AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054616


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054616.t1 MTR_3g101260 96.923 130 4 0 17 146 1 130 6.14e-92 262
MS.gene054616.t1 MTR_4g086730 46.610 118 63 0 29 146 61 178 2.94e-35 120
MS.gene054616.t1 MTR_4g086750 46.610 118 63 0 29 146 62 179 3.06e-35 120
MS.gene054616.t1 MTR_4g086740 46.610 118 63 0 29 146 60 177 3.09e-35 120
MS.gene054616.t1 MTR_4g086710 45.763 118 64 0 29 146 62 179 5.29e-35 120
MS.gene054616.t1 MTR_4g086690 42.529 87 50 0 60 146 21 107 5.54e-20 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054616.t1 AT2G15780 42.478 113 63 1 29 141 142 252 5.42e-25 96.3
MS.gene054616.t1 AT2G15770 38.793 116 69 1 26 141 141 254 1.31e-23 93.6
MS.gene054616.t1 AT4G33930 35.897 117 58 6 39 144 229 339 4.77e-12 62.4
MS.gene054616.t1 AT4G34300 35.652 115 56 6 39 141 198 306 2.08e-11 60.5

Find 47 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCCAATGTGTCATTTATT+TGG 0.160335 3.4:-89152056 None:intergenic
CTTCCTTGTGATTGCTTCAA+TGG 0.264782 3.4:+89151921 MS.gene054616:CDS
TCCAACCAAGATGCTTCTTT+TGG 0.296074 3.4:-89151971 None:intergenic
GTGATTGCTTCAATGGTTGC+AGG 0.311734 3.4:+89151928 MS.gene054616:CDS
GGGAATTGGACTAAATTAAA+AGG 0.331947 3.4:-89152553 None:intergenic
TCATCAGAGGCAAAGTAATA+AGG 0.345121 3.4:-89152468 None:intergenic
TACACGACGTGTGAATTTAG+AGG 0.385924 3.4:+89152375 MS.gene054616:CDS
GCTTCAATGGTTGCAGGGTC+AGG 0.401233 3.4:+89151934 MS.gene054616:CDS
GACTCTGAAGGTTGGCGTGC+AGG 0.411668 3.4:+89151994 MS.gene054616:CDS
AATTAAAAGGAACGTGTAGA+TGG 0.428002 3.4:-89152540 None:intergenic
TATTACTTTGCCTCTGATGA+AGG 0.434564 3.4:+89152471 MS.gene054616:CDS
AATGCCTATGACTGTATTGC+TGG 0.454610 3.4:+89152495 MS.gene054616:CDS
GAGTCCAGCAATACAGTCAT+AGG 0.464321 3.4:-89152499 None:intergenic
GTCGTGTAACTCCACATATT+CGG 0.471065 3.4:-89152360 None:intergenic
CAATGTGTCATTTATTTGGA+AGG 0.485349 3.4:-89152052 None:intergenic
TTTAGAGGAGCAAAGTTGCT+TGG 0.490765 3.4:+89152390 MS.gene054616:CDS
TTTACTTGCTACCGAATATG+TGG 0.498287 3.4:+89152349 MS.gene054616:CDS
TTCCAAATAAATGACACATT+GGG 0.508285 3.4:+89152054 MS.gene054616:CDS
ATGTGTCATTTATTTGGAAG+GGG 0.525400 3.4:-89152050 None:intergenic
AATGTGTCATTTATTTGGAA+GGG 0.530429 3.4:-89152051 None:intergenic
CTTCCAAATAAATGACACAT+TGG 0.530831 3.4:+89152053 MS.gene054616:CDS
CAGAACCAAAAGAAGCATCT+TGG 0.539687 3.4:+89151966 MS.gene054616:CDS
ACCAAAAGAAGCATCTTGGT+TGG 0.551375 3.4:+89151970 MS.gene054616:CDS
GGTTGCAGGGTCAGGAAGCA+AGG 0.552711 3.4:+89151942 MS.gene054616:CDS
CAGGCACTAACTACACCCAA+TGG 0.558303 3.4:+89152013 MS.gene054616:CDS
GCTGATCAAGGTGGTGGTGA+GGG 0.565763 3.4:+89152417 MS.gene054616:CDS
TGATTGCTTCAATGGTTGCA+GGG 0.566600 3.4:+89151929 MS.gene054616:CDS
TTCGGTAGCAAGTAAACGCT+GGG 0.568902 3.4:-89152342 None:intergenic
TGGTTGGAGACTCTGAAGGT+TGG 0.582794 3.4:+89151986 MS.gene054616:CDS
AGGCACTAACTACACCCAAT+GGG 0.584087 3.4:+89152014 MS.gene054616:CDS
ATTCGGTAGCAAGTAAACGC+TGG 0.587303 3.4:-89152343 None:intergenic
