AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71532


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71532.t1 MTR_3g083080 42.073 164 73 5 6 152 30 188 4.61e-26 99.0
MS.gene71532.t1 MTR_3g082420 36.527 167 88 6 3 152 39 204 4.37e-24 94.4
MS.gene71532.t1 MTR_3g080680 40.000 180 77 7 1 152 5 181 8.42e-24 92.8
MS.gene71532.t1 MTR_3g083030 40.462 173 77 7 2 155 49 214 3.55e-22 89.4
MS.gene71532.t1 MTR_3g082340 34.524 168 90 6 4 152 39 205 3.17e-20 84.3
MS.gene71532.t1 MTR_3g083050 39.623 159 72 6 13 155 41 191 5.01e-20 83.2
MS.gene71532.t1 MTR_4g055800 34.706 170 83 6 11 164 127 284 1.13e-18 81.3
MS.gene71532.t1 MTR_8g461300 38.068 176 72 9 2 150 14 179 2.92e-17 75.9
MS.gene71532.t1 MTR_3g083150 39.252 107 57 4 50 151 91 194 2.59e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGTATTATATCACCTTTC+AGG 0.222077 3.4:+78232092 MS.gene71532:CDS
TGCGGTTGTGGTCCCAATTC+AGG 0.229825 3.4:-78231547 None:intergenic
AAGATCTTCGGTTAAGTTAA+TGG 0.250637 3.4:-78231859 None:intergenic
CAAAATGTTGAAACCTGAAT+TGG 0.269249 3.4:+78231534 None:intergenic
TCGTATTTCGATTGCGGTTG+TGG 0.305044 3.4:-78231559 None:intergenic
GCTATCGTGGAGTACGGATA+TGG 0.366721 3.4:+78233481 MS.gene71532:CDS
GTCAGCAATTAGTTCATCTA+TGG 0.376229 3.4:-78231662 None:intergenic
AGATCTTCGGTTAAGTTAAT+GGG 0.384715 3.4:-78231858 None:intergenic
CCATGCTATAACAACTTTCC+AGG 0.403448 3.4:+78232143 MS.gene71532:CDS
GTACGACGATGACGACTTTG+CGG 0.444713 3.4:+78231627 MS.gene71532:CDS
ACTGCTGTTGCCTGTGGTGG+TGG 0.453533 3.4:+78232066 MS.gene71532:CDS
AAAATGTTGAAACCTGAATT+GGG 0.454585 3.4:+78231535 None:intergenic
GAATTACAATCAAAATAATC+AGG 0.466466 3.4:+78231920 MS.gene71532:CDS
CCACATAACTCTAGAACGGC+TGG 0.510258 3.4:-78231825 None:intergenic
AAAGTCGTCATCGTCGTACA+TGG 0.527955 3.4:-78231623 None:intergenic
GAGAGTAGGACGAAGATCTT+CGG 0.537282 3.4:-78231871 None:intergenic
ACCACTGCTGTTGCCTGTGG+TGG 0.537702 3.4:+78232063 MS.gene71532:CDS
CATCATCCCATACTTCGGCC+TGG 0.538029 3.4:-78232161 None:intergenic
TCCGAATCGTATTTCGATTG+CGG 0.541557 3.4:-78231565 None:intergenic
ATTCAGGCTATCGTGGAGTA+CGG 0.559342 3.4:+78233475 MS.gene71532:intron
AGTTGTTATAGCATGGCTGT+TGG 0.561797 3.4:-78232136 None:intergenic
GTTATAGCATGGCTGTTGGA+AGG 0.561860 3.4:-78232132 None:intergenic
TCAGAGAGAGTAACGAGAGT+AGG 0.562238 3.4:-78231885 None:intergenic
ATACAAATCACCACCACCAC+AGG 0.565336 3.4:-78232076 None:intergenic
