AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09704

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09704.t1 MTR_5g013530 88.202 178 15 2 1 177 1 173 8.40e-115 323
MS.gene09704.t1 MTR_5g013520 93.151 146 10 0 30 175 1 146 7.40e-100 284
MS.gene09704.t1 MTR_5g013530 87.333 150 13 2 29 177 7 151 1.43e-92 266
MS.gene09704.t1 MTR_5g013515 73.188 138 29 3 31 161 1 137 4.28e-68 204
MS.gene09704.t1 MTR_2g042900 44.785 163 43 6 25 156 99 245 6.78e-34 120
MS.gene09704.t1 MTR_2g042900 34.731 167 39 5 25 130 99 256 1.67e-19 83.2
MS.gene09704.t1 MTR_4g124960 35.849 159 72 6 5 162 73 202 2.69e-19 81.3
MS.gene09704.t1 MTR_8g021380 33.065 124 74 2 24 138 85 208 2.05e-15 71.6
MS.gene09704.t1 MTR_4g124960 35.115 131 56 5 5 135 73 174 2.67e-15 70.1
MS.gene09704.t1 MTR_2g044910 27.679 112 66 1 44 140 15 126 2.68e-12 62.0
MS.gene09704.t1 MTR_4g124950 32.374 139 66 5 5 141 7 119 2.81e-12 61.2
MS.gene09704.t1 MTR_2g044910 27.679 112 66 1 44 140 58 169 5.37e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09704.t1 AT1G19180 40.152 132 70 3 37 159 53 184 3.01e-24 94.0
MS.gene09704.t1 AT1G19180 39.552 134 72 3 37 161 119 252 7.24e-24 94.7
MS.gene09704.t1 AT1G19180 39.552 134 72 3 37 161 119 252 7.24e-24 94.7
MS.gene09704.t1 AT1G74950 39.855 138 64 4 37 157 112 247 7.56e-23 91.7
MS.gene09704.t1 AT1G74950 40.909 110 49 2 37 130 112 221 8.10e-18 77.8
MS.gene09704.t1 AT1G17380 36.885 122 63 2 33 140 58 179 3.69e-16 73.9
MS.gene09704.t1 AT5G20900 33.571 140 71 4 24 141 28 167 6.60e-16 72.0
MS.gene09704.t1 AT1G17380 36.885 122 63 2 33 140 87 208 7.14e-16 73.6
MS.gene09704.t1 AT1G72450 37.063 143 68 4 39 165 101 237 8.54e-15 70.5
MS.gene09704.t1 AT1G70700 30.496 141 82 3 13 138 82 221 2.37e-11 60.8
MS.gene09704.t1 AT1G17380 33.333 114 62 2 33 132 87 200 5.68e-11 59.3

Find 41 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTACAAGAGATTCCTATTT+TGG 0.046444 5.2:+5538041 MS.gene09704:CDS
CCATCTATACCTGTTATTTA+TGG 0.164541 5.2:+5538440 MS.gene09704:CDS
CTTGGATTGCTTGTTTGATA+TGG 0.217861 5.2:-5539071 None:intergenic
ATTGGTTTATTAATGCTTCT+TGG 0.268448 5.2:-5539089 None:intergenic
AGCTTCACTTCATCGGTTCT+TGG 0.292747 5.2:+5538588 MS.gene09704:CDS
CATGTCATGGATTCATCAAT+TGG 0.320863 5.2:-5539107 None:intergenic
CCAAAATAGGAATCTCTTGT+AGG 0.331403 5.2:-5538041 None:intergenic
