AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09703

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09703.t1 MTR_5g013530 86.413 184 14 3 1 184 1 173 2.42e-110 312
MS.gene09703.t1 MTR_5g013530 86.538 156 10 3 29 184 7 151 1.83e-90 261
MS.gene09703.t1 MTR_5g013520 84.211 152 17 3 30 181 1 145 1.36e-87 253
MS.gene09703.t1 MTR_5g013515 71.034 145 27 5 31 168 1 137 5.33e-64 194
MS.gene09703.t1 MTR_2g042900 47.273 165 43 7 25 163 99 245 9.82e-35 123
MS.gene09703.t1 MTR_2g042900 37.500 168 39 7 25 136 99 256 1.35e-19 83.6
MS.gene09703.t1 MTR_2g044910 30.172 116 72 1 40 146 11 126 2.42e-13 65.1
MS.gene09703.t1 MTR_2g044910 30.172 116 72 1 40 146 54 169 5.51e-13 64.7
MS.gene09703.t1 MTR_8g021380 31.298 131 84 3 19 144 79 208 6.65e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09703.t1 AT1G19180 43.284 134 70 4 37 166 53 184 1.55e-27 102
MS.gene09703.t1 AT1G19180 43.284 134 70 4 37 166 119 250 1.06e-26 102
MS.gene09703.t1 AT1G19180 43.284 134 70 4 37 166 119 250 1.06e-26 102
MS.gene09703.t1 AT1G74950 39.130 138 72 3 37 164 112 247 2.13e-22 90.9
MS.gene09703.t1 AT1G74950 40.000 110 56 2 37 136 112 221 3.68e-17 76.3
MS.gene09703.t1 AT1G17380 35.714 126 73 2 33 150 58 183 8.55e-16 73.2
MS.gene09703.t1 AT1G72450 36.066 122 66 3 39 152 101 218 2.02e-15 72.4
MS.gene09703.t1 AT1G17380 35.714 126 73 2 33 150 87 212 2.96e-15 72.0
MS.gene09703.t1 AT5G20900 37.719 114 58 3 44 147 57 167 6.72e-15 69.7
MS.gene09703.t1 AT1G70700 34.884 129 74 4 44 167 119 242 1.53e-12 64.3
MS.gene09703.t1 AT1G17380 33.929 112 66 2 33 136 87 198 6.20e-11 59.7

Find 38 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTACAAGAGATTCCTAATT+TGG 0.066386 5.2:+5552586 MS.gene09703:CDS
CCATCTATACCTGTTATTTA+TGG 0.164541 5.2:+5552988 MS.gene09703:CDS
ATTCATCAATTGACTTATTT+AGG 0.185988 5.2:-5554018 None:intergenic
AGCTTCACTTCATCGGTTCT+TGG 0.292747 5.2:+5553132 MS.gene09703:CDS
TACCTGGAGTTTCCCAAATT+AGG 0.318968 5.2:-5552599 None:intergenic
CCAAATTAGGAATCTCTTGT+AGG 0.328797 5.2:-5552586 None:intergenic
CTACAAGAGATTCCTAATTT+GGG 0.331956 5.2:+5552587 MS.gene09703:CDS
GGAAAAGTCCATGATGTCTT+TGG 0.411671 5.2:-5552851 None:intergenic
ATGTCTTTGGCTTTATCAGC+TGG 0.417227 5.2:-5552838 None:intergenic
GCTGGATTACTTGTTTGATA+AGG 0.423471 5.2:-5553989 None:intergenic