ACCGCAATCGAAATACGATT+CGG 0.566744 3.4:+78231564 MS.gene71532:CDS
CGACTTTGCGGAAGAGAGAG+AGG 0.588174 3.4:+78231639 MS.gene71532:CDS
CCTGGAAAGTTGTTATAGCA+TGG 0.593345 3.4:-78232143 None:intergenic
TGTACCACTGCTGTTGCCTG+TGG 0.600572 3.4:+78232060 MS.gene71532:CDS
CAGCAGTGGTACACTTGACA+AGG 0.618690 3.4:-78232050 None:intergenic
CCAGCCGTTCTAGAGTTATG+TGG 0.626689 3.4:+78231825 MS.gene71532:CDS
ACAGCCACATAACTCTAGAA+CGG 0.642024 3.4:-78231829 None:intergenic
ACCACCACAGGCAACAGCAG+TGG 0.646579 3.4:-78232064 None:intergenic
GGATGATAGATAGCATCGAA+CGG 0.667704 3.4:-78231804 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATCAAATACAATTTCAT+AGG - chr3.4:78232319-78232338 None:intergenic 15.0%
!! AATTGTTCTTCTTAATTATT+AGG + chr3.4:78232005-78232024 MS.gene71532:intron 15.0%
!! AATTTCATGAAGAAATAAAA+TGG - chr3.4:78232363-78232382 None:intergenic 15.0%
!! ATTGTTCTTCTTAATTATTA+GGG + chr3.4:78232006-78232025 MS.gene71532:intron 15.0%
!! AAAAATTAAACATGTAAGGA+TGG - chr3.4:78232258-78232277 None:intergenic 20.0%
!! CAAGAAAAATTAAACATGTA+AGG - chr3.4:78232262-78232281 None:intergenic 20.0%
!! GAATTACAATCAAAATAATC+AGG + chr3.4:78231920-78231939 MS.gene71532:CDS 20.0%
!!! CTTACATGTTTAATTTTTCT+TGG + chr3.4:78232260-78232279 MS.gene71532:intron 20.0%
! CCATATAGATAATCAGAATT+CGG + chr3.4:78232819-78232838 MS.gene71532:intron 25.0%
! GAATATAAAAGTGATAGAAC+TGG - chr3.4:78233459-78233478 None:intergenic 25.0%
! GAGATAAGTTACAATGAATA+AGG - chr3.4:78233312-78233331 None:intergenic 25.0%
! GATTTATTACAACAAACTCT+GGG - chr3.4:78233403-78233422 None:intergenic 25.0%
! GGAAATACTGTAATAGAATA+AGG - chr3.4:78233291-78233310 None:intergenic 25.0%
! TAAAATCTAATACACTACCT+TGG + chr3.4:78232221-78232240 MS.gene71532:intron 25.0%
! TGATTTATTACAACAAACTC+TGG - chr3.4:78233404-78233423 None:intergenic 25.0%
! TTCATTGTAACTTATCTCTA+TGG + chr3.4:78233314-78233333 MS.gene71532:intron 25.0%
! TTTGTATTATATCACCTTTC+AGG + chr3.4:78232092-78232111 MS.gene71532:CDS 25.0%
!! ACAAGAACTAATGGTAATTT+TGG - chr3.4:78233263-78233282 None:intergenic 25.0%
!! ACTGTGTTTTTCTCTTTATT+TGG + chr3.4:78232487-78232506 MS.gene71532:intron 25.0%
!! AGAATAAACCATAAAGCATT+TGG + chr3.4:78232998-78233017 MS.gene71532:intron 25.0%
!! CTTATATTCCTTTTAGCAAT+GGG - chr3.4:78232980-78232999 None:intergenic 25.0%
!! GGTAGTGTATTAGATTTTAA+TGG - chr3.4:78232220-78232239 None:intergenic 25.0%