ATCCATGACATGGCTCTCTT+TGG 0.358156 5.2:+5539118 MS.gene09704:CDS
TACCTGGAGTTTCCCAAAAT+AGG 0.395618 5.2:-5538054 None:intergenic
GGAAAAGTCCATGATGTCTT+TGG 0.411671 5.2:-5538321 None:intergenic
ATGTCTTTGGCTTTATCAGC+TGG 0.417227 5.2:-5538308 None:intergenic
AGTGAAGCTTTCCTAGTCAT+TGG 0.425048 5.2:-5538574 None:intergenic
TGAAGTACTAGTAATTCCTT+TGG 0.431697 5.2:-5538345 None:intergenic
GCTTCTGCAGAATTGTAGCC+AGG 0.440659 5.2:+5539045 MS.gene09704:intron
CAAATGACAATCTTCTATGA+TGG 0.453411 5.2:+5538260 MS.gene09704:CDS
TTCATCGGTTCTTGGAGAAA+AGG 0.463618 5.2:+5538596 MS.gene09704:CDS
GGAAGTTGTTGAAAATTCAT+TGG 0.467496 5.2:-5538009 None:intergenic
AGTAAGCATAGTTGTTATTG+TGG 0.472037 5.2:-5538373 None:intergenic
CCATAAATAACAGGTATAGA+TGG 0.477854 5.2:-5538440 None:intergenic
ATTGTCATTTGTGCACATCT+AGG 0.485611 5.2:-5538248 None:intergenic
AGTACTAGTAATTCCTTTGG+TGG 0.499055 5.2:-5538342 None:intergenic
GCTTGTTTGATATGGTGCCC+TGG 0.504181 5.2:-5539063 None:intergenic
CTACACTCAGATTTGTGTTG+TGG 0.517732 5.2:-5539152 None:intergenic
CTAGGAAAGCTTCACTTCAT+CGG 0.529148 5.2:+5538581 MS.gene09704:CDS
CAGGTATAGATGGTACTTGA+GGG 0.533329 5.2:-5538430 None:intergenic
AAATGACAATCTTCTATGAT+GGG 0.538308 5.2:+5538261 MS.gene09704:CDS
GATTTGTGTTGTGGTGATTG+TGG 0.542480 5.2:-5539143 None:intergenic
AATGAAGGCTAATATTAAGA+AGG 0.546955 5.2:+5538220 MS.gene09704:CDS
ATCTCTTGTAGGAAGAGATG+AGG 0.564072 5.2:-5538030 None:intergenic
TCTTGGAGAAAAGGAAGGAT+AGG 0.567398 5.2:+5538605 MS.gene09704:CDS
ACAGGTATAGATGGTACTTG+AGG 0.569787 5.2:-5538431 None:intergenic
TGCCAAAGAGAGCCATGTCA+TGG 0.583954 5.2:-5539120 None:intergenic
TGATAAAGCCAAAGACATCA+TGG 0.585378 5.2:+5538313 MS.gene09704:CDS
TCGGTTCTTGGAGAAAAGGA+AGG 0.585705 5.2:+5538600 MS.gene09704:CDS
ATTCAGATTTACCAATGACT+AGG 0.608086 5.2:+5538563 MS.gene09704:intron
TTAAAGTAACACATGGGTGG+AGG 0.612419 5.2:-5539180 None:intergenic
CTTCTGCAGAATTGTAGCCA+GGG 0.619958 5.2:+5539046 MS.gene09704:intron
CAATTGATGAATCCATGACA+TGG 0.622850 5.2:+5539108 MS.gene09704:CDS
AAAACAGTTAAAGTAACACA+TGG 0.639241 5.2:-5539187 None:intergenic
CAGTTAAAGTAACACATGGG+TGG 0.664883 5.2:-5539183 None:intergenic
AAACAGTTAAAGTAACACAT+GGG 0.695262 5.2:-5539186 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAATTAAATGTAAGTT+TGG + chr5.2:5538721-5538740 MS.gene09704:intron 10.0%
!!! TTTATGGTAATTTTTTTTTT+TGG + chr5.2:5538456-5538475 MS.gene09704:intron 10.0%
