! CTATATATGTATTCATTTGG+GGG - chr5.2:56859664-56859683 MS.gene010060:intron 25.0%
! TCACTCAAAGATATTTCTTT+GGG - chr5.2:56859151-56859170 MS.gene010060:intron 25.0%
! TTCACTCAAAGATATTTCTT+TGG - chr5.2:56859150-56859169 MS.gene010060:intron 25.0%
! TTTATGCAATACTTACAAAC+AGG + chr5.2:56860081-56860100 None:intergenic 25.0%
! TTTCCTTAAAGATGATAGAT+GGG - chr5.2:56860656-56860675 MS.gene010060:intron 25.0%
! TTTGACCAATTGTGAAAATT+TGG - chr5.2:56859210-56859229 MS.gene010060:intron 25.0%
! TTTGGAGAGTTTGAAAAAAT+TGG - chr5.2:56859228-56859247 MS.gene010060:intron 25.0%
!!! CTTCTATTTTCTCTAAAGAT+TGG - chr5.2:56858747-56858766 MS.gene010060:CDS 25.0%
!!! GTTGTTGTTGTTTATATTGT+AGG - chr5.2:56860449-56860468 MS.gene010060:intron 25.0%
!!! GTTTTGCCTACTTATTTTTA+TGG - chr5.2:56859058-56859077 MS.gene010060:intron 25.0%
!!! TTTTATTGTTTTGCTCTCTT+GGG - chr5.2:56859687-56859706 MS.gene010060:intron 25.0%
AAATTGTTGATGCTCAAAGA+AGG - chr5.2:56858843-56858862 MS.gene010060:CDS 30.0%
AATCATTGCTTTCAAAGAAG+CGG - chr5.2:56858718-56858737 MS.gene010060:CDS 30.0%
AATTGTTGATGCTCAAAGAA+GGG - chr5.2:56858844-56858863 MS.gene010060:CDS 30.0%
ATGAGCTCATTAAACAATTC+AGG + chr5.2:56858947-56858966 None:intergenic 30.0%
ATTACTTACTTTCTCACTCA+TGG - chr5.2:56860606-56860625 MS.gene010060:intron 30.0%
GAAAATGTTCTACTGCTTTA+CGG + chr5.2:56860695-56860714 None:intergenic 30.0%
GAACTCTTCTTTGTTAAAGT+TGG - chr5.2:56858809-56858828 MS.gene010060:CDS 30.0%
GATACTCCACAAATTCAAAA+CGG + chr5.2:56859995-56860014 None:intergenic 30.0%
TCCAAAAGCTTCAACTAATT+TGG - chr5.2:56860722-56860741 MS.gene010060:CDS 30.0%
TTACTTACTTTCTCACTCAT+GGG - chr5.2:56860607-56860626 MS.gene010060:intron 30.0%
TTGAAGGAAATCGAGATTAA+GGG - chr5.2:56860552-56860571 MS.gene010060:intron 30.0%
TTTGAAGGAAATCGAGATTA+AGG - chr5.2:56860551-56860570 MS.gene010060:intron 30.0%
! ACTCTCCAAATTTTCACAAT+TGG + chr5.2:56859218-56859237 None:intergenic 30.0%
! CTTCTTTGAAAGCAATGATT+CGG + chr5.2:56858718-56858737 None:intergenic 30.0%
! GTAAAGCAGTAGAACATTTT+CGG - chr5.2:56860694-56860713 MS.gene010060:intron 30.0%
! TCATGGATATATGACACTTT+TGG - chr5.2:56859321-56859340 MS.gene010060:intron 30.0%
! TCCAAATTAGTTGAAGCTTT+TGG + chr5.2:56860726-56860745 None:intergenic 30.0%
! TGTGAATTTTTGTAGTAGGT+TGG - chr5.2:56860289-56860308 MS.gene010060:CDS 30.0%
! TTCTTTGAAAGCAATGATTC+GGG + chr5.2:56858717-56858736 None:intergenic 30.0%
!! CTTAGGTTTCAAAGTTTTAG+AGG - chr5.2:56859756-56859775 MS.gene010060:intron 30.0%
!! GTTTTATTGTTTTGCTCTCT+TGG - chr5.2:56859686-56859705 MS.gene010060:intron 30.0%
!!! GTTCGTTTTGCTTTAAGAAA+TGG - chr5.2:56858977-56858996 MS.gene010060:intron 30.0%
AAGAAATGGAGTCAAGGATT+TGG - chr5.2:56858991-56859010 MS.gene010060:intron 35.0%
AATCGAGATTAAGGGCTTTA+AGG - chr5.2:56860560-56860579 MS.gene010060:intron 35.0%
ACAAATTCAAAACGGTGGAA+AGG + chr5.2:56859987-56860006 None:intergenic 35.0%
AGTAAATGCGCCAAATCTAA+AGG - chr5.2:56859288-56859307 MS.gene010060:intron 35.0%
