AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene44768

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44768.t1 MTR_7g017880 96.335 191 7 0 1 191 1 191 4.23e-135 375
MS.gene44768.t1 MTR_6g016375 67.582 182 53 5 1 177 1 181 8.13e-65 198
MS.gene44768.t1 MTR_7g029400 53.968 189 72 7 9 190 8 188 6.50e-50 160
MS.gene44768.t1 MTR_8g015250 53.514 185 68 10 9 190 8 177 9.77e-47 151
MS.gene44768.t1 MTR_4g070860 52.326 86 38 2 70 155 16 98 1.64e-17 75.9
MS.gene44768.t1 MTR_1g022495 44.330 97 54 0 61 157 4 100 7.47e-17 74.3
MS.gene44768.t1 MTR_3g117120 50.000 80 40 0 76 155 19 98 2.09e-16 73.2
MS.gene44768.t1 MTR_4g097440 33.974 156 85 3 37 174 7 162 5.40e-16 72.4
MS.gene44768.t1 MTR_1g087040 42.553 94 49 2 62 155 7 95 6.58e-13 63.5
MS.gene44768.t1 MTR_5g015090 36.885 122 72 1 56 172 25 146 2.39e-12 62.4
MS.gene44768.t1 MTR_5g028850 37.736 106 61 2 54 154 272 377 2.36e-11 62.0
MS.gene44768.t1 MTR_5g028850 37.736 106 61 2 54 154 270 375 2.91e-11 61.6
MS.gene44768.t1 MTR_8g086020 32.292 96 65 0 60 155 8 103 9.54e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44768.t1 AT3G30530 57.396 169 56 7 11 176 12 167 3.60e-49 157
MS.gene44768.t1 AT5G38800 57.042 142 56 3 39 176 20 160 2.80e-43 142
MS.gene44768.t1 AT2G04038 64.583 96 34 0 67 162 54 149 2.64e-36 124
MS.gene44768.t1 AT5G15830 61.616 99 38 0 65 163 52 150 7.78e-35 121
MS.gene44768.t1 AT1G13600 44.375 160 83 3 8 165 9 164 2.75e-34 120
MS.gene44768.t1 AT1G68880 44.348 115 59 1 51 165 16 125 1.64e-23 91.3
MS.gene44768.t1 AT5G60830 51.724 87 41 1 79 164 62 148 4.48e-19 81.3
MS.gene44768.t1 AT2G18160 50.000 72 36 0 84 155 28 99 2.12e-15 70.9
MS.gene44768.t1 AT1G75390 40.187 107 61 1 52 155 3 109 2.69e-15 70.5
MS.gene44768.t1 AT3G62420 46.575 73 39 0 83 155 21 93 4.63e-15 69.3
MS.gene44768.t1 AT1G75390 39.815 108 62 1 52 156 3 110 1.66e-14 67.4
MS.gene44768.t1 AT4G34590 45.946 74 40 0 82 155 22 95 2.45e-12 62.4