!! AAAAAATTACCATAAATAAC+AGG - chr5.2:5538452-5538471 None:intergenic 15.0%
!! ATTACTAATACTATGATGTT+TGG + chr5.2:5538990-5539009 MS.gene09704:intron 20.0%
!! TATCAAACATAAATCACTAA+AGG + chr5.2:5538899-5538918 MS.gene09704:intron 20.0%
!! TTACTAATACTATGATGTTT+GGG + chr5.2:5538991-5539010 MS.gene09704:intron 20.0%
!!! GTTAATAAACTTCACTTTTT+GGG + chr5.2:5538671-5538690 MS.gene09704:intron 20.0%
!!! TGTTAATAAACTTCACTTTT+TGG + chr5.2:5538670-5538689 MS.gene09704:intron 20.0%
!!! TTAATAAACTTCACTTTTTG+GGG + chr5.2:5538672-5538691 MS.gene09704:intron 20.0%
! AAACATGTCAAAATCAATCT+TGG - chr5.2:5538764-5538783 None:intergenic 25.0%
! AAATGACAATCTTCTATGAT+GGG + chr5.2:5538261-5538280 MS.gene09704:CDS 25.0%
! AACAAACATATCAGTCAATA+TGG - chr5.2:5539022-5539041 None:intergenic 25.0%
! AATGAAGGCTAATATTAAGA+AGG + chr5.2:5538220-5538239 MS.gene09704:CDS 25.0%
!! ATTGGTTTATTAATGCTTCT+TGG - chr5.2:5539092-5539111 None:intergenic 25.0%
!! TGGATATTTTATGTTTGAGA+GGG + chr5.2:5538476-5538495 MS.gene09704:intron 25.0%
!! TTGGATATTTTATGTTTGAG+AGG + chr5.2:5538475-5538494 MS.gene09704:intron 25.0%
!!! GTTTTATTACAGTGTAATGA+AGG + chr5.2:5538205-5538224 MS.gene09704:intron 25.0%
AAAAAGAACATGTATGTACC+TGG - chr5.2:5538073-5538092 None:intergenic 30.0%
AATCTTGGATTATCCAAAAG+TGG - chr5.2:5538749-5538768 None:intergenic 30.0%
ATTCAGATTTACCAATGACT+AGG + chr5.2:5538563-5538582 MS.gene09704:intron 30.0%
CAAAATCTATTCAACTGATG+CGG - chr5.2:5538791-5538810 None:intergenic 30.0%
CAAATGACAATCTTCTATGA+TGG + chr5.2:5538260-5538279 MS.gene09704:CDS 30.0%
CATACTAGTAGTATACAACA+TGG + chr5.2:5538152-5538171 MS.gene09704:intron 30.0%
CCATAAATAACAGGTATAGA+TGG - chr5.2:5538443-5538462 None:intergenic 30.0%
GGAAGTTGTTGAAAATTCAT+TGG - chr5.2:5538012-5538031 None:intergenic 30.0%
! AATAGATTTTGCCTACAGAA+TGG + chr5.2:5538800-5538819 MS.gene09704:intron 30.0%
! AGTAAGCATAGTTGTTATTG+TGG - chr5.2:5538376-5538395 None:intergenic 30.0%
! CCATCTATACCTGTTATTTA+TGG + chr5.2:5538440-5538459 MS.gene09704:CDS 30.0%
! CTACAAGAGATTCCTATTTT+GGG + chr5.2:5538042-5538061 MS.gene09704:CDS 30.0%
! TGAAGTACTAGTAATTCCTT+TGG - chr5.2:5538348-5538367 None:intergenic 30.0%
ACATTTGATTGAGAGAGATC+TGG - chr5.2:5538639-5538658 None:intergenic 35.0%
AGTACTAGTAATTCCTTTGG+TGG - chr5.2:5538345-5538364 None:intergenic 35.0%