AGTGAAGCTTTCCTAGTCAT+TGG 0.425048 5.2:-5553118 None:intergenic
GACTTATTTAGGAATGCTGC+TGG 0.431039 5.2:-5554007 None:intergenic
GTAGTCTTGAAGAGAATTGT+TGG 0.442893 5.2:-5552956 None:intergenic
CAAATGACAATCTTCTATGA+TGG 0.453411 5.2:+5552790 MS.gene09703:CDS
TGAAGTACTAGTAATTCCTT+TGG 0.455465 5.2:-5552875 None:intergenic
TTCATCGGTTCTTGGAGAAA+AGG 0.463618 5.2:+5553140 MS.gene09703:CDS
CCATAAATAACAGGTATAGA+TGG 0.477854 5.2:-5552988 None:intergenic
AGTACTAGTAATTCCTTTGG+TGG 0.499055 5.2:-5552872 None:intergenic
ATCCATGTCATGGCTATCCT+TGG 0.509457 5.2:+5554039 MS.gene09703:CDS
AGCAAGCATAGTTGTTATTG+TGG 0.514503 5.2:-5552909 None:intergenic
TTCCTAATTTGGGAAACTCC+AGG 0.526778 5.2:+5552597 MS.gene09703:CDS
CTAGGAAAGCTTCACTTCAT+CGG 0.529148 5.2:+5553125 MS.gene09703:CDS
AAATGACAATCTTCTATGAT+GGG 0.538308 5.2:+5552791 MS.gene09703:CDS
CTACATTCAGATTTGTGTTG+CGG 0.544643 5.2:-5554073 None:intergenic
GGATGCTGTTGAAAATTCAT+AGG 0.552738 5.2:-5552554 None:intergenic
AATGAAGGCTAATATTAAGA+AGG 0.556826 5.2:+5552750 MS.gene09703:CDS
GGCTAATATTAAGAAGGAAG+AGG 0.566182 5.2:+5552756 MS.gene09703:CDS
TCTTGGAGAAAAGGAAGGAT+AGG 0.567398 5.2:+5553149 MS.gene09703:CDS
ATCTCTTGTAGGAAGAGATG+AGG 0.580197 5.2:-5552575 None:intergenic
TGATAAAGCCAAAGACATCA+TGG 0.585378 5.2:+5552843 MS.gene09703:CDS
TCGGTTCTTGGAGAAAAGGA+AGG 0.585705 5.2:+5553144 MS.gene09703:CDS
GTTTCTGCAGAATTGCTGCA+AGG 0.606526 5.2:+5553963 MS.gene09703:intron
ATTCAGATTTACCAATGACT+AGG 0.608086 5.2:+5553107 MS.gene09703:intron
TTTCTGCAGAATTGCTGCAA+GGG 0.611240 5.2:+5553964 MS.gene09703:intron
CAATTGATGAATCCATGTCA+TGG 0.612586 5.2:+5554029 MS.gene09703:CDS
TGCCAAGGATAGCCATGACA+TGG 0.617530 5.2:-5554041 None:intergenic
GATTTGTGTTGCGGTGAATG+TGG 0.622415 5.2:-5554064 None:intergenic
TTGCGGTGAATGTGGTGCCA+AGG 0.648709 5.2:-5554056 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTATGGTAATTTTTTT+TGG + chr5.2:5553001-5553020 MS.gene09703:intron 10.0%
!! AAAAAATTACCATAAATAAC+AGG - chr5.2:5553000-5553019 None:intergenic 15.0%
!!! TACACTATTATAATCAATTT+TGG + chr5.2:5553768-5553787 MS.gene09703:intron 15.0%
!!! TGATAGATAAATCAATTTTA+AGG + chr5.2:5553407-5553426 MS.gene09703:intron 15.0%
!!! TTTTTACTTATAATAGTGAT+TGG + chr5.2:5553532-5553551 MS.gene09703:intron 15.0%
!! TATTGCTAAAAATATGTTGA+TGG - chr5.2:5552657-5552676 None:intergenic 20.0%
