AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053581


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053581.t1 MTR_4g093660 98.824 85 1 0 1 85 1 85 4.01e-58 172
MS.gene053581.t1 MTR_2g009660 85.882 85 12 0 1 85 63 147 2.55e-50 155
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053581.t1 AT4G33640 80.769 78 15 0 1 78 1 78 1.09e-41 132
MS.gene053581.t1 AT4G33640 80.769 78 15 0 1 78 67 144 3.34e-41 132

Find 17 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCATTGTGAAGGTCACATT+TGG 0.398089 4.4:-21393348 MS.gene053581:intron
GAGTGATTTCCACATTATCA+TGG 0.446001 4.4:+21393208 None:intergenic
GAACACTCTTTCACGATGAT+CGG 0.491735 4.4:-21393326 MS.gene053581:CDS
AAGAGGAGGTTGAAAAGCTG+AGG 0.496528 4.4:-21394095 MS.gene053581:CDS
CCGAATCAGTTAGCAGCAGC+AGG 0.502169 4.4:+21393174 None:intergenic
CAGTTAGCAGCAGCAGGAGC+AGG 0.504867 4.4:+21393180 None:intergenic
CTTGGAAATGTTCAAGCAGA+TGG 0.516658 4.4:-21394057 MS.gene053581:CDS
AGGGAAGAAATCAAGAGGCT+TGG 0.527446 4.4:-21394075 MS.gene053581:CDS
TGTGAAGATGAACGTAGAAG+AGG 0.563453 4.4:-21394112 None:intergenic
GAAGATGAACGTAGAAGAGG+AGG 0.565552 4.4:-21394109 None:intergenic
AGAGGAGGTTGAAAAGCTGA+GGG 0.572997 4.4:-21394094 MS.gene053581:CDS
AATATATTTGAAGCACTCGT+CGG 0.601303 4.4:-21393297 MS.gene053581:CDS
TCAAGCAGATGGTTCTTGCA+AGG 0.604584 4.4:-21394046 MS.gene053581:intron
AGCTGAGGGAAGAAATCAAG+AGG 0.626324 4.4:-21394080 MS.gene053581:CDS
GACGGTGAACTACTGTTGCA+AGG 0.632747 4.4:-21393234 MS.gene053581:CDS
GCAAGGAGTCCATGATAATG+TGG 0.676630 4.4:-21393217 MS.gene053581:CDS
CGTAAAGTAGTTGCATACGA+CGG 0.749247 4.4:-21393252 MS.gene053581:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAAACAAATTAATGTAT+AGG + chr4.4:21393550-21393569 None:intergenic 10.0%
!! ATAATTGTAATTAAATGTGT+TGG - chr4.4:21393722-21393741 MS.gene053581:intron 15.0%
!! TATTATTGATATGATGTTTA+GGG + chr4.4:21393684-21393703 None:intergenic 15.0%
!!! AATTTGTTTATTATAAACCA+TGG - chr4.4:21393557-21393576 MS.gene053581:intron 15.0%
!! GAATCAAGTTCTTAATTAAA+AGG + chr4.4:21393344-21393363 None:intergenic 20.0%
!! GTATTATTGATATGATGTTT+AGG + chr4.4:21393685-21393704 None:intergenic 20.0%
!! TTTCATATGATATTTCGTAA+TGG + chr4.4:21393477-21393496 None:intergenic 20.0%
! AAATATGTAATGCATTGTGA+AGG - chr4.4:21393926-21393945 MS.gene053581:intron 25.0%
! ATGCATCATGAAAATGTATA+TGG + chr4.4:21393306-21393325 None:intergenic 25.0%
! CATTCCATATAAAACTGATA+TGG - chr4.4:21393603-21393622 MS.gene053581:intron 25.0%
! TAATGTATAGGTAGATACAT+TGG + chr4.4:21393538-21393557 None:intergenic 25.0%
! TCAGATCTAGATATATTGAT+GGG - chr4.4:21393362-21393381 MS.gene053581:intron 25.0%
! TTCAGATCTAGATATATTGA+TGG - chr4.4:21393361-21393380 MS.gene053581:intron 25.0%
! TTGTTTATTATAAACCATGG+AGG - chr4.4:21393560-21393579 MS.gene053581:intron 25.0%
!! GAAAATGTATATGGTTTGTA+AGG + chr4.4:21393297-21393316 None:intergenic 25.0%
!!! AATTTGCTGAAATAGTACTA+TGG - chr4.4:21393782-21393801 MS.gene053581:intron 25.0%
!!! CATATCAGTTTTATATGGAA+TGG + chr4.4:21393605-21393624 None:intergenic 25.0%
TATAGTGAGTGATGGTTAAT+TGG - chr4.4:21393832-21393851 MS.gene053581:intron 30.0%
TTCTTGCAAGGTATAACAAA+AGG - chr4.4:21393250-21393269 MS.gene053581:CDS 30.0%
! AATATATTTGAAGCACTCGT+CGG - chr4.4:21393987-21394006 MS.gene053581:intron 30.0%
! CTATATCTTCAGTTGATTCA+TGG + chr4.4:21393817-21393836 None:intergenic 30.0%
! TGATGGGTATTTATTGAATG+TGG - chr4.4:21393378-21393397 MS.gene053581:intron 30.0%
! TGGTCACTTTCTTATTCTTA+TGG - chr4.4:21393398-21393417 MS.gene053581:intron 30.0%
!! CTAGCCATATCAGTTTTATA+TGG + chr4.4:21393610-21393629 None:intergenic 30.0%
ACTGAAGATATAGTGAGTGA+TGG - chr4.4:21393824-21393843 MS.gene053581:intron 35.0%
GAGTGATTTCCACATTATCA+TGG + chr4.4:21394079-21394098 None:intergenic 35.0%
GTTAATGCGCATATGTGAAT+TGG - chr4.4:21393862-21393881 MS.gene053581:intron 35.0%
TCTTATGGATCTAGATCACA+AGG - chr4.4:21393413-21393432 MS.gene053581:intron 35.0%
CACAAGGTCATTCACAACAT+TGG - chr4.4:21393429-21393448 MS.gene053581:intron 40.0%
CGTAAAGTAGTTGCATACGA+CGG - chr4.4:21394032-21394051 MS.gene053581:intron 40.0%
CTTGGAAATGTTCAAGCAGA+TGG - chr4.4:21393227-21393246 MS.gene053581:CDS 40.0%
GAACACTCTTTCACGATGAT+CGG - chr4.4:21393958-21393977 MS.gene053581:intron 40.0%
TGCATTGTGAAGGTCACATT+TGG - chr4.4:21393936-21393955 MS.gene053581:intron 40.0%
AAGAGGAGGTTGAAAAGCTG+AGG - chr4.4:21393189-21393208 MS.gene053581:CDS 45.0%
AGAGGAGGTTGAAAAGCTGA+GGG - chr4.4:21393190-21393209 MS.gene053581:CDS 45.0%
AGCTGAGGGAAGAAATCAAG+AGG - chr4.4:21393204-21393223 MS.gene053581:CDS 45.0%
AGGGAAGAAATCAAGAGGCT+TGG - chr4.4:21393209-21393228 MS.gene053581:CDS 45.0%
TCAAGCAGATGGTTCTTGCA+AGG - chr4.4:21393238-21393257 MS.gene053581:CDS 45.0%
! GCAAGGAGTCCATGATAATG+TGG - chr4.4:21394067-21394086 MS.gene053581:CDS 45.0%
CGCATGATATCTCTCCTCCA+TGG + chr4.4:21393577-21393596 None:intergenic 50.0%
GACGGTGAACTACTGTTGCA+AGG - chr4.4:21394050-21394069 MS.gene053581:CDS 50.0%
CAGTTAGCAGCAGCAGGAGC+AGG + chr4.4:21394107-21394126 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 21393179 21394127 21393179 ID=MS.gene053581
chr4.4 mRNA 21393179 21394127 21393179 ID=MS.gene053581.t1;Parent=MS.gene053581
chr4.4 exon 21394047 21394127 21394047 ID=MS.gene053581.t1.exon1;Parent=MS.gene053581.t1
chr4.4 CDS 21394047 21394127 21394047 ID=cds.MS.gene053581.t1;Parent=MS.gene053581.t1
chr4.4 exon 21393179 21393358 21393179 ID=MS.gene053581.t1.exon2;Parent=MS.gene053581.t1
chr4.4 CDS 21393179 21393358 21393179 ID=cds.MS.gene053581.t1;Parent=MS.gene053581.t1
Gene Sequence