CAATTGATGAATCCATGACA+TGG + chr5.2:5539108-5539127 MS.gene09704:CDS 35.0%
CATGTCATGGATTCATCAAT+TGG - chr5.2:5539110-5539129 None:intergenic 35.0%
CCAAAATAGGAATCTCTTGT+AGG - chr5.2:5538044-5538063 None:intergenic 35.0%
CTTGGATTGCTTGTTTGATA+TGG - chr5.2:5539074-5539093 None:intergenic 35.0%
TCAAGTAGAATCCATTCTGT+AGG - chr5.2:5538814-5538833 None:intergenic 35.0%
TGATAAAGCCAAAGACATCA+TGG + chr5.2:5538313-5538332 MS.gene09704:CDS 35.0%
! ATTGTCATTTGTGCACATCT+AGG - chr5.2:5538251-5538270 None:intergenic 35.0%
! CCTACAAGAGATTCCTATTT+TGG + chr5.2:5538041-5538060 MS.gene09704:CDS 35.0%
!! TGTAAGTTTGGTTCCACTTT+TGG + chr5.2:5538733-5538752 MS.gene09704:intron 35.0%
ACAGGTATAGATGGTACTTG+AGG - chr5.2:5538434-5538453 None:intergenic 40.0%
AGTGAAGCTTTCCTAGTCAT+TGG - chr5.2:5538577-5538596 None:intergenic 40.0%
ATCTCTTGTAGGAAGAGATG+AGG - chr5.2:5538033-5538052 None:intergenic 40.0%
CAGGTATAGATGGTACTTGA+GGG - chr5.2:5538433-5538452 None:intergenic 40.0%
CTACACTCAGATTTGTGTTG+TGG - chr5.2:5539155-5539174 None:intergenic 40.0%
CTAGGAAAGCTTCACTTCAT+CGG + chr5.2:5538581-5538600 MS.gene09704:CDS 40.0%
GATTTGTGTTGTGGTGATTG+TGG - chr5.2:5539146-5539165 None:intergenic 40.0%
GGAAAAGTCCATGATGTCTT+TGG - chr5.2:5538324-5538343 None:intergenic 40.0%
TACCTGGAGTTTCCCAAAAT+AGG - chr5.2:5538057-5538076 None:intergenic 40.0%
TCTTGGAGAAAAGGAAGGAT+AGG + chr5.2:5538605-5538624 MS.gene09704:CDS 40.0%
TTAAAGTAACACATGGGTGG+AGG - chr5.2:5539183-5539202 None:intergenic 40.0%
! ATCATGGACTTTTCCACCAA+AGG + chr5.2:5538329-5538348 MS.gene09704:CDS 40.0%
!! ATGTCTTTGGCTTTATCAGC+TGG - chr5.2:5538311-5538330 None:intergenic 40.0%
!! TTCATCGGTTCTTGGAGAAA+AGG + chr5.2:5538596-5538615 MS.gene09704:CDS 40.0%
!! TTCCTATTTTGGGAAACTCC+AGG + chr5.2:5538052-5538071 MS.gene09704:CDS 40.0%
ATCCATGACATGGCTCTCTT+TGG + chr5.2:5539118-5539137 MS.gene09704:CDS 45.0%
CTTCTGCAGAATTGTAGCCA+GGG + chr5.2:5539046-5539065 MS.gene09704:intron 45.0%
TCGGTTCTTGGAGAAAAGGA+AGG + chr5.2:5538600-5538619 MS.gene09704:CDS 45.0%
TTGATTGAGAGAGATCTGGC+TGG - chr5.2:5538635-5538654 None:intergenic 45.0%
!! AGCTTCACTTCATCGGTTCT+TGG + chr5.2:5538588-5538607 MS.gene09704:CDS 45.0%
GCTTCTGCAGAATTGTAGCC+AGG + chr5.2:5539045-5539064 MS.gene09704:intron 50.0%
GCTTGTTTGATATGGTGCCC+TGG - chr5.2:5539066-5539085 None:intergenic 50.0%
