AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0579520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0579520 MtrunA17_Chr4g0042801 86.275 102 14 0 1 102 140 241 6.30e-55 172
Msa0579520 MtrunA17_Chr4g0042781 68.033 122 39 0 1 122 163 284 1.68e-51 164
Msa0579520 MtrunA17_Chr4g0042791 63.492 126 42 2 1 122 155 280 2.98e-34 119
Msa0579520 MtrunA17_Chr4g0042811 37.903 124 58 3 4 111 195 315 2.79e-17 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0579520 AT3G11810.1 41.129 124 50 2 11 111 202 325 2.51e-18 79.0
Msa0579520 AT2G03330.1 41.935 124 49 3 11 111 239 362 4.32e-12 62.0

Find 22 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATAAAACTATGGAATTA+AGG 0.231917 4_1:+84277830 None:intergenic
ATTGAAAAGAAGTTGGAAAT+TGG 0.291924 4_1:-84278090 Msa0579520:CDS
TTTCGATCTGTTACTTGTTT+GGG 0.296706 4_1:-84278043 Msa0579520:CDS
GGTGGAATCAAGCTGGGGTT+TGG 0.409217 4_1:-84278117 Msa0579520:CDS
TTGTTGTGGTGGAATCAAGC+TGG 0.436772 4_1:-84278124 Msa0579520:CDS
TGGAACCATTGAAAAGAAGT+TGG 0.460136 4_1:-84278097 Msa0579520:CDS
AGCATAAGCATTGTTTGTAT+AGG 0.477285 4_1:+84277957 None:intergenic
TGTTGTGGTGGAATCAAGCT+GGG 0.493170 4_1:-84278123 Msa0579520:CDS
TGGAGAGGAGGAATTTGAGA+AGG 0.502925 4_1:-84277874 Msa0579520:CDS
GTGATATTGCTATGGATAAG+TGG 0.521603 4_1:-84278011 Msa0579520:CDS
AAGGAGAAGCACACTGAAGT+TGG 0.523808 4_1:-84277894 Msa0579520:CDS
GGTGAAAGGAATGAGAAAGT+TGG 0.528700 4_1:-84278069 Msa0579520:CDS
TCTTAGAAGTGATATTGCTA+TGG 0.547707 4_1:-84278019 Msa0579520:CDS
GCACACTGAAGTTGGAGAGG+AGG 0.554051 4_1:-84277886 Msa0579520:CDS
ATTTGAGAAGGCAAAGGACG+AGG 0.569011 4_1:-84277862 Msa0579520:CDS
AGAAGTTGGAAATTGGTGAA+AGG 0.577351 4_1:-84278083 Msa0579520:CDS
AGTGAAAGTTATTGTTGTGG+TGG 0.580518 4_1:-84278135 Msa0579520:CDS
GAAGCACACTGAAGTTGGAG+AGG 0.605440 4_1:-84277889 Msa0579520:CDS
GGAGGAATTTGAGAAGGCAA+AGG 0.622313 4_1:-84277868 Msa0579520:CDS
CTTAGTGAAAGTTATTGTTG+TGG 0.623664 4_1:-84278138 Msa0579520:CDS
GTTGTGGTGGAATCAAGCTG+GGG 0.681004 4_1:-84278122 Msa0579520:CDS
GGTGGTATACATATACTGCA+AGG 0.690547 4_1:-84277913 Msa0579520:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTACAATATTGCTGTTTTTA+CGG - chr4_1:84278090-84278109 Msa0579520:CDS 20.0%
!! AATTTCCAACTTCTTTTCAA+TGG + chr4_1:84277935-84277954 None:intergenic 25.0%
! ATTGAAAAGAAGTTGGAAAT+TGG - chr4_1:84277934-84277953 Msa0579520:CDS 25.0%
!!! GCTTGTTTTTATGACGTATT+TGG - chr4_1:84277850-84277869 Msa0579520:CDS 30.0%
CTTAGTGAAAGTTATTGTTG+TGG - chr4_1:84277886-84277905 Msa0579520:CDS 30.0%
!! TTTTCGATCTGTTACTTGTT+TGG - chr4_1:84277980-84277999 Msa0579520:CDS 30.0%
