AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene73707

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTAAGTTTCTTGCTGAAAT+TGG 0.181561 6.3:-35250827 None:intergenic
AACGCACCATCCCTACTATA+TGG 0.339161 6.3:-35251238 None:intergenic
GAAGATATACTGCTAGATAT+TGG 0.387033 6.3:+35251385 MS.gene73707:CDS
GCCTTTGTATTCCATATAGT+AGG 0.387617 6.3:+35251227 MS.gene73707:CDS
CAACTGCTTTCACTAGATAA+TGG 0.398746 6.3:+35251048 MS.gene73707:CDS
ATGGTGTTGTAGAATGCTTA+AGG 0.434944 6.3:+35251158 MS.gene73707:intron
TATGGAATACAAAGGCCAAT+AGG 0.452781 6.3:-35251220 None:intergenic
ATTTGTTACTAGGCTTTGGA+TGG 0.480492 6.3:+35251341 MS.gene73707:intron
TCAGCAAGAAACTTAAGCTA+TGG 0.487709 6.3:+35250833 MS.gene73707:CDS
CCTTTGTATTCCATATAGTA+GGG 0.498392 6.3:+35251228 MS.gene73707:CDS
AGAAACTTAAGCTATGGATC+TGG 0.503060 6.3:+35250839 MS.gene73707:CDS
TTTGTTACTAGGCTTTGGAT+GGG 0.557463 6.3:+35251342 MS.gene73707:intron
TGTATTCCATATAGTAGGGA+TGG 0.560836 6.3:+35251232 MS.gene73707:CDS
CCTAATTTCATGTAATCACT+GGG 0.561960 6.3:-35251410 None:intergenic
CTTTGGATGGGAATCATATG+TGG 0.565052 6.3:+35251354 MS.gene73707:CDS
TGGGAATCATATGTGGACTT+TGG 0.581283 6.3:+35251361 MS.gene73707:CDS
CCCTACTATATGGAATACAA+AGG 0.640596 6.3:-35251228 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAACATATATATTTATT+TGG - chr6.3:35251110-35251129 None:intergenic 10.0%
!!! ATTATGATTTTTTTTTGACT+TGG + chr6.3:35250918-35250937 MS.gene73707:intron 15.0%
!! ACAAAATATCTCATTGTTAA+GGG + chr6.3:35251269-35251288 MS.gene73707:intron 20.0%
!!! AATTACTTTTACTATCCTAT+TGG + chr6.3:35251205-35251224 MS.gene73707:CDS 20.0%
!!! CTAAATTGAAATTTGTTACT+AGG + chr6.3:35251331-35251350 MS.gene73707:intron 20.0%
!!! TCTTTTTATGTTTGATATGA+GGG + chr6.3:35250891-35250910 MS.gene73707:intron 20.0%
!!! TTCTTTTTATGTTTGATATG+AGG + chr6.3:35250890-35250909 MS.gene73707:intron 20.0%
! CACAAAATATCTCATTGTTA+AGG + chr6.3:35251268-35251287 MS.gene73707:intron 25.0%
! TTAGCTATTATGTACATGAT+AGG + chr6.3:35251128-35251147 MS.gene73707:intron 25.0%
! TTTCAATTTAGTAAGCATGA+AGG - chr6.3:35251322-35251341 None:intergenic 25.0%
CCTTTGTATTCCATATAGTA+GGG + chr6.3:35251228-35251247 MS.gene73707:CDS 30.0%
CTTAAGTTTCTTGCTGAAAT+TGG - chr6.3:35250830-35250849 None:intergenic 30.0%
GAAGATATACTGCTAGATAT+TGG + chr6.3:35251385-35251404 MS.gene73707:CDS 30.0%
GTACATGATAGGAGAATTTA+TGG + chr6.3:35251139-35251158 MS.gene73707:intron 30.0%
!! TGAAATTTGTTACTAGGCTT+TGG + chr6.3:35251337-35251356 MS.gene73707:intron 30.0%
AGAAACTTAAGCTATGGATC+TGG + chr6.3:35250839-35250858 MS.gene73707:CDS 35.0%
CAACTGCTTTCACTAGATAA+TGG + chr6.3:35251048-35251067 MS.gene73707:CDS 35.0%
CCCTACTATATGGAATACAA+AGG - chr6.3:35251231-35251250 None:intergenic 35.0%
GCCTTTGTATTCCATATAGT+AGG + chr6.3:35251227-35251246 MS.gene73707:CDS 35.0%
TATGGAATACAAAGGCCAAT+AGG - chr6.3:35251223-35251242 None:intergenic 35.0%
TCAGCAAGAAACTTAAGCTA+TGG + chr6.3:35250833-35250852 MS.gene73707:CDS 35.0%
TGGTTTAGTACTGCATTACT+AGG + chr6.3:35250938-35250957 MS.gene73707:intron 35.0%
TGTATTCCATATAGTAGGGA+TGG + chr6.3:35251232-35251251 MS.gene73707:CDS 35.0%
!! ATGGTGTTGTAGAATGCTTA+AGG + chr6.3:35251158-35251177 MS.gene73707:intron 35.0%
!! ATTTGTTACTAGGCTTTGGA+TGG + chr6.3:35251341-35251360 MS.gene73707:intron 35.0%
!! TTTGTTACTAGGCTTTGGAT+GGG + chr6.3:35251342-35251361 MS.gene73707:intron 35.0%
CTTTGGATGGGAATCATATG+TGG + chr6.3:35251354-35251373 MS.gene73707:CDS 40.0%
TGGGAATCATATGTGGACTT+TGG + chr6.3:35251361-35251380 MS.gene73707:CDS 40.0%
AACGCACCATCCCTACTATA+TGG - chr6.3:35251241-35251260 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 35250787 35251417 35250787 ID=MS.gene73707
chr6.3 mRNA 35250787 35251417 35250787 ID=MS.gene73707.t1;Parent=MS.gene73707
chr6.3 exon 35250787 35250880 35250787 ID=MS.gene73707.t1.exon1;Parent=MS.gene73707.t1
chr6.3 CDS 35250787 35250880 35250787 ID=cds.MS.gene73707.t1;Parent=MS.gene73707.t1
chr6.3 exon 35251010 35251069 35251010 ID=MS.gene73707.t1.exon2;Parent=MS.gene73707.t1
chr6.3 CDS 35251010 35251069 35251010 ID=cds.MS.gene73707.t1;Parent=MS.gene73707.t1
chr6.3 exon 35251170 35251253 35251170 ID=MS.gene73707.t1.exon3;Parent=MS.gene73707.t1
chr6.3 CDS 35251170 35251253 35251170 ID=cds.MS.gene73707.t1;Parent=MS.gene73707.t1
chr6.3 exon 35251353 35251417 35251353 ID=MS.gene73707.t1.exon4;Parent=MS.gene73707.t1
chr6.3 CDS 35251353 35251417 35251353 ID=cds.MS.gene73707.t1;Parent=MS.gene73707.t1
Gene Sequence