ATGTTATCCCAGAGAGATAT+TGG - chr5.2:56860490-56860509 MS.gene010060:intron 35.0%
CATCCCATCTATCATCTTTA+AGG + chr5.2:56860662-56860681 None:intergenic 35.0%
CTTTGAGCATCAACAATTTC+AGG + chr5.2:56858842-56858861 None:intergenic 35.0%
GGACATGAATAACAACTACA+TGG + chr5.2:56859896-56859915 None:intergenic 35.0%
GTCTAAACTTACTACTCTAC+CGG - chr5.2:56860360-56860379 MS.gene010060:CDS 35.0%
TGATATTCAATCACCTGCAT+TGG - chr5.2:56859348-56859367 MS.gene010060:intron 35.0%
TGCAGGTGATTGAATATCAA+CGG + chr5.2:56859347-56859366 None:intergenic 35.0%
TGTTATCCCAGAGAGATATT+GGG - chr5.2:56860491-56860510 MS.gene010060:intron 35.0%
TTCTATCGATATCTCTCTCA+AGG + chr5.2:56859917-56859936 None:intergenic 35.0%
TTTCAGCTTTCGTGAGAAAA+TGG - chr5.2:56858870-56858889 MS.gene010060:CDS 35.0%
! ATCGAGATTAAGGGCTTTAA+GGG - chr5.2:56860561-56860580 MS.gene010060:intron 35.0%
! CTTTGGGTTACATGAGAATA+AGG - chr5.2:56859167-56859186 MS.gene010060:intron 35.0%
! TTCGTGTATTTTGCTTGGTT+GGG - chr5.2:56859710-56859729 MS.gene010060:intron 35.0%
!! AATAAGGCACTGTGCTATTA+AGG - chr5.2:56859183-56859202 MS.gene010060:intron 35.0%
!! ATGTGTGAAAAAGCGTTTGA+AGG - chr5.2:56860536-56860555 MS.gene010060:intron 35.0%
!! TGCTTTAAGAAATGGAGTCA+AGG - chr5.2:56858985-56859004 MS.gene010060:intron 35.0%
!! TTTCCACCGTTTTGAATTTG+TGG - chr5.2:56859986-56860005 MS.gene010060:CDS 35.0%
!!! GGTTTCAAAGTTTTAGAGGA+TGG - chr5.2:56859760-56859779 MS.gene010060:intron 35.0%
ACTCCACAAATTCAAAACGG+TGG + chr5.2:56859992-56860011 None:intergenic 40.0%
AGATTAACCTCATCCAATGC+AGG + chr5.2:56859364-56859383 None:intergenic 40.0%
ATCCTTGACAACGATGTTCA+GGG + chr5.2:56859396-56859415 None:intergenic 40.0%
GAACATCGTTGTCAAGGATA+TGG - chr5.2:56859397-56859416 MS.gene010060:intron 40.0%
TATCCTTGACAACGATGTTC+AGG + chr5.2:56859397-56859416 None:intergenic 40.0%
TGTATGCAGCTACTTACTTC+AGG - chr5.2:56859471-56859490 MS.gene010060:intron 40.0%
! ATTGTGAGACGCTCTAAGTA+AGG + chr5.2:56860037-56860056 None:intergenic 40.0%
! GTTCGTGTATTTTGCTTGGT+TGG - chr5.2:56859709-56859728 MS.gene010060:intron 40.0%
! TTGGGTTCGTGTATTTTGCT+TGG - chr5.2:56859705-56859724 MS.gene010060:intron 40.0%
! TTGTGAGACGCTCTAAGTAA+GGG + chr5.2:56860036-56860055 None:intergenic 40.0%
AGTCGACCCAATATCTCTCT+GGG + chr5.2:56860500-56860519 None:intergenic 45.0%
TCAATCACCTGCATTGGATG+AGG - chr5.2:56859354-56859373 MS.gene010060:intron 45.0%
TCCTTGACAACGATGTTCAG+GGG + chr5.2:56859395-56859414 None:intergenic 45.0%
GAGTCGACCCAATATCTCTC+TGG + chr5.2:56860501-56860520 None:intergenic 50.0%
TACATGGTGCAGCTACTGTG+AGG + chr5.2:56859880-56859899 None:intergenic 50.0%
TCCCCTGAACATCGTTGTCA+AGG - chr5.2:56859391-56859410 MS.gene010060:intron 50.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 56858681 56860761 56858681 ID=MS.gene010060
chr5.2 mRNA 56858681 56860761 56858681 ID=MS.gene010060.t1;Parent=MS.gene010060
chr5.2 exon 56860703 56860761 56860703 ID=MS.gene010060.t1.exon1;Parent=MS.gene010060.t1
