AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1422270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1422270 MtrunA17_Chr3g0129411 97.647 85 2 0 1 85 35 119 1.24e-57 172
Msa1422270 MtrunA17_Chr8g0383481 52.941 85 32 4 1 85 36 112 9.19e-21 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAAATAGTGCACAAATTT+TGG 0.112038 tig0025353:-38953 Msa1422270:exon
CCATATGGATATGTTAATTT+AGG 0.228692 tig0025353:+39406 None:intergenic
TCCTATATATAGACACATTT+TGG 0.251593 tig0025353:+39429 None:intergenic
TCCATCCATATTCAAGTAAA+AGG 0.259194 tig0025353:-39263 Msa1422270:intron
CAATTAACCATGTTAGTATC+TGG 0.347082 tig0025353:-38764 Msa1422270:three_prime_UTR
ATAAGGTGGTGATAATGTTT+TGG 0.354103 tig0025353:-38732 Msa1422270:three_prime_UTR
TGCACTATTTAATTGTGAAT+TGG 0.396593 tig0025353:+38963 None:intergenic
GTATCTGGATCTAGAATATA+AGG 0.397126 tig0025353:-38749 Msa1422270:three_prime_UTR
GCCAAAATGTGTCTATATAT+AGG 0.397555 tig0025353:-39430 Msa1422270:five_prime_UTR
ATTGGTGGTTTCCTTGATGC+TGG 0.439868 tig0025353:+38981 None:intergenic
TGTTGACATCCTCACTACTT+TGG 0.458998 tig0025353:+39099 None:intergenic
CAACAAAGCTCAACAACATA+AGG 0.461599 tig0025353:-39081 Msa1422270:CDS
ACTATTTAATTGTGAATTGG+TGG 0.515565 tig0025353:+38966 None:intergenic
CCTAAATTAACATATCCATA+TGG 0.523592 tig0025353:-39406 Msa1422270:five_prime_UTR
GACATGTTTAAGCTAAAAGA+AGG 0.527331 tig0025353:-39047 Msa1422270:CDS
AAATAGCTATTCTATAGCTA+TGG 0.532562 tig0025353:-38887 Msa1422270:three_prime_UTR
TATGGATGGAGAAGAAGCAA+AGG 0.568511 tig0025353:+39276 None:intergenic
TGGATTATACTCCAGCATCA+AGG 0.596772 tig0025353:-38992 Msa1422270:CDS
AATAAACAACCAAAGTAGTG+AGG 0.645718 tig0025353:-39108 Msa1422270:CDS
CAAAGCTCAACAACATAAGG+AGG 0.647677 tig0025353:-39078 Msa1422270:CDS
ATGTTTAAGCTAAAAGAAGG+AGG 0.667536 tig0025353:-39044 Msa1422270:CDS
AAAGAAGGAGGAGATAACGT+TGG 0.669136 tig0025353:-39032 Msa1422270:CDS
TCTAGATCCAGATACTAACA+TGG 0.690048 tig0025353:+38757 None:intergenic
TCTGGATCTAGAATATAAGG+TGG 0.701138 tig0025353:-38746 Msa1422270:three_prime_UTR
TGATGCTGGAGTATAATCCA+TGG 0.719915 tig0025353:+38995 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAAATATTACAACAT+TGG - tig0025353:38939-38958 Msa1422270:three_prime_UTR 10.0%
!! AATTAAACAGAAAATAAAAA+TGG + tig0025353:38978-38997 None:intergenic 10.0%
!!! AATTTTTCTTACATTTTTTT+TGG - tig0025353:38998-39017 Msa1422270:CDS 10.0%
!!! TGTAATATTTTTTTTAGCTA+TGG + tig0025353:38935-38954 None:intergenic 15.0%
!!! AATTGCTTTTAACTTTAAGA+TGG - tig0025353:38811-38830 Msa1422270:three_prime_UTR 20.0%
!!! ATTAAATAGTGCACAAATTT+TGG - tig0025353:39200-39219 Msa1422270:intron 20.0%
!! TCCTATATATAGACACATTT+TGG + tig0025353:38727-38746 None:intergenic 25.0%
! CCATATGGATATGTTAATTT+AGG + tig0025353:38750-38769 None:intergenic 25.0%
! CCTAAATTAACATATCCATA+TGG - tig0025353:38747-38766 Msa1422270:three_prime_UTR 25.0%
!! CTTTTTCTGAATATACCATA+TGG + tig0025353:38765-38784 None:intergenic 25.0%
! ACTATTTAATTGTGAATTGG+TGG + tig0025353:39190-39209 None:intergenic 25.0%