! TTTCGATCTGTTACTTGTTT+GGG - chr4_1:84277981-84278000 Msa0579520:CDS 30.0%
TCTTAGAAGTGATATTGCTA+TGG - chr4_1:84278005-84278024 Msa0579520:CDS 30.0%
! AGCATAAGCATTGTTTGTAT+AGG + chr4_1:84278070-84278089 None:intergenic 30.0%
AGTGAAAGTTATTGTTGTGG+TGG - chr4_1:84277889-84277908 Msa0579520:CDS 35.0%
TGGAACCATTGAAAAGAAGT+TGG - chr4_1:84277927-84277946 Msa0579520:CDS 35.0%
AGAAGTTGGAAATTGGTGAA+AGG - chr4_1:84277941-84277960 Msa0579520:CDS 35.0%
GTGATATTGCTATGGATAAG+TGG - chr4_1:84278013-84278032 Msa0579520:CDS 35.0%
!!! CAATATTGCTGTTTTTACGG+TGG - chr4_1:84278093-84278112 Msa0579520:CDS 35.0%
GGTGAAAGGAATGAGAAAGT+TGG - chr4_1:84277955-84277974 Msa0579520:CDS 40.0%
GGTGGTATACATATACTGCA+AGG - chr4_1:84278111-84278130 Msa0579520:CDS 40.0%
! TTGTTGTGGTGGAATCAAGC+TGG - chr4_1:84277900-84277919 Msa0579520:CDS 45.0%
! TGTTGTGGTGGAATCAAGCT+GGG - chr4_1:84277901-84277920 Msa0579520:CDS 45.0%
! AAGGAGAAGCACACTGAAGT+TGG - chr4_1:84278130-84278149 Msa0579520:CDS 45.0%
TGGAGAGGAGGAATTTGAGA+AGG - chr4_1:84278150-84278169 Msa0579520:CDS 45.0%
GGAGGAATTTGAGAAGGCAA+AGG - chr4_1:84278156-84278175 Msa0579520:CDS 45.0%
ATTTGAGAAGGCAAAGGACG+AGG - chr4_1:84278162-84278181 Msa0579520:CDS 45.0%
! GTTGTGGTGGAATCAAGCTG+GGG - chr4_1:84277902-84277921 Msa0579520:CDS 50.0%
GAAGCACACTGAAGTTGGAG+AGG - chr4_1:84278135-84278154 Msa0579520:CDS 50.0%
GGTGGAATCAAGCTGGGGTT+TGG - chr4_1:84277907-84277926 Msa0579520:CDS 55.0%
GCACACTGAAGTTGGAGAGG+AGG - chr4_1:84278138-84278157 Msa0579520:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 84277839 84278207 84277839 ID=Msa0579520;Name=Msa0579520
chr4_1 mRNA 84277839 84278207 84277839 ID=Msa0579520-mRNA-1;Parent=Msa0579520;Name=Msa0579520-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|-1|0|1|-1|1|1|0|122
chr4_1 exon 84277839 84278207 84277839 ID=Msa0579520-mRNA-1:exon:30836;Parent=Msa0579520-mRNA-1
chr4_1 CDS 84277839 84278207 84277839 ID=Msa0579520-mRNA-1:cds;Parent=Msa0579520-mRNA-1
Gene Sequence

>Msa0579520

ATGGTTTTAATGCTTGTTTTTATGACGTATTTGGTAGTTAACTTGAGCTTAGTGAAAGTTATTGTTGTGGTGGAATCAAGCTGGGGTTTGGAACCATTGAAAAGAAGTTGGAAATTGGTGAAAGGAATGAGAAAGTTGGTATTTTCGATCTGTTACTTGTTTGGGTTCTTAGAAGTGATATTGCTATGGATAAGTGGTTACAATTTAGTACTGATTTTCGTGATTTCTCCTATACAAACAATGCTTATGCTTTACAATATTGCTGTTTTTACGGTGGTATACATATACTGCAAGGAGAAGCACACTGAAGTTGGAGAGGAGGAATTTGAGAAGGCAAAGGACGAGGCTAGTTTGTCCTTAATTCCATAG

Protein sequence

>Msa0579520

MVLMLVFMTYLVVNLSLVKVIVVVESSWGLEPLKRSWKLVKGMRKLVFSICYLFGFLEVILLWISGYNLVLIFVISPIQTMLMLYNIAVFTVVYIYCKEKHTEVGEEEFEKAKDEASLSLIP*