Find 39 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGAGATGGATCTAAATT+TGG 0.177056 7.4:+82493360 None:intergenic
TAGAATTGGTTGGAGAGTTT+TGG 0.269358 7.4:+82493285 None:intergenic
GGAGAATTTGAATAGGGTTT+TGG 0.279223 7.4:+82493253 None:intergenic
AAACTCTCCAACCAATTCTA+TGG 0.313604 7.4:-82493282 MS.gene44768:CDS
TGAGGTGTTTGGATGGTGTT+TGG 0.320608 7.4:+82493312 None:intergenic
AGCTTTGGTCACAGGTTGTT+TGG 0.326268 7.4:-82493068 MS.gene44768:CDS
CTTTCAATTGAACATTCTCT+TGG 0.350205 7.4:+82492977 None:intergenic
AGGGAGATGGATCTAAATTT+GGG 0.357619 7.4:+82493361 None:intergenic
TTTGGTTGAAACCATAGAAT+TGG 0.382996 7.4:+82493271 None:intergenic
AAGTCTTGGAGAATTTGAAT+AGG 0.394409 7.4:+82493246 None:intergenic
GAGGTGTTTGGATGGTGTTT+GGG 0.397868 7.4:+82493313 None:intergenic
AAAAGCAGCTTGATGAGCTT+TGG 0.402088 7.4:-82493083 MS.gene44768:CDS
GCTTGATGAGCTTTGGTCAC+AGG 0.419095 7.4:-82493076 MS.gene44768:CDS
AGTCTTGGAGAATTTGAATA+GGG 0.420567 7.4:+82493247 None:intergenic
AGCTTCAGAACTTCGACAAA+TGG 0.463372 7.4:-82492950 MS.gene44768:CDS
GTTATAGTTACAAGATGGAT+AGG 0.474326 7.4:+82493341 None:intergenic
TGGATGTTGAGGTGTTTGGA+TGG 0.476729 7.4:+82493305 None:intergenic
GGTCACAGGTTGTTTGGCTA+AGG 0.480861 7.4:-82493062 MS.gene44768:CDS
TTTGTTTCCTCATTCGCGAC+CGG 0.492636 7.4:+82493103 None:intergenic
AGGATGGAGGACTGAAGTCT+TGG 0.496834 7.4:+82493232 None:intergenic
ATTAATCTCTCTAGTTTGCA+TGG 0.500778 7.4:+82493404 None:intergenic
GCGACCGGCGTGCTGACTCT+CGG 0.500855 7.4:+82493118 None:intergenic
GTTGAAACCATAGAATTGGT+TGG 0.501172 7.4:+82493275 None:intergenic
CAGCACGCCGGTCGCGAATG+AGG 0.513300 7.4:-82493110 MS.gene44768:CDS
CAAACTAGAGAGATTAATAC+AGG 0.518960 7.4:-82493399 MS.gene44768:CDS
CGAAAGAAAACATCGAAGAA+TGG 0.528388 7.4:-82493148 MS.gene44768:CDS
ACATTTGATGAAGTGATGCT+AGG 0.529651 7.4:+82492871 None:intergenic
TTCTTTCGTTGATTAGACCT+AGG 0.573011 7.4:+82493163 None:intergenic
ATCATGTTATAGTTACAAGA+TGG 0.577997 7.4:+82493336 None:intergenic
TTACAAGATGGATAGGGAGA+TGG 0.578971 7.4:+82493348 None:intergenic
CAACTCAACGTCCGACGAAG+CGG 0.581363 7.4:-82493196 MS.gene44768:CDS
ACATCTTCAAGAGGACTCAA+AGG 0.584334 7.4:+82492895 None:intergenic
TTATAGTTACAAGATGGATA+GGG 0.602516 7.4:+82493342 None:intergenic
TTGCTGCTTATGCATGAGGA+TGG 0.607001 7.4:+82493216 None:intergenic
TGAGTTGCTGCTTATGCATG+AGG 0.633239 7.4:+82493212 None:intergenic
CTGCTTATGCATGAGGATGG+AGG 0.633472 7.4:+82493219 None:intergenic
ATGCTAGGAACATCTTCAAG+AGG 0.640644 7.4:+82492886 None:intergenic
GAAGCGGACGAACAAAACCT+AGG 0.674445 7.4:-82493180 MS.gene44768:CDS
CGAACCGAGAGTCAGCACGC+CGG 0.746941 7.4:-82493122 MS.gene44768:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATCATGTTATAGTTACAAGA+TGG + chr7.4:82492918-82492937 None:intergenic 25.0%
! TTATAGTTACAAGATGGATA+GGG + chr7.4:82492912-82492931 None:intergenic 25.0%
AAGTCTTGGAGAATTTGAAT+AGG + chr7.4:82493008-82493027 None:intergenic 30.0%
AGTCTTGGAGAATTTGAATA+GGG + chr7.4:82493007-82493026 None:intergenic 30.0%
CAAACTAGAGAGATTAATAC+AGG - chr7.4:82492852-82492871 MS.gene44768:CDS 30.0%
CTTTCAATTGAACATTCTCT+TGG + chr7.4:82493277-82493296 None:intergenic 30.0%
GTTATAGTTACAAGATGGAT+AGG + chr7.4:82492913-82492932 None:intergenic 30.0%
TTTGGTTGAAACCATAGAAT+TGG + chr7.4:82492983-82493002 None:intergenic 30.0%
AAACTCTCCAACCAATTCTA+TGG - chr7.4:82492969-82492988 MS.gene44768:CDS 35.0%
ACATTTGATGAAGTGATGCT+AGG + chr7.4:82493383-82493402 None:intergenic 35.0%
AGGGAGATGGATCTAAATTT+GGG + chr7.4:82492893-82492912 None:intergenic 35.0%
CGAAAGAAAACATCGAAGAA+TGG - chr7.4:82493103-82493122 MS.gene44768:CDS 35.0%
GTTGAAACCATAGAATTGGT+TGG + chr7.4:82492979-82492998 None:intergenic 35.0%
TAGGGAGATGGATCTAAATT+TGG + chr7.4:82492894-82492913 None:intergenic 35.0%
! GGAGAATTTGAATAGGGTTT+TGG + chr7.4:82493001-82493020 None:intergenic 35.0%
! TAGAATTGGTTGGAGAGTTT+TGG + chr7.4:82492969-82492988 None:intergenic 35.0%
! TTCTTTCGTTGATTAGACCT+AGG + chr7.4:82493091-82493110 None:intergenic 35.0%
AAAAGCAGCTTGATGAGCTT+TGG - chr7.4:82493168-82493187 MS.gene44768:CDS 40.0%
ACATCTTCAAGAGGACTCAA+AGG + chr7.4:82493359-82493378 None:intergenic 40.0%
AGCTTCAGAACTTCGACAAA+TGG - chr7.4:82493301-82493320 MS.gene44768:CDS 40.0%
ATGCTAGGAACATCTTCAAG+AGG + chr7.4:82493368-82493387 None:intergenic 40.0%
TTACAAGATGGATAGGGAGA+TGG + chr7.4:82492906-82492925 None:intergenic 40.0%
!! GTTTTGGATGTTGAGGTGTT+TGG + chr7.4:82492953-82492972 None:intergenic 40.0%
!!! TTGGAGAGTTTTGGATGTTG+AGG + chr7.4:82492960-82492979 None:intergenic 40.0%
TTTGTTTCCTCATTCGCGAC+CGG + chr7.4:82493151-82493170 None:intergenic 45.0%
! AGCTTTGGTCACAGGTTGTT+TGG - chr7.4:82493183-82493202 MS.gene44768:CDS 45.0%
! GAGGTGTTTGGATGGTGTTT+GGG + chr7.4:82492941-82492960 None:intergenic 45.0%
! TGAGGTGTTTGGATGGTGTT+TGG + chr7.4:82492942-82492961 None:intergenic 45.0%
! TGAGTTGCTGCTTATGCATG+AGG + chr7.4:82493042-82493061 None:intergenic 45.0%
! TGGATGTTGAGGTGTTTGGA+TGG + chr7.4:82492949-82492968 None:intergenic 45.0%
! TTGCTGCTTATGCATGAGGA+TGG + chr7.4:82493038-82493057 None:intergenic 45.0%
AGGATGGAGGACTGAAGTCT+TGG + chr7.4:82493022-82493041 None:intergenic 50.0%
CTGCTTATGCATGAGGATGG+AGG + chr7.4:82493035-82493054 None:intergenic 50.0%
GAAGCGGACGAACAAAACCT+AGG - chr7.4:82493071-82493090 MS.gene44768:CDS 50.0%
GGTCACAGGTTGTTTGGCTA+AGG - chr7.4:82493189-82493208 MS.gene44768:CDS 50.0%
! GCTTGATGAGCTTTGGTCAC+AGG - chr7.4:82493175-82493194 MS.gene44768:CDS 50.0%
!! GTTTTGTTCGTCCGCTTCGT+CGG + chr7.4:82493069-82493088 None:intergenic 50.0%
CAACTCAACGTCCGACGAAG+CGG - chr7.4:82493055-82493074 MS.gene44768:CDS 55.0%
CGAACCGAGAGTCAGCACGC+CGG - chr7.4:82493129-82493148 MS.gene44768:CDS 65.0%
CAGCACGCCGGTCGCGAATG+AGG - chr7.4:82493141-82493160 MS.gene44768:CDS 70.0%
!! GCGACCGGCGTGCTGACTCT+CGG + chr7.4:82493136-82493155 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 82492849 82493424 82492849 ID=MS.gene44768
chr7.4 mRNA 82492849 82493424 82492849 ID=MS.gene44768.t1;Parent=MS.gene44768
chr7.4 exon 82492849 82493424 82492849 ID=MS.gene44768.t1.exon1;Parent=MS.gene44768.t1
chr7.4 CDS 82492849 82493424 82492849 ID=cds.MS.gene44768.t1;Parent=MS.gene44768.t1
Gene Sequence

