AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene074278

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 32 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCCTCGGCTCATCAGTTT+TGG 0.286371 6.2:-13761282 None:intergenic
CAACCCTCAGGTATGTCATT+TGG 0.310524 6.2:+13761454 MS.gene074278:CDS
AACCCTCAGGTATGTCATTT+GGG 0.353608 6.2:+13761455 MS.gene074278:CDS
GATTTGCTTCCACCTGGTGC+TGG 0.403266 6.2:+13761074 MS.gene074278:CDS
GCAATTCAAACGGATCATAT+TGG 0.403266 6.2:-13761205 None:intergenic
CCTTGTGTGAGGGAACAAAA+AGG 0.407725 6.2:-13761240 None:intergenic
CCGAGGAGGCATTGTAGAAA+GGG 0.473376 6.2:+13761296 MS.gene074278:CDS
ATCTATGAAATAACGAACAT+AGG 0.482241 6.2:-13761491 None:intergenic
AAAACGCAATCAAAACTAGT+TGG 0.483313 6.2:+13761405 MS.gene074278:CDS
GCCGAGGAGGCATTGTAGAA+AGG 0.491519 6.2:+13761295 MS.gene074278:CDS
TCTATGAAATAACGAACATA+GGG 0.500536 6.2:-13761490 None:intergenic
TGCTGGAGTTGATGATGTGT+TGG 0.510278 6.2:+13761337 MS.gene074278:CDS
CCCTTTCTACAATGCCTCCT+CGG 0.527304 6.2:-13761296 None:intergenic
GCAATGGATTTGCTTCCACC+TGG 0.532019 6.2:+13761068 None:intergenic
CAAACGGATCATATTGGTAC+AGG 0.534644 6.2:-13761199 None:intergenic
GAAGGGACGAAGCCAGCACC+AGG 0.543610 6.2:-13761086 None:intergenic
TGGAGTTGATGATGTGTTGG+TGG 0.544087 6.2:+13761340 MS.gene074278:CDS
GCTGTCGGAGATATTACTGC+TGG 0.559286 6.2:+13761320 MS.gene074278:CDS
TGAGCAAGATGCAATTCAAA+CGG 0.561766 6.2:-13761215 None:intergenic
CAGTAAAACTCCCTTGTGTG+AGG 0.577220 6.2:-13761251 None:intergenic
CACTCAGGTTAACAACCCTC+AGG 0.577476 6.2:+13761442 MS.gene074278:CDS
TAACAAGGAGTTCGTCAGAA+GGG 0.582203 6.2:-13761103 None:intergenic
CATTGTAGAAAGGGAGCTGT+CGG 0.587159 6.2:+13761305 MS.gene074278:CDS
TTCCCAAATGACATACCTGA+GGG 0.589048 6.2:-13761457 None:intergenic
GGAGTTGATGATGTGTTGGT+GGG 0.604152 6.2:+13761341 MS.gene074278:CDS
AGTAAAACTCCCTTGTGTGA+GGG 0.618109 6.2:-13761250 None:intergenic
TTTCCCAAATGACATACCTG+AGG 0.629144 6.2:-13761458 None:intergenic
CCAAAACTGATGAGCCGAGG+AGG 0.639982 6.2:+13761282 MS.gene074278:CDS
GGGACGAAGCCAGCACCAGG+TGG 0.645386 6.2:-13761083 None:intergenic
CTAACAAGGAGTTCGTCAGA+AGG 0.653784 6.2:-13761104 None:intergenic
CTGCCAAAACTGATGAGCCG+AGG 0.655541 6.2:+13761279 MS.gene074278:CDS
GACTATGTACGAATACACTC+AGG 0.677311 6.2:+13761427 MS.gene074278:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCTCTCTTCTTTTTCTATAT+AGG + chr6.2:13761371-13761390 MS.gene074278:CDS 25.0%
!!! AACCTCTTAATTGTTTTTGT+TGG - chr6.2:13761141-13761160 None:intergenic 25.0%
AAAACGCAATCAAAACTAGT+TGG + chr6.2:13761405-13761424 MS.gene074278:CDS 30.0%
TGCCAACAAAAACAATTAAG+AGG + chr6.2:13761136-13761155 MS.gene074278:intron 30.0%
!!! CTTAATTGTTTTTGTTGGCA+AGG - chr6.2:13761136-13761155 None:intergenic 30.0%
!!! TAGTTTTGATTGCGTTTTGA+GGG - chr6.2:13761403-13761422 None:intergenic 30.0%
GCAATTCAAACGGATCATAT+TGG - chr6.2:13761208-13761227 None:intergenic 35.0%
TAAGAGGTTCAGAATTTCCA+TGG + chr6.2:13761152-13761171 MS.gene074278:intron 35.0%
TGAGCAAGATGCAATTCAAA+CGG - chr6.2:13761218-13761237 None:intergenic 35.0%
!!! AGTTTTGATTGCGTTTTGAG+GGG - chr6.2:13761402-13761421 None:intergenic 35.0%
!!! CTAGTTTTGATTGCGTTTTG+AGG - chr6.2:13761404-13761423 None:intergenic 35.0%
AGTAAAACTCCCTTGTGTGA+GGG - chr6.2:13761253-13761272 None:intergenic 40.0%
CAAACGGATCATATTGGTAC+AGG - chr6.2:13761202-13761221 None:intergenic 40.0%
GACTATGTACGAATACACTC+AGG + chr6.2:13761427-13761446 MS.gene074278:CDS 40.0%
TAACAAGGAGTTCGTCAGAA+GGG - chr6.2:13761106-13761125 None:intergenic 40.0%
TTCCCAAATGACATACCTGA+GGG - chr6.2:13761460-13761479 None:intergenic 40.0%
TTTCCCAAATGACATACCTG+AGG - chr6.2:13761461-13761480 None:intergenic 40.0%
! AACCCTCAGGTATGTCATTT+GGG + chr6.2:13761455-13761474 MS.gene074278:CDS 40.0%
! CTTTTTGTTCCCTCACACAA+GGG + chr6.2:13761241-13761260 MS.gene074278:CDS 40.0%
CAACCCTCAGGTATGTCATT+TGG + chr6.2:13761454-13761473 MS.gene074278:CDS 45.0%
CAGTAAAACTCCCTTGTGTG+AGG - chr6.2:13761254-13761273 None:intergenic 45.0%
CATTGTAGAAAGGGAGCTGT+CGG + chr6.2:13761305-13761324 MS.gene074278:CDS 45.0%
CCTTAATCAGGTCAGAACCA+TGG - chr6.2:13761172-13761191 None:intergenic 45.0%
CCTTGTGTGAGGGAACAAAA+AGG - chr6.2:13761243-13761262 None:intergenic 45.0%
CTAACAAGGAGTTCGTCAGA+AGG - chr6.2:13761107-13761126 None:intergenic 45.0%
TGGCAAGGTAGTAGCTAACA+AGG - chr6.2:13761121-13761140 None:intergenic 45.0%
! CCTTTTTGTTCCCTCACACA+AGG + chr6.2:13761240-13761259 MS.gene074278:CDS 45.0%
!! CCATGGTTCTGACCTGATTA+AGG + chr6.2:13761169-13761188 MS.gene074278:intron 45.0%
!! GGAGTTGATGATGTGTTGGT+GGG + chr6.2:13761341-13761360 MS.gene074278:CDS 45.0%
!! TGCTGGAGTTGATGATGTGT+TGG + chr6.2:13761337-13761356 MS.gene074278:CDS 45.0%
!! TGGAGTTGATGATGTGTTGG+TGG + chr6.2:13761340-13761359 MS.gene074278:CDS 45.0%
CACTCAGGTTAACAACCCTC+AGG + chr6.2:13761442-13761461 MS.gene074278:CDS 50.0%
CCCTTTCTACAATGCCTCCT+CGG - chr6.2:13761299-13761318 None:intergenic 50.0%
GCTGTCGGAGATATTACTGC+TGG + chr6.2:13761320-13761339 MS.gene074278:CDS 50.0%
!! CCGAGGAGGCATTGTAGAAA+GGG + chr6.2:13761296-13761315 MS.gene074278:CDS 50.0%
ACAGGCGCAGCTCCTTAATC+AGG - chr6.2:13761184-13761203 None:intergenic 55.0%
CCAAAACTGATGAGCCGAGG+AGG + chr6.2:13761282-13761301 MS.gene074278:CDS 55.0%
CTGCCAAAACTGATGAGCCG+AGG + chr6.2:13761279-13761298 MS.gene074278:CDS 55.0%
! CCTCCTCGGCTCATCAGTTT+TGG - chr6.2:13761285-13761304 None:intergenic 55.0%
! GATTTGCTTCCACCTGGTGC+TGG + chr6.2:13761074-13761093 MS.gene074278:CDS 55.0%
!! GCCGAGGAGGCATTGTAGAA+AGG + chr6.2:13761295-13761314 MS.gene074278:CDS 55.0%
GAAGGGACGAAGCCAGCACC+AGG - chr6.2:13761089-13761108 None:intergenic 65.0%
GGGACGAAGCCAGCACCAGG+TGG - chr6.2:13761086-13761105 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 13761071 13761511 13761071 ID=MS.gene074278
chr6.2 mRNA 13761071 13761511 13761071 ID=MS.gene074278.t1;Parent=MS.gene074278
chr6.2 exon 13761071 13761121 13761071 ID=MS.gene074278.t1.exon1;Parent=MS.gene074278.t1
chr6.2 CDS 13761071 13761121 13761071 ID=cds.MS.gene074278.t1;Parent=MS.gene074278.t1
chr6.2 exon 13761191 13761511 13761191 ID=MS.gene074278.t1.exon2;Parent=MS.gene074278.t1
chr6.2 CDS 13761191 13761511 13761191 ID=cds.MS.gene074278.t1;Parent=MS.gene074278.t1
Gene Sequence