TGCCAAAGAGAGCCATGTCA+TGG - chr5.2:5539123-5539142 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 5537988 5539202 5537988 ID=MS.gene09704
chr5.2 mRNA 5537988 5539202 5537988 ID=MS.gene09704.t1;Parent=MS.gene09704
chr5.2 exon 5537988 5538073 5537988 ID=MS.gene09704.t1.exon1;Parent=MS.gene09704.t1
chr5.2 CDS 5537988 5538073 5537988 ID=cds.MS.gene09704.t1;Parent=MS.gene09704.t1
chr5.2 exon 5538217 5538461 5538217 ID=MS.gene09704.t1.exon2;Parent=MS.gene09704.t1
chr5.2 CDS 5538217 5538461 5538217 ID=cds.MS.gene09704.t1;Parent=MS.gene09704.t1
chr5.2 exon 5538569 5538626 5538569 ID=MS.gene09704.t1.exon3;Parent=MS.gene09704.t1
chr5.2 CDS 5538569 5538626 5538569 ID=cds.MS.gene09704.t1;Parent=MS.gene09704.t1
chr5.2 exon 5539055 5539202 5539055 ID=MS.gene09704.t1.exon4;Parent=MS.gene09704.t1
chr5.2 CDS 5539055 5539202 5539055 ID=cds.MS.gene09704.t1;Parent=MS.gene09704.t1
Gene Sequence

>MS.gene09704

ATGAATCATCACAACATGACACCAATGAATTTTCAACAACTTCCTCATCTCTTCCTACAAGAGATTCCTATTTTGGGAAACTCCAGGTACATACATGTTCTTTTTTCTACTTTAACTTGTTAAGTACATCAACATTTTTTTAGCAAAATTCAAATTCATTAATTCATACTAGTAGTATACAACATGGTCAATTTGCATTAAATTAATTATTAATGTTGTTTTATTACAGTGTAATGAAGGCTAATATTAAGAAGGAAGAACCTAGATGTGCACAAATGACAATCTTCTATGATGGGAAAGTAATTGTGTTTGATGATGTTCCAGCTGATAAAGCCAAAGACATCATGGACTTTTCCACCAAAGGAATTACTAGTACTTCACAAAACCACAATAACAACTATGCTTACTCTTCATTTCTTGCTAGAAATTCTCTTCAAGACTACCCTCAAGTACCATCTATACCTGTTATTTATGGTAATTTTTTTTTTTGGATATTTTATGTTTGAGAGGGTGCTTGATTTGTGTCATATTTTAGTTTTGTGTGTGCTTTTAATTAATGAACTTTCTTTTTATGTATTCAGATTTACCAATGACTAGGAAAGCTTCACTTCATCGGTTCTTGGAGAAAAGGAAGGATAGGTAAGCCAGCCAGATCTCTCTCAATCAAATGTTGTTTGATCTTTGTTAATAAACTTCACTTTTTGGGGAAAAATCAAATATCAAGTCAATTGAAAATAAAATTAAATGTAAGTTTGGTTCCACTTTTGGATAATCCAAGATTGATTTTGACATGTTTTGTTCCGCATCAGTTGAATAGATTTTGCCTACAGAATGGATTCTACTTGAAATTCAAAATTGTTGCTTCTGATTTTACATTCAAATTTATTATTCAATTCATTTTTACGTGAATGTATCAAACATAAATCACTAAAGGTAGAATCAATTTTACATAATCAATTTATTCAAAATCAATTTTTCTCGTAGCAGAACAAAAGATACACTATTACTAATACTATGATGTTTGGGATGATCCATATTGACTGATATGTTTGTTTATGCTTCTGCAGAATTGTAGCCAGGGCACCATATCAAACAAGCAATCCAAGAAGCATTAATAAACCAATTGATGAATCCATGACATGGCTCTCTTTGGCACCACAATCACCACAACACAAATCTGAGTGTAGCAGCTCCTCCACCCATGTGTTACTTTAA
Protein sequence

>MS.gene09704.t1

MNHHNMTPMNFQQLPHLFLQEIPILGNSSVMKANIKKEEPRCAQMTIFYDGKVIVFDDVPADKAKDIMDFSTKGITSTSQNHNNNYAYSSFLARNSLQDYPQVPSIPVIYDLPMTRKASLHRFLEKRKDRIVARAPYQTSNPRSINKPIDESMTWLSLAPQSPQHKSECSSSSTHVLL