!!! AATTTTAAGGAACCAATTTT+AGG + chr5.2:5553420-5553439 MS.gene09703:intron 20.0%
!!! AGTGTAATTTTGTGTATTTT+AGG + chr5.2:5553376-5553395 MS.gene09703:intron 20.0%
!!! ATTCATCAATTGACTTATTT+AGG - chr5.2:5554021-5554040 None:intergenic 20.0%
! AAATGACAATCTTCTATGAT+GGG + chr5.2:5552791-5552810 MS.gene09703:CDS 25.0%
! AATGAAGGCTAATATTAAGA+AGG + chr5.2:5552750-5552769 MS.gene09703:CDS 25.0%
! ATCCTCTCAAAACTAATATA+TGG + chr5.2:5553881-5553900 MS.gene09703:intron 25.0%
! GATAACCAATTTACTGAAAT+TGG - chr5.2:5553864-5553883 None:intergenic 25.0%
! GTTACAAAAATTGATTGAAC+TGG + chr5.2:5553275-5553294 MS.gene09703:intron 25.0%
! TAAAAAAAAGAACATGTACC+TGG - chr5.2:5552618-5552637 None:intergenic 25.0%
! TGGATATATTATGTTTGAGA+GGG + chr5.2:5553021-5553040 MS.gene09703:intron 25.0%
! TTGCGTTTATATAATAGTGA+CGG - chr5.2:5553454-5553473 None:intergenic 25.0%
! TTGGATATATTATGTTTGAG+AGG + chr5.2:5553020-5553039 MS.gene09703:intron 25.0%
AACACACTACTTAACAATTG+AGG - chr5.2:5553245-5553264 None:intergenic 30.0%
AAGTAGTGTGTTTGATTCTA+CGG + chr5.2:5553253-5553272 MS.gene09703:intron 30.0%
ATATTTGATTGAGAGAGATC+TGG - chr5.2:5553183-5553202 None:intergenic 30.0%
ATTCAGATTTACCAATGACT+AGG + chr5.2:5553107-5553126 MS.gene09703:intron 30.0%
ATTCATGCTAGTATATAGCA+TGG + chr5.2:5552682-5552701 MS.gene09703:intron 30.0%
CAAATGACAATCTTCTATGA+TGG + chr5.2:5552790-5552809 MS.gene09703:CDS 30.0%
CCAAACATCACAATAGAAAA+GGG - chr5.2:5553911-5553930 None:intergenic 30.0%
CCATAAATAACAGGTATAGA+TGG - chr5.2:5552991-5553010 None:intergenic 30.0%
CTACAAGAGATTCCTAATTT+GGG + chr5.2:5552587-5552606 MS.gene09703:CDS 30.0%
GACAAACATATCAGTCAATA+TGG - chr5.2:5553940-5553959 None:intergenic 30.0%
TCCAAACATCACAATAGAAA+AGG - chr5.2:5553912-5553931 None:intergenic 30.0%
TGATGACTTTCTCACTTTAA+AGG + chr5.2:5553600-5553619 MS.gene09703:intron 30.0%
TGCGTTTATATAATAGTGAC+GGG - chr5.2:5553453-5553472 None:intergenic 30.0%
TTAAAGTGAGAAAGTCATCA+TGG - chr5.2:5553600-5553619 None:intergenic 30.0%
! ACTTTCTCACTTTAAAGGTA+GGG + chr5.2:5553605-5553624 MS.gene09703:intron 30.0%
! CCATCTATACCTGTTATTTA+TGG + chr5.2:5552988-5553007 MS.gene09703:CDS 30.0%
! GTGATTTTGCTAAAAGTGAA+TGG + chr5.2:5553308-5553327 MS.gene09703:intron 30.0%
! TGAAGTACTAGTAATTCCTT+TGG - chr5.2:5552878-5552897 None:intergenic 30.0%