>MS.gene074278

ATGGATTTGCTTCCACCTGGTGCTGGCTTCGTCCCTTCTGACGAACTCCTTGTTAGCTACTACCTTGCCAACAAAAACAATTAAGAGGTTCAGAATTTCCATGGTTCTGACCTGATTAAGGAGCTGCGCCTGTACCAATATGATCCGTTTGAATTGCATCTTGCTCAGTCCTTTTTGTTCCCTCACACAAGGGAGTTTTACTGCTTCACTGCCAAAACTGATGAGCCGAGGAGGCATTGTAGAAAGGGAGCTGTCGGAGATATTACTGCTGGAGTTGATGATGTGTTGGTGGGAAAGAAGTCTCTCTTCTTTTTCTATATAGGAAATTCCCCTCAAAACGCAATCAAAACTAGTTGGACTATGTACGAATACACTCAGGTTAACAACCCTCAGGTATGTCATTTGGGAAAACTAACTTTCCCTATGTTCGTTATTTCATAG
Protein sequence

>MS.gene074278.t1

MDLLPPGAGFVPSDELLELRLYQYDPFELHLAQSFLFPHTREFYCFTAKTDEPRRHCRKGAVGDITAGVDDVLVGKKSLFFFYIGNSPQNAIKTSWTMYEYTQVNNPQVCHLGKLTFPMFVIS