AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98607

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98607.t1 MTR_4g052060 95.055 182 8 1 1 181 1 182 8.56e-125 349
MS.gene98607.t1 MTR_4g052040 71.271 181 41 4 1 174 1 177 3.35e-76 226
MS.gene98607.t1 MTR_5g079710 44.720 161 83 4 4 163 6 161 2.61e-33 119
MS.gene98607.t1 MTR_7g105790 36.207 174 88 2 1 154 1 171 4.71e-23 91.3
MS.gene98607.t1 MTR_0907s0020 59.701 67 27 0 95 161 104 170 9.15e-22 87.4
MS.gene98607.t1 MTR_8g103520 41.558 77 45 0 86 162 217 293 9.68e-13 65.1
MS.gene98607.t1 MTR_5g075210 49.180 61 31 0 96 156 283 343 7.87e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98607.t1 AT3G52525 59.091 66 26 1 89 153 61 126 2.62e-20 83.2
MS.gene98607.t1 AT2G36026 59.016 61 25 0 98 158 91 151 8.71e-19 79.7
MS.gene98607.t1 AT5G22240 37.864 103 60 2 58 159 63 162 1.32e-12 63.5
MS.gene98607.t1 AT5G19650 44.776 67 37 0 92 158 153 219 2.29e-12 63.5

