AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39883

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39883.t1 MTR_1g070250 99.194 124 1 0 1 124 1 124 4.60e-89 256
MS.gene39883.t1 MTR_1g075430 68.000 50 14 1 22 71 4 51 4.51e-16 70.9
MS.gene39883.t1 MTR_4g064873 62.745 51 18 1 28 78 11 60 2.83e-15 68.6
MS.gene39883.t1 MTR_1g044225 47.692 65 34 0 16 80 4 68 1.18e-14 66.6
MS.gene39883.t1 MTR_7g063220 61.364 44 17 0 35 78 21 64 1.25e-14 65.9
MS.gene39883.t1 MTR_5g014400 36.538 104 50 2 38 125 80 183 2.46e-13 64.7
MS.gene39883.t1 MTR_2g076060 44.928 69 32 1 18 80 24 92 2.56e-12 61.6
MS.gene39883.t1 MTR_1g070265 52.727 55 13 2 26 67 10 64 7.94e-12 59.7
MS.gene39883.t1 MTR_5g008280 44.615 65 32 1 3 67 15 75 1.04e-11 60.8
MS.gene39883.t1 MTR_5g080660 51.852 54 21 1 34 87 43 91 2.38e-11 58.9
MS.gene39883.t1 MTR_3g068095 68.571 35 11 0 38 72 55 89 8.81e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39883.t1 AT5G43540 47.059 68 33 1 40 107 35 99 4.13e-14 64.7
MS.gene39883.t1 AT3G23130 60.870 46 15 1 25 67 29 74 1.51e-13 64.7
MS.gene39883.t1 AT3G09290 67.568 37 12 0 31 67 26 62 3.26e-12 60.5
MS.gene39883.t1 AT3G53820 64.103 39 14 0 37 75 18 56 5.26e-12 59.3
MS.gene39883.t1 AT2G37740 40.506 79 44 1 27 102 26 104 6.52e-12 61.2

