RetrogeneDB ID: retro_opri_406

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1101:222007..222454(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KHDC3L
• Ensembl ID: ENSOPRG00000013565
• Aliases: None
• Description: KH domain containing 3-like, subcortical maternal complex member [Source:HGNC Symbol;Acc:33699]

Sequence

>retro_opri_406
CTGCAGCAGCGGAAAGGAGAGCTATCCCAGGTGCTGGGGAACCTCACCAAACCGCCCAAGTGGTTCCACTCCGAATTCCT
CAAGAGTCCGAAGGCAGTCCGCCTGGAGGCTTGGTTGGTGGAAGCGATCTTTGGCCCGGGCGGAGAACACATCCCGCACG
TCGAGTGTGTGTCCAACACCCTCCTGCATGTGAACCAATGGGACCCCGAAGGCAATGCTGAGATCTTGATATGTGGACAA
CCTTATTATCAGAAGGACGTATCCAAGCTCATTATGAACTCGGCCGACTATCACTACCAGCTCTGGCTGCAAAGCTCCAA
GAAGGCCGGAAGACCGCAGTCTCCTGTGGAAGTCCACGAGGTTGAGACTCTGCCATCTCCCACCCATGTTGGCGAGGCCA
GCATGTAGCAGTCCCAGACCAAGGTCAATGAGGCTGAGACACAGGGC

Alignment

ORF - retro_opri_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 91.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQQREGELSQVLGNLTKPPKWFHSEFLKSPKAVRLEAWLVEAIFGPGGEHIPHVECVSNTLLHVNEWDPE
          LQQR.GELSQVLGNLTKPPKWFHSEFLKSPKAVRLEAWLVEAIFGPGGEHIPHVECVSNTLLHVN.WDPE
Retrocopy LQQRKGELSQVLGNLTKPPKWFHSEFLKSPKAVRLEAWLVEAIFGPGGEHIPHVECVSNTLLHVNQWDPE

Parental  GDAEILICGRPYYQKDVSKLIMNLADYHRQLRLQSSKKAGRPQSPVEVHGVGAPPSPTHVGEASTRQSQT
          G.AEILICG.PYYQKDVSKLIMN.ADYH.QL.LQSSKKAGRPQSPVEVH.V...PSPTHVGEAS..QSQT
Retrocopy GNAEILICGQPYYQKDVSKLIMNSADYHYQLWLQSSKKAGRPQSPVEVHEVETLPSPTHVGEASM*QSQT

Parental  KVDEAGTQG
          KV.EA.TQG
Retrocopy KVNEAETQG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_406 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007887	1 retrocopy	retro_amel_1880,
Callithrix jacchus	ENSCJAG00000009947	1 retrocopy	retro_cjac_1153,
Myotis lucifugus	ENSMLUG00000004469	1 retrocopy	retro_mluc_2196,
Ochotona princeps	ENSOPRG00000013565	3 retrocopies	retro_opri_322, retro_opri_406 , retro_opri_651,
Sorex araneus	ENSSARG00000003714	1 retrocopy	retro_sara_631,