! TTTATATAATAGTGACGGGA+GGG - chr5.2:5553449-5553468 None:intergenic 30.0%
!! AACGGATTGAAGCTATAATT+TGG - chr5.2:5553668-5553687 None:intergenic 30.0%
!! ATTGATTTTGCTTCCAGAAA+CGG - chr5.2:5553686-5553705 None:intergenic 30.0%
!! GTTTTATTACAGTGCAATGA+AGG + chr5.2:5552735-5552754 MS.gene09703:intron 30.0%
!!! AGCCATATATTAGTTTTGAG+AGG - chr5.2:5553886-5553905 None:intergenic 30.0%
!!! GTCAATAGACTTCACTTTTT+AGG + chr5.2:5553215-5553234 MS.gene09703:intron 30.0%
AGATATAGTGACTTTGGTGA+TGG + chr5.2:5553335-5553354 MS.gene09703:intron 35.0%
AGGAGCCAATTTCAGTAAAT+TGG + chr5.2:5553856-5553875 MS.gene09703:intron 35.0%
AGTACTAGTAATTCCTTTGG+TGG - chr5.2:5552875-5552894 None:intergenic 35.0%
CAATTGATGAATCCATGTCA+TGG + chr5.2:5554029-5554048 MS.gene09703:CDS 35.0%
CCAAATTAGGAATCTCTTGT+AGG - chr5.2:5552589-5552608 None:intergenic 35.0%
CCTACAAGAGATTCCTAATT+TGG + chr5.2:5552586-5552605 MS.gene09703:CDS 35.0%
CTACAAAAATAACACAGAGG+TGG - chr5.2:5554101-5554120 None:intergenic 35.0%
CTACATTCAGATTTGTGTTG+CGG - chr5.2:5554076-5554095 None:intergenic 35.0%
GCTGGATTACTTGTTTGATA+AGG - chr5.2:5553992-5554011 None:intergenic 35.0%
GGATGCTGTTGAAAATTCAT+AGG - chr5.2:5552557-5552576 None:intergenic 35.0%
GGATTGAGATATAGTGACTT+TGG + chr5.2:5553329-5553348 MS.gene09703:intron 35.0%
GGCTAATATTAAGAAGGAAG+AGG + chr5.2:5552756-5552775 MS.gene09703:CDS 35.0%
TGATAAAGCCAAAGACATCA+TGG + chr5.2:5552843-5552862 MS.gene09703:CDS 35.0%
TTATAGCTTCAATCCGTTTC+TGG + chr5.2:5553670-5553689 MS.gene09703:intron 35.0%
! AGCAAGCATAGTTGTTATTG+TGG - chr5.2:5552912-5552931 None:intergenic 35.0%
! CACTTTAAAGGTAGGGAATT+TGG + chr5.2:5553612-5553631 MS.gene09703:intron 35.0%
! CCCTTTTCTATTGTGATGTT+TGG + chr5.2:5553908-5553927 MS.gene09703:intron 35.0%
! GACTTTCTCACTTTAAAGGT+AGG + chr5.2:5553604-5553623 MS.gene09703:intron 35.0%
! GATATAGTGACTTTGGTGAT+GGG + chr5.2:5553336-5553355 MS.gene09703:intron 35.0%
! GTAGTCTTGAAGAGAATTGT+TGG - chr5.2:5552959-5552978 None:intergenic 35.0%
! GTTTATATAATAGTGACGGG+AGG - chr5.2:5553450-5553469 None:intergenic 35.0%
! TGGAGTTTTTGTCTCTACAT+TGG - chr5.2:5553648-5553667 None:intergenic 35.0%
AGTGAAGCTTTCCTAGTCAT+TGG - chr5.2:5553121-5553140 None:intergenic 40.0%
ATCTCTTGTAGGAAGAGATG+AGG - chr5.2:5552578-5552597 None:intergenic 40.0%
