AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70439


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70439.t1 MTR_3g083030 66.250 240 70 3 1 239 1 230 2.09e-104 301
MS.gene70439.t1 MTR_3g083080 62.185 238 57 3 1 238 1 205 4.54e-100 290
MS.gene70439.t1 MTR_3g083050 53.333 240 78 3 1 239 1 207 6.98e-74 223
MS.gene70439.t1 MTR_3g082340 35.628 247 125 8 1 238 1 222 1.49e-35 126
MS.gene70439.t1 MTR_3g082420 38.261 230 119 9 17 238 7 221 1.53e-34 123
MS.gene70439.t1 MTR_3g086030 51.852 108 44 1 54 161 4 103 3.05e-28 105
MS.gene70439.t1 MTR_3g083150 36.327 245 117 8 1 239 1 212 1.66e-25 99.8
MS.gene70439.t1 MTR_3g080680 38.462 208 105 10 39 238 6 198 4.29e-21 87.8
MS.gene70439.t1 MTR_3g083100 42.857 126 58 3 128 239 49 174 1.33e-20 85.9
MS.gene70439.t1 MTR_8g461300 38.728 173 81 10 83 238 34 198 8.52e-19 81.6
MS.gene70439.t1 MTR_4g055800 30.345 145 79 5 86 222 143 273 1.40e-13 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 62 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAATTCCGGTTCGGATTTC+AGG 0.202617 3.1:+66318928 None:intergenic
TGCAGAGGGGAGTGAGTTTA+AGG 0.216980 3.1:+66318451 None:intergenic
TTCAGTTCCGGTGGCAATTC+CGG 0.272860 3.1:+66318879 None:intergenic
TCGCCAGAGCTAAGCATAAA+AGG 0.284068 3.1:-66318656 MS.gene70439:CDS
TCCGGTTCCGACTTCAGTTC+GGG 0.301504 3.1:+66318897 None:intergenic
TCGGGTTCAGGTTGCAATTC+CGG 0.306399 3.1:+66318915 None:intergenic
TCATATTTCTGTCTCTGTTT+CGG 0.331334 3.1:+66318819 None:intergenic
TCCGACTTCAGTTCGGGTTC+AGG 0.333407 3.1:+66318903 None:intergenic
TTCGGTTGCGACTTCAGTTC+CGG 0.367780 3.1:+66318837 None:intergenic
TCCGGTTCCAACTTCAGTTC+CGG 0.379777 3.1:+66318867 None:intergenic
TTCCGGTTCCGACTTCAGTT+CGG 0.385258 3.1:+66318896 None:intergenic
GCGATTTACGTATAAGAATA+AGG 0.390721 3.1:-66318709 MS.gene70439:CDS
GCAATACAATGCTAAGAATC+AGG 0.399334 3.1:-66318415 MS.gene70439:intron
AAGGCGAAGATCATCGGTTA+TGG 0.404672 3.1:+66318470 None:intergenic
GAAAATTATAACAGGTCTGT+TGG 0.444773 3.1:+66318203 None:intergenic
TCTTGTTCCATACGTGGGCC+TGG 0.449501 3.1:+66318181 None:intergenic
TTCAGGTTGCAATTCCGGTT+CGG 0.449691 3.1:+66318920 None:intergenic
GAATCACATACATGTTTGTT+CGG 0.450921 3.1:-66318996 MS.gene70439:CDS
CACGTATGGAACAAGAGGCC+TGG 0.458410 3.1:-66318174 MS.gene70439:CDS
ACCCGAACTGAAGTCGGAAC+CGG 0.459886 3.1:-66318898 MS.gene70439:CDS
CGCACACACTTAAACACAAA+AGG 0.462554 3.1:+66318729 None:intergenic
TCCCCTCTGCAAGCTTGCGT+TGG 0.466151 3.1:-66318439 MS.gene70439:CDS
AACAGAGACAGAAATATGAA+TGG 0.466188 3.1:-66318815 MS.gene70439:CDS