Find 33 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTGGCTAATGGAAATTT+TGG 0.176660 4.2:-50122226 None:intergenic
TGGATGAAGCCTTGCTAATT+TGG 0.245892 4.2:-50122242 None:intergenic
GCTTCATCCAACACAACTTT+AGG 0.315005 4.2:+50122255 MS.gene98607:CDS
AGCCTTGCTAATTTGGCTAA+TGG 0.359333 4.2:-50122235 None:intergenic
TCATAAACATGTATATTAGA+AGG 0.359929 4.2:-50122630 None:intergenic
AGAGTGTTCTCAACAAATAT+TGG 0.365412 4.2:+50122147 MS.gene98607:CDS
AAACACTGTGGTTGTTGAAA+AGG 0.406424 4.2:+50122392 MS.gene98607:CDS
GAGTGCTTGAAATCATGATA+TGG 0.426047 4.2:-50122426 None:intergenic
ATGATCTTCGAGTTCTTCTT+CGG 0.426591 4.2:+50122490 MS.gene98607:CDS
ACAACCACAGTGTTTGATAG+AGG 0.460583 4.2:-50122384 None:intergenic
CACAACTTTAGGTGAAAGAA+AGG 0.468235 4.2:+50122266 MS.gene98607:CDS
TCTTTCACCTAAAGTTGTGT+TGG 0.468817 4.2:-50122262 None:intergenic
GCTGTGGTCGACGCTACAAC+CGG 0.476684 4.2:-50122292 None:intergenic
AGCTTCAGAGAAAGTGGTGG+TGG 0.499280 4.2:-50122325 None:intergenic
TATGCTTCAAATGATCTTCG+AGG 0.503327 4.2:+50122449 MS.gene98607:CDS
TCAACAAATATTGGAAGTTG+TGG 0.506051 4.2:+50122156 MS.gene98607:CDS
GTAGTAGTACAAACCTTGTC+GGG 0.514681 4.2:-50122591 None:intergenic
TGTTTCAGCTTCAGAGAAAG+TGG 0.518295 4.2:-50122331 None:intergenic
GTTTGATAGAGGGCTATGCT+TGG 0.522411 4.2:-50122373 None:intergenic
TTCCATTAGCCAAATTAGCA+AGG 0.533087 4.2:+50122233 MS.gene98607:CDS
TTTGATAGAGGGCTATGCTT+GGG 0.544333 4.2:-50122372 None:intergenic
AGTACACGAGCCTATTCAAA+AGG 0.546512 4.2:+50122203 MS.gene98607:CDS
CTTCGAGGATGAGATCGATT+CGG 0.564919 4.2:+50122464 MS.gene98607:CDS
GATAGAGGGCTATGCTTGGG+TGG 0.581428 4.2:-50122369 None:intergenic
AGTAGTAGTACAAACCTTGT+CGG 0.598934 4.2:-50122592 None:intergenic
CAACCACAGTGTTTGATAGA+GGG 0.606410 4.2:-50122383 None:intergenic
TTAGGTGAAAGAAAGGGTGC+CGG 0.615123 4.2:+50122273 MS.gene98607:CDS
ACAACTTTAGGTGAAAGAAA+GGG 0.626599 4.2:+50122267 MS.gene98607:CDS
TTCAGCTTCAGAGAAAGTGG+TGG 0.661349 4.2:-50122328 None:intergenic
CGAGGATGAGATCGATTCGG+AGG 0.665085 4.2:+50122467 MS.gene98607:CDS
TAAAGACTTTAACGATGACA+AGG 0.672661 4.2:-50122545 None:intergenic
TGGTGGAGAAATCGTCGCTG+TGG 0.708398 4.2:-50122308 None:intergenic
TAGCCCTCTATCAAACACTG+TGG 0.798981 4.2:+50122380 MS.gene98607:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATAAACATGTATATTAGA+AGG - chr4.2:50122633-50122652 None:intergenic 20.0%
!! AATTTGGCTAATGGAAATTT+TGG - chr4.2:50122229-50122248 None:intergenic 25.0%
ACAACTTTAGGTGAAAGAAA+GGG + chr4.2:50122267-50122286 MS.gene98607:CDS 30.0%
TAAAGACTTTAACGATGACA+AGG - chr4.2:50122548-50122567 None:intergenic 30.0%
TCAACAAATATTGGAAGTTG+TGG + chr4.2:50122156-50122175 MS.gene98607:CDS 30.0%
! AGAGTGTTCTCAACAAATAT+TGG + chr4.2:50122147-50122166 MS.gene98607:CDS 30.0%
!! GAAATTTTGGCCTTTTGAAT+AGG - chr4.2:50122216-50122235 None:intergenic 30.0%
AAACACTGTGGTTGTTGAAA+AGG + chr4.2:50122392-50122411 MS.gene98607:CDS 35.0%
AGTAGTAGTACAAACCTTGT+CGG - chr4.2:50122595-50122614 None:intergenic 35.0%
CACAACTTTAGGTGAAAGAA+AGG + chr4.2:50122266-50122285 MS.gene98607:CDS 35.0%
GAGTGCTTGAAATCATGATA+TGG - chr4.2:50122429-50122448 None:intergenic 35.0%
TATGCTTCAAATGATCTTCG+AGG + chr4.2:50122449-50122468 MS.gene98607:CDS 35.0%
TCTTTCACCTAAAGTTGTGT+TGG - chr4.2:50122265-50122284 None:intergenic 35.0%
TTCCATTAGCCAAATTAGCA+AGG + chr4.2:50122233-50122252 MS.gene98607:CDS 35.0%
! ATGATCTTCGAGTTCTTCTT+CGG + chr4.2:50122490-50122509 MS.gene98607:CDS 35.0%
! TCTCACAAGTCTTTTCTTGT+TGG - chr4.2:50122127-50122146 None:intergenic 35.0%
ACAACCACAGTGTTTGATAG+AGG - chr4.2:50122387-50122406 None:intergenic 40.0%
AGCCTTGCTAATTTGGCTAA+TGG - chr4.2:50122238-50122257 None:intergenic 40.0%
AGTACACGAGCCTATTCAAA+AGG + chr4.2:50122203-50122222 MS.gene98607:CDS 40.0%
CAACCACAGTGTTTGATAGA+GGG - chr4.2:50122386-50122405 None:intergenic 40.0%
GCTTCATCCAACACAACTTT+AGG + chr4.2:50122255-50122274 MS.gene98607:CDS 40.0%
GTAGTAGTACAAACCTTGTC+GGG - chr4.2:50122594-50122613 None:intergenic 40.0%
TGGATGAAGCCTTGCTAATT+TGG - chr4.2:50122245-50122264 None:intergenic 40.0%
TGTTTCAGCTTCAGAGAAAG+TGG - chr4.2:50122334-50122353 None:intergenic 40.0%
TTTGATAGAGGGCTATGCTT+GGG - chr4.2:50122375-50122394 None:intergenic 40.0%
CTTCGAGGATGAGATCGATT+CGG + chr4.2:50122464-50122483 MS.gene98607:CDS 45.0%
GTTTGATAGAGGGCTATGCT+TGG - chr4.2:50122376-50122395 None:intergenic 45.0%
TAGCCCTCTATCAAACACTG+TGG + chr4.2:50122380-50122399 MS.gene98607:CDS 45.0%
TTCAGCTTCAGAGAAAGTGG+TGG - chr4.2:50122331-50122350 None:intergenic 45.0%
! TCATGAAGCTTTTCCCGACA+AGG + chr4.2:50122578-50122597 MS.gene98607:CDS 45.0%
! TTAGGTGAAAGAAAGGGTGC+CGG + chr4.2:50122273-50122292 MS.gene98607:CDS 45.0%
AGCTTCAGAGAAAGTGGTGG+TGG - chr4.2:50122328-50122347 None:intergenic 50.0%
GATAGAGGGCTATGCTTGGG+TGG - chr4.2:50122372-50122391 None:intergenic 55.0%
TGGTGGAGAAATCGTCGCTG+TGG - chr4.2:50122311-50122330 None:intergenic 55.0%
!! CGAGGATGAGATCGATTCGG+AGG + chr4.2:50122467-50122486 MS.gene98607:CDS 55.0%
GCTGTGGTCGACGCTACAAC+CGG - chr4.2:50122295-50122314 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 50122117 50122662 50122117 ID=MS.gene98607
chr4.2 mRNA 50122117 50122662 50122117 ID=MS.gene98607.t1;Parent=MS.gene98607
chr4.2 exon 50122117 50122662 50122117 ID=MS.gene98607.t1.exon1;Parent=MS.gene98607.t1
chr4.2 CDS 50122117 50122662 50122117 ID=cds.MS.gene98607.t1;Parent=MS.gene98607.t1
Gene Sequence