!! TCTCTCTTTTTCTCTTAATT+GGG + chr3.4:78233099-78233118 MS.gene71532:intron 25.0%
!! TCTTATATTCCTTTTAGCAA+TGG - chr3.4:78232981-78233000 None:intergenic 25.0%
!! TTGCTTTAACACTGAATTTT+TGG + chr3.4:78232716-78232735 MS.gene71532:intron 25.0%
!! TTTGTTTGTTGGAAATACTT+TGG + chr3.4:78232445-78232464 MS.gene71532:intron 25.0%
!!! AAATCATATTTTAGGAATGG+AGG - chr3.4:78233223-78233242 None:intergenic 25.0%
!!! AGGAAATCATATTTTAGGAA+TGG - chr3.4:78233226-78233245 None:intergenic 25.0%
!!! CTGTGTTTTTCTCTTTATTT+GGG + chr3.4:78232488-78232507 MS.gene71532:intron 25.0%
!!! GTTCTATCACTTTTATATTC+AGG + chr3.4:78233459-78233478 MS.gene71532:intron 25.0%
!!! GTTTGTTGTAATAAATCAGA+AGG + chr3.4:78233406-78233425 MS.gene71532:intron 25.0%
!!! TGTGTTTTTCTCTTTATTTG+GGG + chr3.4:78232489-78232508 MS.gene71532:intron 25.0%
AAGATCTTCGGTTAAGTTAA+TGG - chr3.4:78231862-78231881 None:intergenic 30.0%
AAGCATTACCAAATGCTTTA+TGG - chr3.4:78233009-78233028 None:intergenic 30.0%
ACATATCACAAATGTCTACA+GGG + chr3.4:78233029-78233048 MS.gene71532:intron 30.0%
AGATCTTCGGTTAAGTTAAT+GGG - chr3.4:78231861-78231880 None:intergenic 30.0%
AGATTTATCAGAACAAACTC+TGG - chr3.4:78233353-78233372 None:intergenic 30.0%
ATAGATAGATTCGTACACTT+AGG - chr3.4:78231708-78231727 None:intergenic 30.0%
ATATTGCTACCGAATAAAAC+TGG - chr3.4:78232860-78232879 None:intergenic 30.0%
CCGAATTCTGATTATCTATA+TGG - chr3.4:78232822-78232841 None:intergenic 30.0%
CTTGTAATAAAAACAGGTTC+TGG - chr3.4:78232605-78232624 None:intergenic 30.0%
GATTTATCAGAACAAACTCT+GGG - chr3.4:78233352-78233371 None:intergenic 30.0%
GGATGGAATTATTATTACCA+AGG - chr3.4:78232241-78232260 None:intergenic 30.0%
GTAATAGTGTCTTATCACAA+GGG - chr3.4:78232541-78232560 None:intergenic 30.0%
TACATATCACAAATGTCTAC+AGG + chr3.4:78233028-78233047 MS.gene71532:intron 30.0%
TCCTTGCTTGTAATAAAAAC+AGG - chr3.4:78232611-78232630 None:intergenic 30.0%
TCTTGGTTAATCAATCTTCT+TGG + chr3.4:78232277-78232296 MS.gene71532:intron 30.0%
TGATAACTGAACTTGTATCA+GGG + chr3.4:78232895-78232914 MS.gene71532:intron 30.0%
TTTGGCAAATCAAATTGTTG+TGG + chr3.4:78232734-78232753 MS.gene71532:intron 30.0%
TTTGTTGGAAATACTTTGGA+TGG + chr3.4:78232449-78232468 MS.gene71532:intron 30.0%
! CTCTCTCTTTTTCTCTTAAT+TGG + chr3.4:78233098-78233117 MS.gene71532:intron 30.0%
! TCAAACTAGACTTTGTTTGT+TGG + chr3.4:78232434-78232453 MS.gene71532:intron 30.0%
! TGCTGAGGAAATCATATTTT+AGG - chr3.4:78233231-78233250 None:intergenic 30.0%