TTCAGTTCCGGTGCTAACTC+CGG 0.468654 3.1:+66318849 None:intergenic
TGGGCCTGGAAAATTATAAC+AGG 0.482469 3.1:+66318195 None:intergenic
ACGTATGGAACAAGAGGCCT+GGG 0.488378 3.1:-66318173 MS.gene70439:CDS
ACCGGAACTGAAGTTGGAAC+CGG 0.489325 3.1:-66318868 MS.gene70439:CDS
GACACCACCTCAGGTGGCCC+AGG 0.497237 3.1:+66318156 None:intergenic
ATATATACCACCAGGTCTCC+AGG 0.503658 3.1:+66318269 None:intergenic
TGGAGGAGTAATAGCATCAA+AGG 0.514021 3.1:+66318530 None:intergenic
TCATCGCAGCAATCCGTGGC+AGG 0.518220 3.1:+66318963 None:intergenic
AGAAAAGCAGAAATATGTTA+CGG 0.518698 3.1:-66318507 MS.gene70439:CDS
ATTGCCACCGGAACTGAAGT+TGG 0.518984 3.1:-66318874 MS.gene70439:CDS
CAGGCCTCTTGTTCCATACG+TGG 0.522394 3.1:+66318175 None:intergenic
GAGTTTAAGGCGAAGATCAT+CGG 0.527340 3.1:+66318464 None:intergenic
ACAGAGACAGAAATATGAAT+GGG 0.527605 3.1:-66318814 MS.gene70439:CDS
GAGGCCTGGGCCACCTGAGG+TGG 0.535128 3.1:-66318160 MS.gene70439:CDS
CTCCAACGCAAGCTTGCAGA+GGG 0.537666 3.1:+66318437 None:intergenic
ATGGCACACGACACCACCTC+AGG 0.542265 3.1:+66318147 None:intergenic
CTGACATTGTGAAGACAACC+TGG 0.546641 3.1:-66318287 MS.gene70439:CDS
GAAGTGCCTGAAATCCGAAC+CGG 0.551355 3.1:-66318934 MS.gene70439:CDS
CGGCGTCATCCGACCTGCCA+CGG 0.552704 3.1:-66318976 MS.gene70439:CDS
AGATCATCGGTTATGGAAAG+TGG 0.556078 3.1:+66318477 None:intergenic
AGGCCTCTTGTTCCATACGT+GGG 0.562166 3.1:+66318176 None:intergenic
ACGGATTGCTGCGATGAAAG+AGG 0.563989 3.1:-66318957 MS.gene70439:CDS
CGGATTGCTGCGATGAAAGA+GGG 0.569780 3.1:-66318956 MS.gene70439:CDS
ATTATAACAGGTCTGTTGGA+AGG 0.577695 3.1:+66318207 None:intergenic
ACCTGAACCCGAACTGAAGT+CGG 0.580010 3.1:-66318904 MS.gene70439:CDS
CAAGAGGCCTGGGCCACCTG+AGG 0.581372 3.1:-66318163 MS.gene70439:CDS
CGCAGCAATCCGTGGCAGGT+CGG 0.581919 3.1:+66318967 None:intergenic
GGAGGAGTAATAGCATCAAA+GGG 0.583487 3.1:+66318531 None:intergenic
GTCGGAACCGGAATTGCCAC+CGG 0.601982 3.1:-66318886 MS.gene70439:CDS
GTGAAGACAACCTGGAGACC+TGG 0.604519 3.1:-66318279 MS.gene70439:CDS
TCTTTCATCGCAGCAATCCG+TGG 0.614163 3.1:+66318959 None:intergenic
GTTGGAACCGGAGTTAGCAC+CGG 0.614360 3.1:-66318856 MS.gene70439:CDS
GGTTCCAACTTCAGTTCCGG+TGG 0.621297 3.1:+66318870 None:intergenic
AGGCCCACGTATGGAACAAG+AGG 0.623282 3.1:-66318179 MS.gene70439:CDS
GCACACGACACCACCTCAGG+TGG 0.634060 3.1:+66318150 None:intergenic
GCTCCAACGCAAGCTTGCAG+AGG 0.640098 3.1:+66318436 None:intergenic
GTGATGTAATATATACCACC+AGG 0.685832 3.1:+66318261 None:intergenic
TCCAACGCAAGCTTGCAGAG+GGG 0.750745 3.1:+66318438 None:intergenic