CTAGGAAAGCTTCACTTCAT+CGG + chr5.2:5553125-5553144 MS.gene09703:CDS 40.0%
GACATGACTCTTTGTATCCT+CGG - chr5.2:5553811-5553830 None:intergenic 40.0%
GACTTATTTAGGAATGCTGC+TGG - chr5.2:5554010-5554029 None:intergenic 40.0%
GAGACCATGAACAAAAGTGA+AGG + chr5.2:5553836-5553855 MS.gene09703:intron 40.0%
GGAAAAGTCCATGATGTCTT+TGG - chr5.2:5552854-5552873 None:intergenic 40.0%
TACCTGGAGTTTCCCAAATT+AGG - chr5.2:5552602-5552621 None:intergenic 40.0%
TCTTGGAGAAAAGGAAGGAT+AGG + chr5.2:5553149-5553168 MS.gene09703:CDS 40.0%
TTCCTAATTTGGGAAACTCC+AGG + chr5.2:5552597-5552616 MS.gene09703:CDS 40.0%
TTTCTGCAGAATTGCTGCAA+GGG + chr5.2:5553964-5553983 MS.gene09703:intron 40.0%
! ATCATGGACTTTTCCACCAA+AGG + chr5.2:5552859-5552878 MS.gene09703:CDS 40.0%
!! AGGGTGTTTGATTTGTGTCA+TGG + chr5.2:5553040-5553059 MS.gene09703:intron 40.0%
!! ATGTCTTTGGCTTTATCAGC+TGG - chr5.2:5552841-5552860 None:intergenic 40.0%
!! TTCATCGGTTCTTGGAGAAA+AGG + chr5.2:5553140-5553159 MS.gene09703:CDS 40.0%
ATCCATGTCATGGCTATCCT+TGG + chr5.2:5554039-5554058 MS.gene09703:CDS 45.0%
GATTTGTGTTGCGGTGAATG+TGG - chr5.2:5554067-5554086 None:intergenic 45.0%
GTTTCTGCAGAATTGCTGCA+AGG + chr5.2:5553963-5553982 MS.gene09703:intron 45.0%
TCGGTTCTTGGAGAAAAGGA+AGG + chr5.2:5553144-5553163 MS.gene09703:CDS 45.0%
TTGATTGAGAGAGATCTGGC+AGG - chr5.2:5553179-5553198 None:intergenic 45.0%
!! AGCTTCACTTCATCGGTTCT+TGG + chr5.2:5553132-5553151 MS.gene09703:CDS 45.0%
!! GGCTCCTTCACTTTTGTTCA+TGG - chr5.2:5553843-5553862 None:intergenic 45.0%
ACGGGAGGGAGTCCTAAAAT+TGG - chr5.2:5553435-5553454 None:intergenic 50.0%
TGCCAAGGATAGCCATGACA+TGG - chr5.2:5554044-5554063 None:intergenic 50.0%
! TGTATCCTCGGCTCGACTTT+AGG - chr5.2:5553799-5553818 None:intergenic 50.0%
CTCATCCTAAAGTCGAGCCG+AGG + chr5.2:5553791-5553810 MS.gene09703:intron 55.0%
! TTGCGGTGAATGTGGTGCCA+AGG - chr5.2:5554059-5554078 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 5552533 5554120 5552533 ID=MS.gene09703
chr5.2 mRNA 5552533 5554120 5552533 ID=MS.gene09703.t1;Parent=MS.gene09703
chr5.2 exon 5552533 5552618 5552533 ID=MS.gene09703.t1.exon1;Parent=MS.gene09703.t1
chr5.2 CDS 5552533 5552618 5552533 ID=cds.MS.gene09703.t1;Parent=MS.gene09703.t1
chr5.2 exon 5552747 5553009 5552747 ID=MS.gene09703.t1.exon2;Parent=MS.gene09703.t1