>MS.gene73707

ATGAATAATGCTGAATTCTTTGCAATTACGAGTGCTTTTGCCAATTTCAGCAAGAAACTTAAGCTATGGATCTGGAGCGCAGCTAACAAAAATTGTATGTATTTTCTTTTTATGTTTGATATGAGGGATTCATTATGATTTTTTTTTGACTTGGTTTAGTACTGCATTACTAGGTTTAATATTATATTCATTCTAACTATTTTTTAACATGTTGCTTTTGCAGCAAGTTATTGCACTGTTCACTTTTGTTTTGTATGTAATCAACTGCTTTCACTAGATAATGGTATATCTTTATACTAAGTTATTAGTTTCTTTTCTATCCAAATAAATATATATGTTTGTTAGCTATTATGTACATGATAGGAGAATTTATGGTGTTGTAGAATGCTTAAGGAATGAGCAGAAACTATGTTGTGCGAATTACTTTTACTATCCTATTGGCCTTTGTATTCCATATAGTAGGGATGGTGCGTTTATTTCTCACAAAATATCTCATTGTTAAGGGTTGTGTTTTCTTGTATTTTTGCTTGTTCCTTCATGCTTACTAAATTGAAATTTGTTACTAGGCTTTGGATGGGAATCATATGTGGACTTTGGTGAAGATATACTGCTAGATATTGGATCCCAGTGA
Protein sequence

>MS.gene73707.t1

MNNAEFFAITSAFANFSKKLKLWIWSAANKNSSYCTVHFCFVCNQLLSLDNECLRNEQKLCCANYFYYPIGLCIPYSRDGFGWESYVDFGEDILLDIGSQ