AAGACAACCTGGAGACCTGG+TGG 0.761347 3.1:-66318276 MS.gene70439:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTATGCTTCTTAATTATTA+GGG - chr3.1:66318815-66318834 MS.gene70439:CDS 20.0%
!! TAGTATGCTTCTTAATTATT+AGG - chr3.1:66318814-66318833 MS.gene70439:CDS 20.0%
! AGAAAAGCAGAAATATGTTA+CGG - chr3.1:66318635-66318654 MS.gene70439:intron 25.0%
!!! TAACATATTTCTGCTTTTCT+TGG + chr3.1:66318635-66318654 None:intergenic 25.0%
AACAGAGACAGAAATATGAA+TGG - chr3.1:66318327-66318346 MS.gene70439:intron 30.0%
ACAGAGACAGAAATATGAAT+GGG - chr3.1:66318328-66318347 MS.gene70439:intron 30.0%
GAAAATTATAACAGGTCTGT+TGG + chr3.1:66318942-66318961 None:intergenic 30.0%
GAATCACATACATGTTTGTT+CGG - chr3.1:66318146-66318165 MS.gene70439:CDS 30.0%
GCGATTTACGTATAAGAATA+AGG - chr3.1:66318433-66318452 MS.gene70439:CDS 30.0%
GGCTCAGATTAAAAAAGATA+AGG - chr3.1:66318454-66318473 MS.gene70439:CDS 30.0%
! TCATATTTCTGTCTCTGTTT+CGG + chr3.1:66318326-66318345 None:intergenic 30.0%
!!! TTCTTGTTTTTGTGCTTGAA+AGG + chr3.1:66318906-66318925 None:intergenic 30.0%
ATTATAACAGGTCTGTTGGA+AGG + chr3.1:66318938-66318957 None:intergenic 35.0%
GCAATACAATGCTAAGAATC+AGG - chr3.1:66318727-66318746 MS.gene70439:CDS 35.0%
GTGATGTAATATATACCACC+AGG + chr3.1:66318884-66318903 None:intergenic 35.0%
TCAAGCACAAAAACAAGAAC+AGG - chr3.1:66318907-66318926 MS.gene70439:CDS 35.0%
! CAGACCTGTTATAATTTTCC+AGG - chr3.1:66318943-66318962 MS.gene70439:CDS 35.0%
!! CATATTTCTGCTTTTCTTGG+AGG + chr3.1:66318632-66318651 None:intergenic 35.0%
CGCACACACTTAAACACAAA+AGG + chr3.1:66318416-66318435 None:intergenic 40.0%
GAGATAGATGCGTTACAGAT+AGG + chr3.1:66318523-66318542 None:intergenic 40.0%
GGAGGAGTAATAGCATCAAA+GGG + chr3.1:66318614-66318633 None:intergenic 40.0%
TGGAGGAGTAATAGCATCAA+AGG + chr3.1:66318615-66318634 None:intergenic 40.0%
TGGGCCTGGAAAATTATAAC+AGG + chr3.1:66318950-66318969 None:intergenic 40.0%
! AGATCATCGGTTATGGAAAG+TGG + chr3.1:66318668-66318687 None:intergenic 40.0%
! GAGTTTAAGGCGAAGATCAT+CGG + chr3.1:66318681-66318700 None:intergenic 40.0%
ATATATACCACCAGGTCTCC+AGG + chr3.1:66318876-66318895 None:intergenic 45.0%
CTGACATTGTGAAGACAACC+TGG - chr3.1:66318855-66318874 MS.gene70439:CDS 45.0%
TCGCCAGAGCTAAGCATAAA+AGG - chr3.1:66318486-66318505 MS.gene70439:CDS 45.0%
! AAGGCGAAGATCATCGGTTA+TGG + chr3.1:66318675-66318694 None:intergenic 45.0%
! ACGCCTTTTATGCTTAGCTC+TGG + chr3.1:66318492-66318511 None:intergenic 45.0%
! TAATTTTCCAGGCCCACGTA+TGG - chr3.1:66318954-66318973 MS.gene70439:CDS 45.0%
!! TTCAGGTTGCAATTCCGGTT+CGG + chr3.1:66318225-66318244 None:intergenic 45.0%
