AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029144

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029144.t1 MTR_1g115290 85.526 152 20 1 37 186 1 152 1.29e-92 268
MS.gene029144.t1 MTR_4g045977 62.736 212 71 3 1 204 1 212 2.00e-90 271
MS.gene029144.t1 MTR_4g107170 54.955 222 82 4 1 204 1 222 1.66e-77 233
MS.gene029144.t1 MTR_2g049610 47.959 196 93 3 1 194 1 189 1.72e-59 187
MS.gene029144.t1 MTR_2g049530 45.026 191 96 3 3 192 5 187 9.06e-54 171
MS.gene029144.t1 MTR_2g049630 51.974 152 71 2 2 152 4 154 5.55e-48 161
MS.gene029144.t1 MTR_6g018920 37.975 158 95 1 1 155 1 158 2.64e-37 132
MS.gene029144.t1 MTR_1g114730 38.608 158 94 1 1 155 1 158 1.15e-35 128
MS.gene029144.t1 MTR_6g005440 36.842 171 105 1 1 168 1 171 6.87e-35 125
MS.gene029144.t1 MTR_6g005450 33.520 179 116 1 1 176 1 179 1.90e-33 122
MS.gene029144.t1 MTR_3g466980 28.000 175 111 5 1 165 1 170 1.87e-13 67.0
MS.gene029144.t1 MTR_3g467080 29.448 163 103 4 1 154 1 160 1.01e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029144.t1 AT5G55690 34.416 154 84 4 1 147 1 144 3.47e-16 75.5
MS.gene029144.t1 AT5G55690 34.416 154 84 4 1 147 1 144 3.47e-16 75.5
MS.gene029144.t1 AT1G22590 30.625 160 99 6 1 153 1 155 1.58e-11 60.8
MS.gene029144.t1 AT3G05860 41.429 70 39 1 1 70 1 68 4.21e-11 60.5
MS.gene029144.t1 AT2G28700 37.333 75 44 2 1 75 1 72 5.08e-11 61.2
MS.gene029144.t1 AT3G05860 41.429 70 39 1 1 70 1 68 6.59e-11 60.5
MS.gene029144.t1 AT3G05860 41.429 70 39 1 1 70 1 68 6.96e-11 60.5