>MS.gene98607

ATGTCTTCCAACAAGAAAAGACTTGTGAGAAGAGTGTTCTCAACAAATATTGGAAGTTGTGGCTGTGCAAAAAAGAAAGCAATTGTAGTACACGAGCCTATTCAAAAGGCCAAAATTTCCATTAGCCAAATTAGCAAGGCTTCATCCAACACAACTTTAGGTGAAAGAAAGGGTGCCGGTTGTAGCGTCGACCACAGCGACGATTTCTCCACCACCACTTTCTCTGAAGCTGAAACAACTCAAAACTATTCTCCACCCAAGCATAGCCCTCTATCAAACACTGTGGTTGTTGAAAAGGATTCTGACGATCCATATCATGATTTCAAGCACTCTATGCTTCAAATGATCTTCGAGGATGAGATCGATTCGGAGGATGATCTTCGAGTTCTTCTTCGGTGTTTTCTTCATCTCAATGATACTTATTATCACCTTGTCATCGTTAAAGTCTTTAATGATATATGTCATGAAGCTTTTCCCGACAAGGTTTGTACTACTACTTCGTCTGCTATCAAACCTTCTAATATACATGTTTATGAAAATGAATAA
Protein sequence

>MS.gene98607.t1

MSSNKKRLVRRVFSTNIGSCGCAKKKAIVVHEPIQKAKISISQISKASSNTTLGERKGAGCSVDHSDDFSTTTFSEAETTQNYSPPKHSPLSNTVVVEKDSDDPYHDFKHSMLQMIFEDEIDSEDDLRVLLRCFLHLNDTYYHLVIVKVFNDICHEAFPDKVCTTTSSAIKPSNIHVYENE