chr5.2 CDS 5552747 5553009 5552747 ID=cds.MS.gene09703.t1;Parent=MS.gene09703.t1
chr5.2 exon 5553113 5553170 5553113 ID=MS.gene09703.t1.exon3;Parent=MS.gene09703.t1
chr5.2 CDS 5553113 5553170 5553113 ID=cds.MS.gene09703.t1;Parent=MS.gene09703.t1
chr5.2 exon 5553973 5554120 5553973 ID=MS.gene09703.t1.exon4;Parent=MS.gene09703.t1
chr5.2 CDS 5553973 5554120 5553973 ID=cds.MS.gene09703.t1;Parent=MS.gene09703.t1
Gene Sequence

>MS.gene09703

ATGAAGCATCACAACATAGCACCTATGAATTTTCAACAGCATCCTCATCTCTTCCTACAAGAGATTCCTAATTTGGGAAACTCCAGGTACATGTTCTTTTTTTTACTTTAACTTTTTAAGTCCATCAACATATTTTTAGCAATATTCAAATTCATGCTAGTATATAGCATGGTCAATTTGCATTAAATTAATTGTTAATGTTGTTTTATTACAGTGCAATGAAGGCTAATATTAAGAAGGAAGAGGCTAGATGTGCACAAATGACAATCTTCTATGATGGGAAAGTAATTGTGTTTGATGATGTTCCAGCTGATAAAGCCAAAGACATCATGGACTTTTCCACCAAAGGAATTACTAGTACTTCACAAGCACAAAACCACAATAACAACTATGCTTGCTCTTCATTTCTTGCTAGAAATTCTGCCAACAATTCTCTTCAAGACTACTATCAAGTACCATCTATACCTGTTATTTATGGTAATTTTTTTTGGATATATTATGTTTGAGAGGGTGTTTGATTTGTGTCATGGTTTTGTTTTTTGTGTGTTTTTAACTCATGAAATTCTTTTTATGTATTCAGATTTACCAATGACTAGGAAAGCTTCACTTCATCGGTTCTTGGAGAAAAGGAAGGATAGGTAAGCCTGCCAGATCTCTCTCAATCAAATATTGTTTGATCTTTGTCAATAGACTTCACTTTTTAGGAAAACCTCAATTGTTAAGTAGTGTGTTTGATTCTACGGTTACAAAAATTGATTGAACTGGTTATTTAAAAGTGATTTTGCTAAAAGTGAATGGATTGAGATATAGTGACTTTGGTGATGGGAAAGTAATTATTACTATAGTGTAATTTTGTGTATTTTAGGAAAGAAAATGATAGATAAATCAATTTTAAGGAACCAATTTTAGGACTCCCTCCCGTCACTATTATATAAACGCAAAAAATCACTTTTAAATTTATTCAATAACTAATGTATTGAATGAATCTTAAAAGTTGTTTTTTTACTTATAATAGTGATTGGATGAAAAATATATATATATATAAGAGAAAGATAAACACAAAGCCATGATGACTTTCTCACTTTAAAGGTAGGGAATTTGGATCTGAAAATCCAATGTAGAGACAAAAACTCCAAATTATAGCTTCAATCCGTTTCTGGAAGCAAAATCAATTTCACTTCAAAAACATTCAAACATTTGTTTTTGAAAGAAAGAAAACATGTCAAAATCAATTCTACACTATTATAATCAATTTTGGCTCATCCTAAAGTCGAGCCGAGGATACAAAGAGTCATGTCAAATTGAGACCATGAACAAAAGTGAAGGAGCCAATTTCAGTAAATTGGTTATCCTCTCAAAACTAATATATGGCTGACCCTTTTCTATTGTGATGTTTGGAATTATCCATATTGACTGATATGTTTGTCTATGTTTCTGCAGAATTGCTGCAAGGGCACCTTATCAAACAAGTAATCCAGCAGCATTCCTAAATAAGTCAATTGATGAATCCATGTCATGGCTATCCTTGGCACCACATTCACCGCAACACAAATCTGAATGTAGCTCCACCTCTGTGTTATTTTTGTAG
Protein sequence

>MS.gene09703.t1

MKHHNIAPMNFQQHPHLFLQEIPNLGNSSAMKANIKKEEARCAQMTIFYDGKVIVFDDVPADKAKDIMDFSTKGITSTSQAQNHNNNYACSSFLARNSANNSLQDYYQVPSIPVIYDLPMTRKASLHRFLEKRKDRIAARAPYQTSNPAAFLNKSIDESMSWLSLAPHSPQHKSECSSTSVLFL