! TGCACTATTTAATTGTGAAT+TGG + tig0025353:39193-39212 None:intergenic 25.0%
! AAATAGCTATTCTATAGCTA+TGG - tig0025353:39266-39285 Msa1422270:CDS 25.0%
GCCAAAATGTGTCTATATAT+AGG - tig0025353:38723-38742 Msa1422270:three_prime_UTR 30.0%
TCCATCCATATTCAAGTAAA+AGG - tig0025353:38890-38909 Msa1422270:three_prime_UTR 30.0%
! ACCTTTTACTTGAATATGGA+TGG + tig0025353:38894-38913 None:intergenic 30.0%
! AGGTACCTTTTACTTGAATA+TGG + tig0025353:38898-38917 None:intergenic 30.0%
! CTATGGATATTTGAAGCAAA+AGG + tig0025353:38918-38937 None:intergenic 30.0%
AATAAACAACCAAAGTAGTG+AGG - tig0025353:39045-39064 Msa1422270:CDS 30.0%
GACATGTTTAAGCTAAAAGA+AGG - tig0025353:39106-39125 Msa1422270:CDS 30.0%
ATGTTTAAGCTAAAAGAAGG+AGG - tig0025353:39109-39128 Msa1422270:CDS 30.0%
CAATTAACCATGTTAGTATC+TGG - tig0025353:39389-39408 Msa1422270:five_prime_UTR 30.0%
! GTATCTGGATCTAGAATATA+AGG - tig0025353:39404-39423 Msa1422270:five_prime_UTR 30.0%
!! ATAAGGTGGTGATAATGTTT+TGG - tig0025353:39421-39440 Msa1422270:five_prime_UTR 30.0%
CAACAAAGCTCAACAACATA+AGG - tig0025353:39072-39091 Msa1422270:CDS 35.0%
TCTAGATCCAGATACTAACA+TGG + tig0025353:39399-39418 None:intergenic 35.0%
! TCTGGATCTAGAATATAAGG+TGG - tig0025353:39407-39426 Msa1422270:five_prime_UTR 35.0%
TATGGATGGAGAAGAAGCAA+AGG + tig0025353:38880-38899 None:intergenic 40.0%
TGTTGACATCCTCACTACTT+TGG + tig0025353:39057-39076 None:intergenic 40.0%
CAAAGCTCAACAACATAAGG+AGG - tig0025353:39075-39094 Msa1422270:CDS 40.0%
AAAGAAGGAGGAGATAACGT+TGG - tig0025353:39121-39140 Msa1422270:CDS 40.0%
!!! TGGTTCTGATGTTTTCACCA+TGG - tig0025353:39141-39160 Msa1422270:intron 40.0%
TGATGCTGGAGTATAATCCA+TGG + tig0025353:39161-39180 None:intergenic 40.0%
TGGATTATACTCCAGCATCA+AGG - tig0025353:39161-39180 Msa1422270:intron 40.0%
! ATTGGTGGTTTCCTTGATGC+TGG + tig0025353:39175-39194 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
tig0025353 gene 38716 39459 38716 ID=Msa1422270;Name=Msa1422270
tig0025353 mRNA 38716 39459 38716 ID=Msa1422270-mRNA-1;Parent=Msa1422270;Name=Msa1422270-mRNA-1;_AED=0.08;_eAED=0.08;_QI=114|1|1|1|1|1|2|255|85
tig0025353 exon 38716 39146 38716 ID=Msa1422270-mRNA-1:exon:2477;Parent=Msa1422270-mRNA-1
tig0025353 exon 39264 39459 39264 ID=Msa1422270-mRNA-1:exon:2476;Parent=Msa1422270-mRNA-1
tig0025353 five_prime_UTR 39346 39459 39346 ID=Msa1422270-mRNA-1:five_prime_utr;Parent=Msa1422270-mRNA-1
tig0025353 CDS 39264 39345 39264 ID=Msa1422270-mRNA-1:cds;Parent=Msa1422270-mRNA-1
tig0025353 CDS 38971 39146 38971 ID=Msa1422270-mRNA-1:cds;Parent=Msa1422270-mRNA-1
tig0025353 three_prime_UTR 38716 38970 38716 ID=Msa1422270-mRNA-1:three_prime_utr;Parent=Msa1422270-mRNA-1
Gene Sequence

>Msa1422270

ATGGTTGCTTCACAAAACAAACGCATTCTACAAGTGATTGTTGTTCTCCTTTGCTTCTTCTCCATCCATATTCAAGTAAAAGCAAGAGTATTGAAAGAAATAAACAACCAAAGTAGTGAGGATGTCAACAAAGCTCAACAACATAAGGAGGTACATGCTGACATGTTTAAGCTAAAAGAAGGAGGAGATAACGTTGGTTCTGATGTTTTCACCATGGATTATACTCCAGCATCAAGGAAACCACCAATTCACAATTAA

Protein sequence

>Msa1422270

MVASQNKRILQVIVVLLCFFSIHIQVKARVLKEINNQSSEDVNKAQQHKEVHADMFKLKEGGDNVGSDVFTMDYTPASRKPPIHN*