! TTGATAACTGAACTTGTATC+AGG + chr3.4:78232894-78232913 MS.gene71532:intron 30.0%
!! TAGCAAGTTTTAGCAATGAT+AGG - chr3.4:78232570-78232589 None:intergenic 30.0%
!!! ACCTGTTTTTATTACAAGCA+AGG + chr3.4:78232607-78232626 MS.gene71532:intron 30.0%
!!! TGCAAATCACCAGTTTTATT+CGG + chr3.4:78232848-78232867 MS.gene71532:intron 30.0%
AAAAGAATCATGTTGCAGTC+TGG + chr3.4:78232667-78232686 MS.gene71532:intron 35.0%
AAGGATAGCACAAGAACTAA+TGG - chr3.4:78233272-78233291 None:intergenic 35.0%
ACAAAGGCAGTATCAAATCT+AGG - chr3.4:78233063-78233082 None:intergenic 35.0%
ATCATCATCATCCCATACTT+CGG - chr3.4:78232169-78232188 None:intergenic 35.0%
CGTAATAGTGTCTTATCACA+AGG - chr3.4:78232542-78232561 None:intergenic 35.0%
GACCTGATATCAAACTACAA+AGG - chr3.4:78233079-78233098 None:intergenic 35.0%
GTCAGCAATTAGTTCATCTA+TGG - chr3.4:78231665-78231684 None:intergenic 35.0%
TAATTGGGCTTTCTTAGTGT+TGG + chr3.4:78233114-78233133 MS.gene71532:intron 35.0%
TGCCTTTGTAGTTTGATATC+AGG + chr3.4:78233074-78233093 MS.gene71532:intron 35.0%
TTTCTTTAGCAGTTGTGAGA+TGG - chr3.4:78232776-78232795 None:intergenic 35.0%
! CTTTTATATTCAGGCTATCG+TGG + chr3.4:78233468-78233487 MS.gene71532:intron 35.0%
ACCGCAATCGAAATACGATT+CGG + chr3.4:78231564-78231583 MS.gene71532:CDS 40.0%
AGACGTAACCCATTGCTAAA+AGG + chr3.4:78232969-78232988 MS.gene71532:intron 40.0%
AGTTGTTATAGCATGGCTGT+TGG - chr3.4:78232139-78232158 None:intergenic 40.0%
CCATGCTATAACAACTTTCC+AGG + chr3.4:78232143-78232162 MS.gene71532:CDS 40.0%
CCTGGAAAGTTGTTATAGCA+TGG - chr3.4:78232146-78232165 None:intergenic 40.0%
CTAAAGAAAATGTTGCGCAG+GGG + chr3.4:78232787-78232806 MS.gene71532:intron 40.0%
GCTAAAGAAAATGTTGCGCA+GGG + chr3.4:78232786-78232805 MS.gene71532:intron 40.0%
TCCGAATCGTATTTCGATTG+CGG - chr3.4:78231568-78231587 None:intergenic 40.0%
TGCTAAAGAAAATGTTGCGC+AGG + chr3.4:78232785-78232804 MS.gene71532:intron 40.0%
! ACAGCCACATAACTCTAGAA+CGG - chr3.4:78231832-78231851 None:intergenic 40.0%
! GGATGATAGATAGCATCGAA+CGG - chr3.4:78231807-78231826 None:intergenic 40.0%
!! TTCTTCTGCTTTTGCCTGAA+AGG - chr3.4:78232109-78232128 None:intergenic 40.0%
AAAATGTTGCGCAGGGGATT+AGG + chr3.4:78232793-78232812 MS.gene71532:intron 45.0%
AAAGTCGTCATCGTCGTACA+TGG - chr3.4:78231626-78231645 None:intergenic 45.0%
AACTTTCCAGGCCGAAGTAT+GGG + chr3.4:78232155-78232174 MS.gene71532:intron 45.0%
ATACAAATCACCACCACCAC+AGG - chr3.4:78232079-78232098 None:intergenic 45.0%