chr5.2 CDS 56860703 56860761 56860703 ID=cds.MS.gene010060.t1;Parent=MS.gene010060.t1
chr5.2 exon 56859950 56860448 56859950 ID=MS.gene010060.t1.exon2;Parent=MS.gene010060.t1
chr5.2 CDS 56859950 56860448 56859950 ID=cds.MS.gene010060.t1;Parent=MS.gene010060.t1
chr5.2 exon 56858681 56858971 56858681 ID=MS.gene010060.t1.exon3;Parent=MS.gene010060.t1
chr5.2 CDS 56858681 56858971 56858681 ID=cds.MS.gene010060.t1;Parent=MS.gene010060.t1
Gene Sequence

>MS.gene010060

ATGGGAGTGAGCAATGACATATTGAGTTTAATGCCCGAATCATTGCTTTCAAAGAAGCGGTAAGAACTTCTATTTTCTCTAAAGATTGGGTGAATGTATACAAATCAACAACAAAAATAGAGTTTAATGAACTCTTCTTTGTTAAAGTTGGTGAATCTCCTGAAATTGTTGATGCTCAAAGAAGGGCATTTTCAGCTTTCGTGAGAAAATGGATTGAAAATCACGTAGATGTCATTGATAAATTCTCTTTAAGAATTTTGATGCCTGAATTGTTTAATGAGCTCATTGATCAATGTGTTCGTTTTGCTTTAAGAAATGGAGTCAAGGATTTGGAGCTTGATTTCAGTTATCCTTATGATATTGTTGATGTTGTAGTTGTTTTGCCTACTTATTTTTATGGTTATAGTGGGTTTGAATCTTTGAAATTGTATGCATGTAAATTTGTTGCTAGTCAATGTGTTAATTTTCATTCACTCAAAGATATTTCTTTGGGTTACATGAGAATAAGGCACTGTGCTATTAAGGCACTTTTGACCAATTGTGAAAATTTGGAGAGTTTGAAAAAATTGGTCATCGATATGTGCGATTTTACGTTTAATATTTTTAGAGTAAATGCGCCAAATCTAAAGGTTTTTAATTATCATGGATATATGACACTTTTGGCCGTTGATATTCAATCACCTGCATTGGATGAGGTTAATCTTGACTTTTCCCCTGAACATCGTTGTCAAGGATATGGTTCTTATCTTTACAAATTTTTAAAAGAGGTCTCTTCTTCTAAAGTTATGACTGTATGCAGCTACTTACTTCAGGTACCATTTTTTACCTTTTGTCTTTTTTCTTAAAGTTAAAATTTATTTTTGATAATCAATTTAATTATTATTGCACAATACATTGCTTTTACTGTATTAATTAACTTTATTCGTTGAAACAATTTATAGCTAGATCTACATATTATTTTTCTCTAATTGTTTTGAAGATCTCTATATATGTATTCATTTGGGGGTTTTATTGTTTTGCTCTCTTGGGTTCGTGTATTTTGCTTGGTTGGGCGATGTAAAAAGTATATATTTTTCTTAGGTTTCAAAGTTTTAGAGGATGGCTGCGTTAAAAATTCTAAAGCTAAATTTTTTTATGAGAAACAACTGAGAAGACCATTAACTTTGTGTGAAATTTTCTTTCATTAGACTTAATGACCTCACAGTAGCTGCACCATGTAGTTGTTATTCATGTCCTTGAGAGAGATATCGATAGAATGCATGCAATATCTTATACCTTTCACTAATTTTATTTTTATTCATGTCCTTTCCACCGTTTTGAATTTGTGGAGTATCTTTTATGCTAAGAAGCTGCCCTTACTTAGAGCGTCTCACAATTGAAATTGTTGATGAAAAATACCTGTTTGTAAGTATTGCATAAATTTGATTTAATTTAATTAATTCTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTATGCATCTAATTTGGATACATTGTCGATGTAAAATATAATGAATATCATAGTTTCATTTGATTGAATATATGCATAAAAAAATATTACAATATTGTTTTTTAATTGTGAATTTTTGTAGTAGGTTGGATAAAAATCAAACTATTTTTATAGTTTGATGCTCATGATTGATTGACAGTCTAAACTTACTACTCTACCGGTGCATATAAATTAAATTTTATACTTCATATGACTTTTGATGTAAAATTAAAAACATGGAACTTTTTGTTGTTGTTGTTTATATTGTAGGGTTATGAAGAAATGTTCAATGTTATCCCAGAGAGATATTGGGTCGACTCTATCAAAGTTTACAAATGTGTGAAAAAGCGTTTGAAGGAAATCGAGATTAAGGGCTTTAAGGGAACTAAAGATGAGTTTAGTGTGATTACTTACTTTCTCACTCATGGGAATGTCTTGAGAAAGTTGAGTATCAATTTCCTTAAAGATGATAGATGGGATGTCACTTCTCGCCGTAAAGCAGTAGAACATTTTCGGATGCTTCCAAAAGCTTCAACTAATTTGGAGATATCAATCTATTAG
Protein sequence

>MS.gene010060.t1

MGVSNDILSLMPESLLSKKRNGVKDLELDFSYPYDIVDVVVVLPTYFYGYSGFESLKLYACKFVASQCVNFHSLKDISLGYMRIRHCAIKALLTNCENLESLKKLVIDMCDFTFNIFRVNAPNLKVFNYHGYMTLLAVDIQSPALDEVNLDFSPEHRCQGYGSYLYKFLKEVSSSKVMTVCSYLLQGYEEMFNVIPERYWVDSIKVYKCVKKRLKEIEIKGFKGTKDEFSVITYFLTHGNVLRKLSINFLKDDRWDVTSRRKAVEHFRMLPKASTNLEISIY