Find 40 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCCATGTTAACCAAATT+TGG 0.129467 1.2:-85114519 None:intergenic
TCCAACCTGGCATCCAAATT+TGG 0.186789 1.2:+85114506 MS.gene029144:CDS
CGGTCTTCGGGCCATGTTAT+TGG 0.257464 1.2:-85114330 None:intergenic
TTTACCATTGTACGGTCTTC+GGG 0.322440 1.2:-85114342 None:intergenic
GTTTACCATTGTACGGTCTT+CGG 0.346180 1.2:-85114343 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1.2:-85114409 None:intergenic
ACCGGACTTGACAGTGTATT+GGG 0.378449 1.2:-85114259 None:intergenic
CACCGGACTTGACAGTGTAT+TGG 0.384830 1.2:-85114260 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 1.2:-85114577 None:intergenic
TGTATGACACTGAGTGGGCT+TGG 0.425893 1.2:-85114651 None:intergenic
ATGAGGCAAACCAGCATGAT+TGG 0.434094 1.2:-85114730 None:intergenic
ATCATATGTTTAAATCAAGT+TGG 0.436280 1.2:-85114767 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.441139 1.2:-85114680 None:intergenic
GATGATATCTTTATGCACTT+TGG 0.458740 1.2:-85114472 None:intergenic
GTTAACCAAATTTGGATGCC+AGG 0.463541 1.2:-85114511 None:intergenic
ACCAAATTTGGATGCCAGGT+TGG 0.474376 1.2:-85114507 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.494636 1.2:-85114681 None:intergenic
TCCCAATACACTGTCAAGTC+CGG 0.494797 1.2:+85114258 MS.gene029144:CDS
ACTTTCAAGCAAAGAAAAGC+TGG 0.495334 1.2:+85114219 MS.gene029144:CDS
TGGTTTGTTGATGAATTATG+AGG 0.510382 1.2:-85114747 None:intergenic
GCATCCAAATTTGGTTAACA+TGG 0.520385 1.2:+85114515 MS.gene029144:CDS
CTTTGAAATTAAGAAAGCTA+AGG 0.524267 1.2:+85114434 MS.gene029144:CDS
TTTGTTTGTAGAATGGGTCG+TGG 0.527118 1.2:+85114150 None:intergenic
TTGATTGTGTATGATGATGA+TGG 0.527956 1.2:+85114294 MS.gene029144:CDS
TCGTTGACATCAAATATCTT+GGG 0.530959 1.2:-85114408 None:intergenic
GCATGGAGTTTACCATTGTA+CGG 0.551323 1.2:-85114350 None:intergenic
ATGCTCATACTCTTGAAGCA+TGG 0.571710 1.2:-85114367 None:intergenic
CAATCATGTTAGTGAGATGG+TGG 0.574738 1.2:+85114701 MS.gene029144:CDS
CATCAATCATGTTAGTGAGA+TGG 0.579763 1.2:+85114698 MS.gene029144:CDS
CATGTTGAAAAGTGAGATGG+TGG 0.605793 1.2:+85114608 MS.gene029144:CDS
CAACATGTTGAAAAGTGAGA+TGG 0.617799 1.2:+85114605 MS.gene029144:CDS
TGATGATGATGGCAATAATG+TGG 0.626471 1.2:+85114305 MS.gene029144:CDS
CAGCACTTAAGTCTCTGAGC+TGG 0.631241 1.2:-85114545 None:intergenic
TCAATATCAAATATCCAACC+TGG 0.635175 1.2:+85114493 MS.gene029144:CDS
ATAATGTGGGACCAATAACA+TGG 0.642393 1.2:+85114319 MS.gene029144:CDS
GATGATGATGGCAATAATGT+GGG 0.653668 1.2:+85114306 MS.gene029144:CDS
GTGGATATGACCAATCATGC+TGG 0.656704 1.2:+85114720 MS.gene029144:CDS
TGCTATGTATGACACTGAGT+GGG 0.671421 1.2:-85114656 None:intergenic
ATGCTATGTATGACACTGAG+TGG 0.718974 1.2:-85114657 None:intergenic
ATGGCCCGAAGACCGTACAA+TGG 0.720674 1.2:+85114338 MS.gene029144:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAGCTA+AGG + chr1.2:85114434-85114453 MS.gene029144:CDS 25.0%
GATGATATCTTTATGCACTT+TGG - chr1.2:85114475-85114494 None:intergenic 30.0%
TCAATATCAAATATCCAACC+TGG + chr1.2:85114493-85114512 MS.gene029144:CDS 30.0%
TCGTTGACATCAAATATCTT+GGG - chr1.2:85114411-85114430 None:intergenic 30.0%
! TTGATTGTGTATGATGATGA+TGG + chr1.2:85114294-85114313 MS.gene029144:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG - chr1.2:85114750-85114769 None:intergenic 30.0%
ACTTTCAAGCAAAGAAAAGC+TGG + chr1.2:85114219-85114238 MS.gene029144:CDS 35.0%
ATAATGTGGGACCAATAACA+TGG + chr1.2:85114319-85114338 MS.gene029144:CDS 35.0%
CAACATGTTGAAAAGTGAGA+TGG + chr1.2:85114605-85114624 MS.gene029144:CDS 35.0%
CATCAATCATGTTAGTGAGA+TGG + chr1.2:85114698-85114717 MS.gene029144:CDS 35.0%
GCATCCAAATTTGGTTAACA+TGG + chr1.2:85114515-85114534 MS.gene029144:CDS 35.0%
GCTTCCATGTTAACCAAATT+TGG - chr1.2:85114522-85114541 None:intergenic 35.0%
GTCGTTGACATCAAATATCT+TGG - chr1.2:85114412-85114431 None:intergenic 35.0%
GTGATTACAAGCTTGAATCT+TGG - chr1.2:85114580-85114599 None:intergenic 35.0%
! AATCAAACAAGCTTTTGCAC+CGG - chr1.2:85114280-85114299 None:intergenic 35.0%
! TGATGTGTTGTTGCATTTGA+GGG - chr1.2:85114683-85114702 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG - chr1.2:85114684-85114703 None:intergenic 35.0%
!! GATGATGATGGCAATAATGT+GGG + chr1.2:85114306-85114325 MS.gene029144:CDS 35.0%
!! TGATGATGATGGCAATAATG+TGG + chr1.2:85114305-85114324 MS.gene029144:CDS 35.0%
ATGCTATGTATGACACTGAG+TGG - chr1.2:85114660-85114679 None:intergenic 40.0%
ATGCTCATACTCTTGAAGCA+TGG - chr1.2:85114370-85114389 None:intergenic 40.0%
CAATCATGTTAGTGAGATGG+TGG + chr1.2:85114701-85114720 MS.gene029144:CDS 40.0%
CATGTTGAAAAGTGAGATGG+TGG + chr1.2:85114608-85114627 MS.gene029144:CDS 40.0%
GCATGGAGTTTACCATTGTA+CGG - chr1.2:85114353-85114372 None:intergenic 40.0%
GTTAACCAAATTTGGATGCC+AGG - chr1.2:85114514-85114533 None:intergenic 40.0%
GTTTACCATTGTACGGTCTT+CGG - chr1.2:85114346-85114365 None:intergenic 40.0%
TGCTATGTATGACACTGAGT+GGG - chr1.2:85114659-85114678 None:intergenic 40.0%
TTTACCATTGTACGGTCTTC+GGG - chr1.2:85114345-85114364 None:intergenic 40.0%
ACCAAATTTGGATGCCAGGT+TGG - chr1.2:85114510-85114529 None:intergenic 45.0%
ACCGGACTTGACAGTGTATT+GGG - chr1.2:85114262-85114281 None:intergenic 45.0%
ATGAGGCAAACCAGCATGAT+TGG - chr1.2:85114733-85114752 None:intergenic 45.0%
GTGGATATGACCAATCATGC+TGG + chr1.2:85114720-85114739 MS.gene029144:CDS 45.0%
TCCAACCTGGCATCCAAATT+TGG + chr1.2:85114506-85114525 MS.gene029144:CDS 45.0%
TCCCAATACACTGTCAAGTC+CGG + chr1.2:85114258-85114277 MS.gene029144:CDS 45.0%
CACCGGACTTGACAGTGTAT+TGG - chr1.2:85114263-85114282 None:intergenic 50.0%
CAGCACTTAAGTCTCTGAGC+TGG - chr1.2:85114548-85114567 None:intergenic 50.0%
! TGTATGACACTGAGTGGGCT+TGG - chr1.2:85114654-85114673 None:intergenic 50.0%
ATGGCCCGAAGACCGTACAA+TGG + chr1.2:85114338-85114357 MS.gene029144:CDS 55.0%
CGGTCTTCGGGCCATGTTAT+TGG - chr1.2:85114333-85114352 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 85114162 85114788 85114162 ID=MS.gene029144
chr1.2 mRNA 85114162 85114788 85114162 ID=MS.gene029144.t1;Parent=MS.gene029144
chr1.2 exon 85114162 85114788 85114162 ID=MS.gene029144.t1.exon1;Parent=MS.gene029144.t1
chr1.2 CDS 85114162 85114788 85114162 ID=cds.MS.gene029144.t1;Parent=MS.gene029144.t1
Gene Sequence