ATTCAGGCTATCGTGGAGTA+CGG + chr3.4:78233475-78233494 MS.gene71532:intron 45.0%
GAGAGTAGGACGAAGATCTT+CGG - chr3.4:78231874-78231893 None:intergenic 45.0%
GTTATAGCATGGCTGTTGGA+AGG - chr3.4:78232135-78232154 None:intergenic 45.0%
TCAGAGAGAGTAACGAGAGT+AGG - chr3.4:78231888-78231907 None:intergenic 45.0%
TCGTATTTCGATTGCGGTTG+TGG - chr3.4:78231562-78231581 None:intergenic 45.0%
! TGATGATGATGATGCTGACG+AGG + chr3.4:78232182-78232201 MS.gene71532:intron 45.0%
!!! TTTTGGCTTCAGAGTTGCTG+AGG - chr3.4:78233246-78233265 None:intergenic 45.0%
CAACTTTCCAGGCCGAAGTA+TGG + chr3.4:78232154-78232173 MS.gene71532:intron 50.0%
CAGCAGTGGTACACTTGACA+AGG - chr3.4:78232053-78232072 None:intergenic 50.0%
GCTATCGTGGAGTACGGATA+TGG + chr3.4:78233481-78233500 MS.gene71532:CDS 50.0%
GTACGACGATGACGACTTTG+CGG + chr3.4:78231627-78231646 MS.gene71532:CDS 50.0%
!! CCACATAACTCTAGAACGGC+TGG - chr3.4:78231828-78231847 None:intergenic 50.0%
!! CCAGCCGTTCTAGAGTTATG+TGG + chr3.4:78231825-78231844 MS.gene71532:CDS 50.0%
CATCATCCCATACTTCGGCC+TGG - chr3.4:78232164-78232183 None:intergenic 55.0%
CGACTTTGCGGAAGAGAGAG+AGG + chr3.4:78231639-78231658 MS.gene71532:CDS 55.0%
TGCGGTTGTGGTCCCAATTC+AGG - chr3.4:78231550-78231569 None:intergenic 55.0%
TGTACCACTGCTGTTGCCTG+TGG + chr3.4:78232060-78232079 MS.gene71532:CDS 55.0%
ACCACCACAGGCAACAGCAG+TGG - chr3.4:78232067-78232086 None:intergenic 60.0%
ACCACTGCTGTTGCCTGTGG+TGG + chr3.4:78232063-78232082 MS.gene71532:CDS 60.0%
ACTGCTGTTGCCTGTGGTGG+TGG + chr3.4:78232066-78232085 MS.gene71532:CDS 60.0%
! AACAGGTTCTGGCGCTGCTG+AGG - chr3.4:78232594-78232613 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 78231538 78233552 78231538 ID=MS.gene71532
chr3.4 mRNA 78231538 78233552 78231538 ID=MS.gene71532.t1;Parent=MS.gene71532
chr3.4 exon 78231538 78231711 78231538 ID=MS.gene71532.t1.exon1;Parent=MS.gene71532.t1
chr3.4 CDS 78231538 78231711 78231538 ID=cds.MS.gene71532.t1;Parent=MS.gene71532.t1
chr3.4 exon 78231804 78231941 78231804 ID=MS.gene71532.t1.exon2;Parent=MS.gene71532.t1
chr3.4 CDS 78231804 78231941 78231804 ID=cds.MS.gene71532.t1;Parent=MS.gene71532.t1
chr3.4 exon 78232027 78232170 78232027 ID=MS.gene71532.t1.exon3;Parent=MS.gene71532.t1
chr3.4 CDS 78232027 78232170 78232027 ID=cds.MS.gene71532.t1;Parent=MS.gene71532.t1
chr3.4 exon 78233481 78233552 78233481 ID=MS.gene71532.t1.exon4;Parent=MS.gene71532.t1