Find 19 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGATCATCGTCGTTGTTT+TGG 0.273789 1.4:+57429282 None:intergenic
TGAACTAGGAGGAGCAAAAT+TGG 0.301135 1.4:+57429124 None:intergenic
TTCACAACTGCTCAAGCTTT+AGG 0.324072 1.4:-57429206 MS.gene39883:CDS
CATGATAACTATGGAGATCT+TGG 0.334975 1.4:-57429083 MS.gene39883:CDS
CATGATCATCACATGGGAAT+TGG 0.389791 1.4:-57429263 MS.gene39883:CDS
GTAGTTGATCATGATAACTA+TGG 0.421306 1.4:-57429092 MS.gene39883:CDS
AGCTCTTCGAGTCTTCTTGA+AGG 0.511682 1.4:+57429336 None:intergenic
TCCAAGTCATCTTGCAAGAG+GGG 0.518624 1.4:-57429042 MS.gene39883:CDS
ACTACTAATTTGCTTGAACT+AGG 0.523496 1.4:+57429110 None:intergenic
ACAACTGCTCAAGCTTTAGG+TGG 0.547877 1.4:-57429203 MS.gene39883:CDS
CGATGATCATGATCATCACA+TGG 0.555921 1.4:-57429270 MS.gene39883:CDS
ATCCAAGTCATCTTGCAAGA+GGG 0.566204 1.4:-57429043 MS.gene39883:CDS
TTGAAGGTAGCTGAATTCCA+TGG 0.575818 1.4:+57429352 None:intergenic
TACCTCAGGAGTAGTTGTTG+TGG 0.580075 1.4:+57428998 None:intergenic
ACTAATTTGCTTGAACTAGG+AGG 0.604445 1.4:+57429113 None:intergenic
AATCCAAGTCATCTTGCAAG+AGG 0.624664 1.4:-57429044 MS.gene39883:CDS
CCAAGTCATCTTGCAAGAGG+GGG 0.654928 1.4:-57429041 MS.gene39883:CDS
ATCCACAACAACTACTCCTG+AGG 0.666114 1.4:-57429000 MS.gene39883:intron
GATGATCATGATCATCACAT+GGG 0.724317 1.4:-57429269 MS.gene39883:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GTAGTTGATCATGATAACTA+TGG - chr1.4:57429170-57429189 MS.gene39883:CDS 30.0%
TAATTAAGAGAATCTACCTC+AGG + chr1.4:57429281-57429300 None:intergenic 30.0%
TGTTGTGTGTTGAAAATCAA+AGG - chr1.4:57429342-57429361 MS.gene39883:CDS 30.0%
!! ACTACTAATTTGCTTGAACT+AGG + chr1.4:57429155-57429174 None:intergenic 30.0%
CATGATAACTATGGAGATCT+TGG - chr1.4:57429179-57429198 MS.gene39883:CDS 35.0%
GATGATCATGATCATCACAT+GGG - chr1.4:57428993-57429012 MS.gene39883:intron 35.0%
TCACTATATTGCACATGTGA+AGG + chr1.4:57429320-57429339 None:intergenic 35.0%
!! ACTAATTTGCTTGAACTAGG+AGG + chr1.4:57429152-57429171 None:intergenic 35.0%
!!! AGGAGCAAAATTGGTTTTAG+TGG + chr1.4:57429132-57429151 None:intergenic 35.0%
AATCCAAGTCATCTTGCAAG+AGG - chr1.4:57429218-57429237 MS.gene39883:CDS 40.0%
ATCCAAGTCATCTTGCAAGA+GGG - chr1.4:57429219-57429238 MS.gene39883:CDS 40.0%
CATGATCATCACATGGGAAT+TGG - chr1.4:57428999-57429018 MS.gene39883:intron 40.0%
CGATGATCATGATCATCACA+TGG - chr1.4:57428992-57429011 MS.gene39883:intron 40.0%
TGAACTAGGAGGAGCAAAAT+TGG + chr1.4:57429141-57429160 None:intergenic 40.0%
TTCACAACTGCTCAAGCTTT+AGG - chr1.4:57429056-57429075 MS.gene39883:CDS 40.0%
! CATGATCATCGTCGTTGTTT+TGG + chr1.4:57428983-57429002 None:intergenic 40.0%
! GAGTGTGTGTTTTGCAAAAG+AGG - chr1.4:57429032-57429051 MS.gene39883:CDS 40.0%
AGCTCTTCGAGTCTTCTTGA+AGG + chr1.4:57428929-57428948 None:intergenic 45.0%
ATCCACAACAACTACTCCTG+AGG - chr1.4:57429262-57429281 MS.gene39883:CDS 45.0%
TACCTCAGGAGTAGTTGTTG+TGG + chr1.4:57429267-57429286 None:intergenic 45.0%
TCCAAGTCATCTTGCAAGAG+GGG - chr1.4:57429220-57429239 MS.gene39883:CDS 45.0%
!! ACAACTGCTCAAGCTTTAGG+TGG - chr1.4:57429059-57429078 MS.gene39883:CDS 45.0%
CCAAGTCATCTTGCAAGAGG+GGG - chr1.4:57429221-57429240 MS.gene39883:CDS 50.0%
CCCCCTCTTGCAAGATGACT+TGG + chr1.4:57429224-57429243 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 57428912 57429372 57428912 ID=MS.gene39883
chr1.4 mRNA 57428912 57429372 57428912 ID=MS.gene39883.t1;Parent=MS.gene39883
chr1.4 exon 57429001 57429372 57429001 ID=MS.gene39883.t1.exon1;Parent=MS.gene39883.t1
chr1.4 CDS 57429001 57429372 57429001 ID=cds.MS.gene39883.t1;Parent=MS.gene39883.t1
chr1.4 exon 57428912 57428920 57428912 ID=MS.gene39883.t1.exon2;Parent=MS.gene39883.t1
chr1.4 CDS 57428912 57428920 57428912 ID=cds.MS.gene39883.t1;Parent=MS.gene39883.t1
Gene Sequence

>MS.gene39883

ATGGAATTCAGCTACCTTCAAGAAGACTCGAAGAGCTCGAGCGATGAAAACATCGATCGATCATCTGACCAAAACAACGACGATGATCATGATCATCACATGGGAATTGGTAGATCTTATGAGTGTGTGTTTTGCAAAAGAGGTTTCACAACTGCTCAAGCTTTAGGTGGACACATGAACATACATAGAAAAGATAGAGCAAATAACAACAAAAGTGCCACTAAAACCAATTTTGCTCCTCCTAGTTCAAGCAAATTAGTAGTTGATCATGATAACTATGGAGATCTTGGATTTTATTCAACAATTAATCCAAGTCATCTTGCAAGAGGGGGTTATTATTCTTCAATTTCATCCACAACAACTACTCCTGAGGTAGATTCTCTTAATTATCATCAAATATATTTTCCTTCACATGTGCAATATAGTGAGATGTTGTGTGTTGAAAATCAAAGGATGTTTGA
Protein sequence

>MS.gene39883.t1

MEFSYLQEDSKSSSDENIDRSSDQNNDDDHDHHMGIGRSYECVFCKRGFTTAQALGGHMNIHRKDRANNNKSATKTNFAPPSSSKLVVDHDNYGDLGFYSTINPSHLARGGYYSSISSTTTTPEDV