RetrogeneDB ID: retro_opri_524

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1510:206046..206655(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSOPRG00000015998
• Aliases: None
• Description: retinol dehydrogenase 13 (all-trans/9-cis) [Source:HGNC Symbol;Acc:19978]

Sequence

>retro_opri_524
GAAGAGCCCAGGCTGGATGTGTTGATCAACAATGCGGGAATCTTCCAGTGCCCTTACATGAGGACCGAAGATGGGTTTGA
GATGCAGTTTGGAGTGAACCACCTGGGGCACTTCCTACTCACCAATCTTCTCCTTGGCCTCCTGAAGAACTCAGCTCCCA
GCAGGATCATCGTCGTTTCTTCCAAACTTTATAAATATGGAGACATCAACTTTGACGACCTCAACAGTGAGCAGAGCTAC
AGTAAAAGCTTTTGCTACAGCCAAAGCAAACTGGCTAACATTCTTTTTACCAAAGAATTAGCCCGCCGACTTGAAGGCAC
AAATGTCACTGTGAATGTACTGCATCCTGGGGTGGTGCGGACCAACCTCGGGCGGCACATCCACATCCCACTCTTGGTGA
AGCCCCTTTTCAATTTGGTGTCTTGGGCTTTTTTCAAAACTCCAGCAGAAGGTGCCCAGACTTCCATTTATTTGGCCTCT
TCCCCCGAGGTGGAAGGGGTGTCTGGAAGGTACTTTGGGGACTGTAAAGAGGAAGAGCTACTACCCAAAGCTATGGATGA
GTCTGTTGCGCGGAAACTCTGGGACATCAGTGAAGTGATGGTTGGCATA

Alignment

ORF - retro_opri_524 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.31 %
• Parental protein coverage: 61.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEERVDILINNAAVMRCPHWTTEDGFEMQFGVNHLGHFLLTNLLLDKLKASAPSRIINLSSLAHVAGHID
          EE.R.D.LINNA....CP...TEDGFEMQFGVNHLGHFLLTNLLL..LK.SAPSRII..SS.....G.I.
Retrocopy EEPRLDVLINNAGIFQCPYMRTEDGFEMQFGVNHLGHFLLTNLLLGLLKNSAPSRIIVVSSKLYKYGDIN

Parental  FDDLNWQARRYDTKAAYCQSKLAVVLFTKELSRRLQGTGVTANALHPGVARTELGRHTGMHSSAFSSLTL
          FDDLN.....Y.....Y.QSKLA..LFTKEL.RRL.GT.VT.N.LHPGV.RT.LGRH...H.........
Retrocopy FDDLN-SEQSYSKSFCYSQSKLANILFTKELARRLEGTNVTVNVLHPGVVRTNLGRH--IHIPLLVKPLF

Parental  GPIFWLLVKSPQLAAQPSTYLAVAEELEGVSGKYFDGLREKAAAPEAEDEEVARRLWAESARLVGL
          ....W...K.P...AQ.S.YLA...E.EGVSG.YF....E....P.A.DE.VAR.LW..S...VG.
Retrocopy NLVSWAFFKTPAEGAQTSIYLASSPEVEGVSGRYFGDCKEEELLPKAMDESVARKLWDISEVMVGI

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_524 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.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338,
Ochotona princeps	ENSOPRG00000015998	2 retrocopies	retro_opri_286, retro_opri_524 ,
Petromyzon marinus	ENSPMAG00000009095	1 retrocopy	retro_pmar_3,
Pongo abelii	ENSPPYG00000010398	1 retrocopy	retro_pabe_1972,
Pan troglodytes	ENSPTRG00000011484	1 retrocopy	retro_ptro_1576,
Sorex araneus	ENSSARG00000003600	1 retrocopy	retro_sara_314,
Tupaia belangeri	ENSTBEG00000016531	1 retrocopy	retro_tbel_1570,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,