>MS.gene029144

ATGGGTCGTGGAAAAATAAATATGAAATACATCAAAAATGCGAAAGTACGCAAACAAACTTTCAAGCAAAGAAAAGCTGGACTAATGAAAAAAATTTCCCAATACACTGTCAAGTCCGGTGCAAAAGCTTGTTTGATTGTGTATGATGATGATGGCAATAATGTGGGACCAATAACATGGCCCGAAGACCGTACAATGGTAAACTCCATGCTTCAAGAGTATGAGCATCAAAAGATTGAGAATACACCCAAGATATTTGATGTCAACGACTACTTTGAAATTAAGAAAGCTAAGGTTAAAGCTGAAATTACCAAAGTGCATAAAGATATCATCAATATCAAATATCCAACCTGGCATCCAAATTTGGTTAACATGGAAGCGAGCCAGCTCAGAGACTTAAGTGCTGTTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATCAACATGTTGAAAAGTGAGATGGTGGAAGAGAATGTTGTTTTGAATCCAAGCCCACTCAGTGTCATACATAGCATCCCTCAAATGCAACAACACATCAATCATGTTAGTGAGATGGTGGATATGACCAATCATGCTGGTTTGCCTCATAATTCATCAACAAACCAACTTGATTTAAACATATGA
Protein sequence

>MS.gene029144.t1

MGRGKINMKYIKNAKVRKQTFKQRKAGLMKKISQYTVKSGAKACLIVYDDDGNNVGPITWPEDRTMVNSMLQEYEHQKIENTPKIFDVNDYFEIKKAKVKAEITKVHKDIINIKYPTWHPNLVNMEASQLRDLSAVVDAKIQACNHKINMLKSEMVEENVVLNPSPLSVIHSIPQMQQHINHVSEMVDMTNHAGLPHNSSTNQLDLNI