AACCGTGGAATTTCCTGAAG+GGG 0.598371 3.4:-89152316 None:intergenic
AGATGGAACAGCAATGAACT+TGG 0.599581 3.4:-89152523 None:intergenic
TAAAGATTGAGCTGAATCAG+TGG 0.605281 3.4:+89152442 MS.gene054616:CDS
TGCTGATCAAGGTGGTGGTG+AGG 0.607379 3.4:+89152416 MS.gene054616:CDS
ATAGGCATTGCCTTCATCAG+AGG 0.610448 3.4:-89152481 None:intergenic
ATGTCTAGAATTCTCATACA+AGG 0.613782 3.4:+89151892 MS.gene054616:CDS
GGTAATGCTGATCAAGGTGG+TGG 0.619304 3.4:+89152411 MS.gene054616:CDS
ACCGTGGAATTTCCTGAAGG+GGG 0.620984 3.4:-89152315 None:intergenic
TTGCTTGGTAATGCTGATCA+AGG 0.621103 3.4:+89152405 MS.gene054616:CDS
ATCTTGGTTGGAGACTCTGA+AGG 0.629130 3.4:+89151982 MS.gene054616:CDS
CAACCATTGAAGCAATCACA+AGG 0.631574 3.4:-89151924 None:intergenic
CAACCGTGGAATTTCCTGAA+GGG 0.654328 3.4:-89152317 None:intergenic
ACAACCGTGGAATTTCCTGA+AGG 0.668113 3.4:-89152318 None:intergenic
CTTGGTAATGCTGATCAAGG+TGG 0.670664 3.4:+89152408 MS.gene054616:CDS
GTAAACGCTGGGAACAACCG+TGG 0.691075 3.4:-89152331 None:intergenic
CCGTGGAATTTCCTGAAGGG+GGG 0.694717 3.4:-89152314 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCAAATTATTATCAA+AGG + chr3.4:89152182-89152201 MS.gene054616:intron 10.0%
!! ATAATTTGAAAAAATCAAAG+TGG - chr3.4:89152176-89152195 None:intergenic 15.0%
!! TTAAATATAATTAAATGCGT+TGG - chr3.4:89152153-89152172 None:intergenic 15.0%
!!! TTTGATTGATGGATTAATTT+TGG + chr3.4:89152257-89152276 MS.gene054616:intron 20.0%
! CAATATATATGCACAAACAA+TGG - chr3.4:89152220-89152239 None:intergenic 25.0%
! TTCCAAATAAATGACACATT+GGG + chr3.4:89152054-89152073 MS.gene054616:CDS 25.0%
!!! AATGTGTCATTTATTTGGAA+GGG - chr3.4:89152054-89152073 None:intergenic 25.0%
CTTCCAAATAAATGACACAT+TGG + chr3.4:89152053-89152072 MS.gene054616:CDS 30.0%
CTTCTTCTTCATTTGATTGA+TGG + chr3.4:89152246-89152265 MS.gene054616:intron 30.0%
! ATGTCTAGAATTCTCATACA+AGG + chr3.4:89151892-89151911 MS.gene054616:CDS 30.0%
!! ATGTGTCATTTATTTGGAAG+GGG - chr3.4:89152053-89152072 None:intergenic 30.0%
!! CAATGTGTCATTTATTTGGA+AGG - chr3.4:89152055-89152074 None:intergenic 30.0%
!! TACCCAATGTGTCATTTATT+TGG - chr3.4:89152059-89152078 None:intergenic 30.0%
TAAAGATTGAGCTGAATCAG+TGG + chr3.4:89152442-89152461 MS.gene054616:CDS 35.0%
TATTACTTTGCCTCTGATGA+AGG + chr3.4:89152471-89152490 MS.gene054616:CDS 35.0%
TCATCAGAGGCAAAGTAATA+AGG - chr3.4:89152471-89152490 None:intergenic 35.0%
! TTTACTTGCTACCGAATATG+TGG + chr3.4:89152349-89152368 MS.gene054616:CDS 35.0%
!!! GCTATTTTTTATGGCCCATT+GGG - chr3.4:89152031-89152050 None:intergenic 35.0%
!!! TTGGAAGGGGCTATTTTTTA+TGG - chr3.4:89152040-89152059 None:intergenic 35.0%
AATGCCTATGACTGTATTGC+TGG + chr3.4:89152495-89152514 MS.gene054616:CDS 40.0%
AGATGGAACAGCAATGAACT+TGG - chr3.4:89152526-89152545 None:intergenic 40.0%
CAACCATTGAAGCAATCACA+AGG - chr3.4:89151927-89151946 None:intergenic 40.0%
CTTCCTTGTGATTGCTTCAA+TGG + chr3.4:89151921-89151940 MS.gene054616:CDS 40.0%
GTCGTGTAACTCCACATATT+CGG - chr3.4:89152363-89152382 None:intergenic 40.0%
TACACGACGTGTGAATTTAG+AGG + chr3.4:89152375-89152394 MS.gene054616:CDS 40.0%
