RetrogeneDB ID: retro_opri_651

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2199:42752..43097(+)
• 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_651
CCAGGAGCCACCCCAGCTGCTCACTACCTCCCTGCTCCCCTCGCAGGCCCGGGCGGAGAACACATCCCGCACGTGGAGTG
TGTGTCCAACACCCTCCTGCATGTGAACGAATGGGACCCCGAAGGCGACGCTGAGATCTTGATATGTGGACGACCTTATT
ATCAGAAGGACGTATCCAAGCTCATTATGAACTTGGCCGACTATCACCGCCAGCTCCGGCTGCAAAGTACGGGAATGGGC
GGGGCTACTCAGAGCCAACCCCGGCTCCCAGGGAGGGATTCGCGTGCTTCCGGGCCGCAGCTGGCCTGAGAGGTCTCTGC
CAGAGATGTAAAAGGCCAAATTGAA

Alignment

ORF - retro_opri_651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.48 %
• Parental protein coverage: 70.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKAVRLEAWLVEAIFGPGGEHIPHVECVSNTLLHVNEWDPEGDAEILICGRPYYQKDVSKLIMNLADYHR
          P.A......L.....GPGGEHIPHVECVSNTLLHVNEWDPEGDAEILICGRPYYQKDVSKLIMNLADYHR
Retrocopy PGATPAAHYLPAPLAGPGGEHIPHVECVSNTLLHVNEWDPEGDAEILICGRPYYQKDVSKLIMNLADYHR

Parental  QLRLQSSKKAGRPQSPVEVHGVGAPPS-PTHVGEASTRQSQTKVD
          QLRLQS....G..QS.....G.....S.P....E.S.R.......
Retrocopy QLRLQSTGMGGATQSQPRLPGRDSRASGPQLA*EVSARDVKGQIE

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_651 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,