>MS.gene053581

ATGAACGTAGAAGAGGAGGTTGAAAAGCTGAGGGAAGAAATCAAGAGGCTTGGAAATGTTCAAGCAGATGGTTCTTGCAAGGTATAACAAAAGGATCTATATTCATCATTATTTTCCTTACAAACCATATACATTTTCATGATGCATATAGATAGATATAAGCCTTTTAATTAAGAACTTGATTCAGATCTAGATATATTGATGGGTATTTATTGAATGTGGTCACTTTCTTATTCTTATGGATCTAGATCACAAGGTCATTCACAACATTGGATCTTCATTTTCATTCACAGATCCATTACGAAATATCATATGAAACATGTGTTCTCACGAACATTAAACATATGCATAATTTACCAATGTATCTACCTATACATTAATTTGTTTATTATAAACCATGGAGGAGAGATATCATGCGAGAGTCCATTCCATATAAAACTGATATGGCTAGCAAAATTGAAGATAGTTGTCTCTTTTCAGTGTACAGAAGCATTGAAGTAAGCCCTAAACATCATATCAATAATACTTAGTTAAAACATTTGCATAATTGTAATTAAATGTGTTGGCATAAAGTGTGAATGTTTGTTACGTGTCATATTGATTAATTTGCTGAAATAGTACTATGGTATGAAAATCCATGAATCAACTGAAGATATAGTGAGTGATGGTTAATTGGTTTGCTTGTTAATGCGCATATGTGAATTGGTTTGCTTATGACACAATGCATAGAACTTTATTAGTTGAATGAAATATGTAATGCATTGTGAAGGTCACATTTGGAACACTCTTTCACGATGATCGGTGCGCAAATATATTTGAAGCACTCGTCGGTACACTAAGAGCTGCTAAAAAGCGTAAAGTAGTTGCATACGACGGTGAACTACTGTTGCAAGGAGTCCATGATAATGTGGAAATCACTCTTAATCCTGCTCCTGCTGCTGCTAACTGA

Protein sequence

>MS.gene053581.t1

MNVEEEVEKLREEIKRLGNVQADGSCKVTFGTLFHDDRCANIFEALVGTLRAAKKRKVVAYDGELLLQGVHDNVEITLNPAPAAAN