TGATTGCTTCAATGGTTGCA+GGG + chr3.4:89151929-89151948 MS.gene054616:CDS 40.0%
TTTAGAGGAGCAAAGTTGCT+TGG + chr3.4:89152390-89152409 MS.gene054616:CDS 40.0%
! TCCAACCAAGATGCTTCTTT+TGG - chr3.4:89151974-89151993 None:intergenic 40.0%
!! ACCAAAAGAAGCATCTTGGT+TGG + chr3.4:89151970-89151989 MS.gene054616:CDS 40.0%
!! CAGAACCAAAAGAAGCATCT+TGG + chr3.4:89151966-89151985 MS.gene054616:CDS 40.0%
!! TTGCTTGGTAATGCTGATCA+AGG + chr3.4:89152405-89152424 MS.gene054616:CDS 40.0%
!!! CAAGATGCTTCTTTTGGTTC+TGG - chr3.4:89151968-89151987 None:intergenic 40.0%
!!! GGCTATTTTTTATGGCCCAT+TGG - chr3.4:89152032-89152051 None:intergenic 40.0%
AACCGTGGAATTTCCTGAAG+GGG - chr3.4:89152319-89152338 None:intergenic 45.0%
ACAACCGTGGAATTTCCTGA+AGG - chr3.4:89152321-89152340 None:intergenic 45.0%
AGGCACTAACTACACCCAAT+GGG + chr3.4:89152014-89152033 MS.gene054616:CDS 45.0%
ATCTTGGTTGGAGACTCTGA+AGG + chr3.4:89151982-89152001 MS.gene054616:CDS 45.0%
ATTCGGTAGCAAGTAAACGC+TGG - chr3.4:89152346-89152365 None:intergenic 45.0%
CAACCGTGGAATTTCCTGAA+GGG - chr3.4:89152320-89152339 None:intergenic 45.0%
GAGTCCAGCAATACAGTCAT+AGG - chr3.4:89152502-89152521 None:intergenic 45.0%
GTGATTGCTTCAATGGTTGC+AGG + chr3.4:89151928-89151947 MS.gene054616:CDS 45.0%
TTCGGTAGCAAGTAAACGCT+GGG - chr3.4:89152345-89152364 None:intergenic 45.0%
! ATAGGCATTGCCTTCATCAG+AGG - chr3.4:89152484-89152503 None:intergenic 45.0%
!! CTTGGTAATGCTGATCAAGG+TGG + chr3.4:89152408-89152427 MS.gene054616:CDS 45.0%
ACCGTGGAATTTCCTGAAGG+GGG - chr3.4:89152318-89152337 None:intergenic 50.0%
CAGGCACTAACTACACCCAA+TGG + chr3.4:89152013-89152032 MS.gene054616:CDS 50.0%
GGTAATGCTGATCAAGGTGG+TGG + chr3.4:89152411-89152430 MS.gene054616:CDS 50.0%
! TGGTTGGAGACTCTGAAGGT+TGG + chr3.4:89151986-89152005 MS.gene054616:CDS 50.0%
CCCCCCTTCAGGAAATTCCA+CGG + chr3.4:89152314-89152333 MS.gene054616:CDS 55.0%
CCGTGGAATTTCCTGAAGGG+GGG - chr3.4:89152317-89152336 None:intergenic 55.0%
GCTTCAATGGTTGCAGGGTC+AGG + chr3.4:89151934-89151953 MS.gene054616:CDS 55.0%
GTAAACGCTGGGAACAACCG+TGG - chr3.4:89152334-89152353 None:intergenic 55.0%
GTGTTCAAGTACCCCCCTTC+AGG + chr3.4:89152303-89152322 MS.gene054616:intron 55.0%
! GCTGATCAAGGTGGTGGTGA+GGG + chr3.4:89152417-89152436 MS.gene054616:CDS 55.0%
! TGCTGATCAAGGTGGTGGTG+AGG + chr3.4:89152416-89152435 MS.gene054616:CDS 55.0%
GGTTGCAGGGTCAGGAAGCA+AGG + chr3.4:89151942-89151961 MS.gene054616:CDS 60.0%
! GACTCTGAAGGTTGGCGTGC+AGG + chr3.4:89151994-89152013 MS.gene054616:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 89151892 89152560 89151892 ID=MS.gene054616
chr3.4 mRNA 89151892 89152560 89151892 ID=MS.gene054616.t1;Parent=MS.gene054616
chr3.4 exon 89151892 89152075 89151892 ID=MS.gene054616.t1.exon1;Parent=MS.gene054616.t1
chr3.4 CDS 89151892 89152075 89151892 ID=cds.MS.gene054616.t1;Parent=MS.gene054616.t1
chr3.4 exon 89152304 89152560 89152304 ID=MS.gene054616.t1.exon2;Parent=MS.gene054616.t1
chr3.4 CDS 89152304 89152560 89152304 ID=cds.MS.gene054616.t1;Parent=MS.gene054616.t1
Gene Sequence