!!! TTAATTTAATTTCTTAATTT+TGG - chr3.1:66318573-66318592 MS.gene70439:intron 5.0%
ACCGGAACTGAAGTTGGAAC+CGG - chr3.1:66318274-66318293 MS.gene70439:CDS 50.0%
ACCTGAACCCGAACTGAAGT+CGG - chr3.1:66318238-66318257 MS.gene70439:CDS 50.0%
ACGTATGGAACAAGAGGCCT+GGG - chr3.1:66318969-66318988 MS.gene70439:CDS 50.0%
AGGCCTCTTGTTCCATACGT+GGG + chr3.1:66318969-66318988 None:intergenic 50.0%
ATTGCCACCGGAACTGAAGT+TGG - chr3.1:66318268-66318287 MS.gene70439:CDS 50.0%
CGGATTGCTGCGATGAAAGA+GGG - chr3.1:66318186-66318205 MS.gene70439:CDS 50.0%
TCCGGTTCCAACTTCAGTTC+CGG + chr3.1:66318278-66318297 None:intergenic 50.0%
TCTTTCATCGCAGCAATCCG+TGG + chr3.1:66318186-66318205 None:intergenic 50.0%
TGCAGAGGGGAGTGAGTTTA+AGG + chr3.1:66318694-66318713 None:intergenic 50.0%
TTCAGTTCCGGTGGCAATTC+CGG + chr3.1:66318266-66318285 None:intergenic 50.0%
TTCCGGTTCCGACTTCAGTT+CGG + chr3.1:66318249-66318268 None:intergenic 50.0%
TTCGGTTGCGACTTCAGTTC+CGG + chr3.1:66318308-66318327 None:intergenic 50.0%
! ACGGATTGCTGCGATGAAAG+AGG - chr3.1:66318185-66318204 MS.gene70439:CDS 50.0%
! GAAGTGCCTGAAATCCGAAC+CGG - chr3.1:66318208-66318227 MS.gene70439:CDS 50.0%
! TTCAGTTCCGGTGCTAACTC+CGG + chr3.1:66318296-66318315 None:intergenic 50.0%
!! GCAATTCCGGTTCGGATTTC+AGG + chr3.1:66318217-66318236 None:intergenic 50.0%
!! TCGGGTTCAGGTTGCAATTC+CGG + chr3.1:66318230-66318249 None:intergenic 50.0%
AAGACAACCTGGAGACCTGG+TGG - chr3.1:66318866-66318885 MS.gene70439:CDS 55.0%
ACCCGAACTGAAGTCGGAAC+CGG - chr3.1:66318244-66318263 MS.gene70439:CDS 55.0%
AGGCCCACGTATGGAACAAG+AGG - chr3.1:66318963-66318982 MS.gene70439:CDS 55.0%
CACGTATGGAACAAGAGGCC+TGG - chr3.1:66318968-66318987 MS.gene70439:CDS 55.0%
CAGGCCTCTTGTTCCATACG+TGG + chr3.1:66318970-66318989 None:intergenic 55.0%
CTCCAACGCAAGCTTGCAGA+GGG + chr3.1:66318708-66318727 None:intergenic 55.0%
GGTTCCAACTTCAGTTCCGG+TGG + chr3.1:66318275-66318294 None:intergenic 55.0%
GTGAAGACAACCTGGAGACC+TGG - chr3.1:66318863-66318882 MS.gene70439:CDS 55.0%
GTTGGAACCGGAGTTAGCAC+CGG - chr3.1:66318286-66318305 MS.gene70439:CDS 55.0%
TCCAACGCAAGCTTGCAGAG+GGG + chr3.1:66318707-66318726 None:intergenic 55.0%
TCCGGTTCCGACTTCAGTTC+GGG + chr3.1:66318248-66318267 None:intergenic 55.0%
TCTTGTTCCATACGTGGGCC+TGG + chr3.1:66318964-66318983 None:intergenic 55.0%
! TCCGACTTCAGTTCGGGTTC+AGG + chr3.1:66318242-66318261 None:intergenic 55.0%
ATGGCACACGACACCACCTC+AGG + chr3.1:66318998-66319017 None:intergenic 60.0%
GCTCCAACGCAAGCTTGCAG+AGG + chr3.1:66318709-66318728 None:intergenic 60.0%
GTCGGAACCGGAATTGCCAC+CGG - chr3.1:66318256-66318275 MS.gene70439:CDS 60.0%