>MS.gene44768

ATGCAAACTAGAGAGATTAATACAGGACTCAATTATTTACTCCCAAATTTAGATCCATCTCCCTATCCATCTTGTAACTATAACATGATCCCAAACACCATCCAAACACCTCAACATCCAAAACTCTCCAACCAATTCTATGGTTTCAACCAAAACCCTATTCAAATTCTCCAAGACTTCAGTCCTCCATCCTCATGCATAAGCAGCAACTCAACGTCCGACGAAGCGGACGAACAAAACCTAGGTCTAATCAACGAAAGAAAACATCGAAGAATGGTATCGAACCGAGAGTCAGCACGCCGGTCGCGAATGAGGAAACAAAAGCAGCTTGATGAGCTTTGGTCACAGGTTGTTTGGCTAAGGAATGAGAATCATCAATTACTAGATAAGCTCAACAATTTCTGTGAGACTCATGATAAAGTTGTCCAAGAGAATGTTCAATTGAAAGAACAAGCTTCAGAACTTCGACAAATGGTGTGTGATATGCAGTTACATAGTACTTGTCTTCCTTTGAGTCCTCTTGAAGATGTTCCTAGCATCACTTCATCAAATGTTAAATCTGATTCTTCAAACTAA
Protein sequence

>MS.gene44768.t1

MQTREINTGLNYLLPNLDPSPYPSCNYNMIPNTIQTPQHPKLSNQFYGFNQNPIQILQDFSPPSSCISSNSTSDEADEQNLGLINERKHRRMVSNRESARRSRMRKQKQLDELWSQVVWLRNENHQLLDKLNNFCETHDKVVQENVQLKEQASELRQMVCDMQLHSTCLPLSPLEDVPSITSSNVKSDSSN