>MS.gene054616

ATGTCTAGAATTCTCATACAAGGAGTTATCTTCCTTGTGATTGCTTCAATGGTTGCAGGGTCAGGAAGCAAGGCCAGAACCAAAAGAAGCATCTTGGTTGGAGACTCTGAAGGTTGGCGTGCAGGCACTAACTACACCCAATGGGCCATAAAAAATAGCCCCTTCCAAATAAATGACACATTGGGTATGTATCAATTAACTCGTAGCAGCGATACTACTTCATATCGAAAACATTTGTTTTTTGACACTAACACGAGACCAACGCATTTAATTATATTTAACCACTTTGATTTTTTCAAATTATTATCAAAGGTCGCTTGTATGTCCATTGTTTGTGCATATATATTGATTTTTCTTCTTCTTCATTTGATTGATGGATTAATTTTGGTTTGTGCATACATAAATAATGCAGTGTTCAAGTACCCCCCTTCAGGAAATTCCACGGTTGTTCCCAGCGTTTACTTGCTACCGAATATGTGGAGTTACACGACGTGTGAATTTAGAGGAGCAAAGTTGCTTGGTAATGCTGATCAAGGTGGTGGTGAGGGCATAAAGATTGAGCTGAATCAGTGGAAGCCTTATTACTTTGCCTCTGATGAAGGCAATGCCTATGACTGTATTGCTGGACTCACCAAGTTCATTGCTGTTCCATCTACACGTTCCTTTTAA

Protein sequence

>MS.gene054616.t1

MSRILIQGVIFLVIASMVAGSGSKARTKRSILVGDSEGWRAGTNYTQWAIKNSPFQINDTLVFKYPPSGNSTVVPSVYLLPNMWSYTTCEFRGAKLLGNADQGGGEGIKIELNQWKPYYFASDEGNAYDCIAGLTKFIAVPSTRSF