TCATCGCAGCAATCCGTGGC+AGG + chr3.1:66318182-66318201 None:intergenic 60.0%
TCCCCTCTGCAAGCTTGCGT+TGG - chr3.1:66318703-66318722 MS.gene70439:CDS 60.0%
CGCAGCAATCCGTGGCAGGT+CGG + chr3.1:66318178-66318197 None:intergenic 65.0%
GCACACGACACCACCTCAGG+TGG + chr3.1:66318995-66319014 None:intergenic 65.0%
CAAGAGGCCTGGGCCACCTG+AGG - chr3.1:66318979-66318998 MS.gene70439:CDS 70.0%
CGGCGTCATCCGACCTGCCA+CGG - chr3.1:66318166-66318185 MS.gene70439:CDS 70.0%
GACACCACCTCAGGTGGCCC+AGG + chr3.1:66318989-66319008 None:intergenic 70.0%
GAGGCCTGGGCCACCTGAGG+TGG - chr3.1:66318982-66319001 MS.gene70439:CDS 75.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 66318137 66319027 66318137 ID=MS.gene70439
chr3.1 mRNA 66318137 66319027 66318137 ID=MS.gene70439.t1;Parent=MS.gene70439
chr3.1 exon 66318638 66319027 66318638 ID=MS.gene70439.t1.exon1;Parent=MS.gene70439.t1
chr3.1 CDS 66318638 66319027 66318638 ID=cds.MS.gene70439.t1;Parent=MS.gene70439.t1
chr3.1 exon 66318416 66318553 66318416 ID=MS.gene70439.t1.exon2;Parent=MS.gene70439.t1
chr3.1 CDS 66318416 66318553 66318416 ID=cds.MS.gene70439.t1;Parent=MS.gene70439.t1
chr3.1 exon 66318137 66318328 66318137 ID=MS.gene70439.t1.exon3;Parent=MS.gene70439.t1
chr3.1 CDS 66318137 66318328 66318137 ID=cds.MS.gene70439.t1;Parent=MS.gene70439.t1
Gene Sequence

>MS.gene70439

ATGTCGATGGAATCACATACATGTTTGTTCGGCGTCATCCGACCTGCCACGGATTGCTGCGATGAAAGAGGGAAGTGCCTGAAATCCGAACCGGAATTGCAACCTGAACCCGAACTGAAGTCGGAACCGGAATTGCCACCGGAACTGAAGTTGGAACCGGAGTTAGCACCGGAACTGAAGTCGCAACCGAAACAGAGACAGAAATATGAATGGGAGTTGAAACGCTTTGAAGATCTTGTGATTAGTGACTTCTCTGTGTATGACGATGACATTAAGCCTTTTGTGTTTAAGTGTGTGCGATTTACGTATAAGAATAAGGCTCAGATTAAAAAAGATAAGGAGATTAGAGTCGCCAGAGCTAAGCATAAAAGGCGTTCTCGCAACCTATCTGTAACGCATCTATCTCATTTTGTTTTCAATTTCACTTAATAGTAATTTAATTTAATTTCTTAATTTTGGATCTGAACAACACAGCCCTTTGATGCTATTACTCCTCCAAGAAAAGCAGAAATATGTTACGGTGTAATACCACTTTCCATAACCGATGATCTTCGCCTTAAACTCACTCCCCTCTGCAAGCTTGCGTTGGAGCAATACAATGCTAAGAATCAGGTTCAATATTTGAGTGAAGTTCTGAATATAGCTTGTTTATTTATTAATTCATTGATCAAATAATTTAGTATGCTTCTTAATTATTAGGGTGCAAATTTTGTGTTAGCTGACATTGTGAAGACAACCTGGAGACCTGGTGGTATATATTACATCACCTTTCAAGCACAAAAACAAGAACAGGAAGATCCTTCCAACAGACCTGTTATAATTTTCCAGGCCCACGTATGGAACAAGAGGCCTGGGCCACCTGAGGTGGTGTCGTGTGCCATCAAAACCTAA

Protein sequence

>MS.gene70439.t1

MSMESHTCLFGVIRPATDCCDERGKCLKSEPELQPEPELKSEPELPPELKLEPELAPELKSQPKQRQKYEWELKRFEDLVISDFSVYDDDIKPFVFKCVRFTYKNKAQIKKDKEIRVARAKHKRRSRNLSPFDAITPPRKAEICYGVIPLSITDDLRLKLTPLCKLALEQYNAKNQGANFVLADIVKTTWRPGGIYYITFQAQKQEQEDPSNRPVIIFQAHVWNKRPGPPEVVSCAIKT