chr3.4 CDS 78233481 78233552 78233481 ID=cds.MS.gene71532.t1;Parent=MS.gene71532.t1
Gene Sequence

>MS.gene71532

ATGTTGAAACCTGAATTGGGACCACAACCGCAATCGAAATACGATTCGGAGTACGACGACGATGACGACTTTGCGAAATGCTTCTCCATGTACGACGATGACGACTTTGCGGAAGAGAGAGAGGCCATAGATGAACTAATTGCTGACTATACAGAGAAGTCTTGCAACCTAAGTGTACGAATCTATCTATCTATCTATTTCAATTTATTTTTAATTTTATCATGTTTCGCTCACTCTACTAATTTTGATGATTCTGTACAACACAGCCGTTCGATGCTATCTATCATCCAGCCGTTCTAGAGTTATGTGGCTGTGTCGTACCCATTAACTTAACCGAAGATCTTCGTCCTACTCTCGTTACTCTCTCTGAGCTTGCTTTGAAGAATTACAATCAAAATAATCAGGTACGTTACAGTGTTATATGTTATATGCTGTTTATTCAATTATTCATCAACTAAACTGATAATAATTGTTCTTCTTAATTATTAGGGTACAAGTTTTGTGTTTCATGACCTTGTCAAGTGTACCACTGCTGTTGCCTGTGGTGGTGGTGATTTGTATTATATCACCTTTCAGGCAAAAGCAGAAGAAGATCCTTCCAACAGCCATGCTATAACAACTTTCCAGGCCGAAGTATGGGATGATGATGATGATGATGCTGACGAGGTCATATCGTGTGCCATTAAAATCTAATACACTACCTTGGTAATAATAATTCCATCCTTACATGTTTAATTTTTCTTGGTTAATCAATCTTCTTGGAGATTAGTTTATAGTTCCTATGAAATTGTATTTGATTTTGATATTTATAACAAGCTTCAACCATTTTATTTCTTCATGAAATTCACAATTATGAAAACTTGAAGTTTTTTGTTCAATCATTTCTTGCTTTACTTTCAAACTAGACTTTGTTTGTTGGAAATACTTTGGATGGTGATAAATGAAAGAAACTGTGTTTTTCTCTTTATTTGGGGCTTTCTTCATGTTGTTAGATTTTTTTCCCTTGTGATAAGACACTATTACGTATTACCTATCATTGCTAAAACTTGCTATCCTCAGCAGCGCCAGAACCTGTTTTTATTACAAGCAAGGAAAGAAATTTTTATTTGCTTTGCTGTTTGTACGTTGAAAAAGAATCATGTTGCAGTCTGGTTTAAAAAGCTTTAAATTTATATTAGTTGCTTTAACACTGAATTTTTGGCAAATCAAATTGTTGTGGAGTCTGATTTTGTTAGCCATCTCACAACTGCTAAAGAAAATGTTGCGCAGGGGATTAGGTGACCATATAGATAATCAGAATTCGGTCAATATGCAAATCACCAGTTTTATTCGGTAGCAATATTACTATGCACATAATTGATAACTGAACTTGTATCAGGGTTTTAGTGTTAAGTTGATGTACTCACAGTAGTTAGACATATAGTACATTACAGACGTAACCCATTGCTAAAAGGAATATAAGAATAAACCATAAAGCATTTGGTAATGCTTACATATCACAAATGTCTACAGGGTGAACAGTCCTAGATTTGATACTGCCTTTGTAGTTTGATATCAGGTCTCTCTCTTTTTCTCTTAATTGGGCTTTCTTAGTGTTGGTAGACGTTGCACTGTAGTTAGACGCTGTTATAACTTATAACTTGTATGTTTGAATAATGTTGATATCTTGAAATATAATTTAACCTCCATTCCTAAAATATGATTTCCTCAGCAACTCTGAAGCCAAAATTACCATTAGTTCTTGTGCTATCCTTATTCTATTACAGTATTTCCTTATTCATTGTAACTTATCTCTATGGAAAGATAAATTTCCCAGAGTTTGTTCTGATAAATCTATCTTATCATGTTCGAAAGATAAATTTCCCAGAGTTTGTTGTAATAAATCAGAAGGATTATTCTAGTAATTAGCTATATCTGACCAGTTCTATCACTTTTATATTCAGGCTATCGTGGAGTACGGATATGGATTAGTTGCAGTCAGATTTTCATACAGTCAGTTCAGTCATATAGTCTGA

Protein sequence

>MS.gene71532.t1

MLKPELGPQPQSKYDSEYDDDDDFAKCFSMYDDDDFAEEREAIDELIADYTEKSCNLSPFDAIYHPAVLELCGCVVPINLTEDLRPTLVTLSELALKNYNQNNQGTSFVFHDLVKCTTAVACGGGDLYYITFQAKAEEDPSNSHAITTFQAEAIVEYGYGLVAVRFSYSQFSHIV