RetrogeneDB ID: retro_pabe_1679

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:53590797..53591126(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459C1416
• Ensembl ID: ENSPPYG00000001711
• Aliases: None
• Description: transmembrane protein 50A [Source:RefSeq peptide;Acc:NP_001127413]

Sequence

>retro_pabe_1679
GAATGTATTGACTGGAGTGAGAGAAGAAATGTTGTGGCGTCTGTTGCGACAGGTATATTGTTTTTTACAGGCTGGTGGAT
AATGACGCAGCTGTGGTGTATCGTAGGCCACAACAGTTGAACCGTGACTTTCACACATGTGGTGTATTTCCCACATTGGC
TTTCTTCATGATAAATGCCATATCCAATGCTCAGGTGAGAGGTGATAGCTATGAAAGTGGTTATTTAGGAAGAACAGGTC
CTTGAGTTTGGCTTTTCGTTGGTTTCATGTTGATGTTTGGGGTACTTATTGCTTCCATGTGGATTCTTTTTGGTGCATAT
GTTACCCAA

Alignment

ORF - retro_pabe_1679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.39 %
• Parental protein coverage: 70.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECIDWGEKRNTIASIAAGVLFFTGWWIII-DAAVIYPTMKDFNHSYHACGVIATIAFLMINAVSNGQVRG
          ECIDW.E.RN..AS.A.G.LFFTG.W.I..DAAV.Y......N...H.CGV..T.AF.MINA.SN.QVRG
Retrocopy ECIDWSERRNVVASVATGILFFTG-WWIM<DAAVVYRRPQQLNRDFHTCGVFPTLAFFMINAISNAQVRG

Parental  DSYSEGCLGQTGARIWLFIGFMLAFGSLIASMWILFGGYVAK
          DSY..G.LG.TG...WLF.GFML.FG.LIASMWILFG.YV..
Retrocopy DSYESGYLGRTGP*VWLFVGFMLMFGVLIASMWILFGAYVTQ

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	2.32 RPM	71.27 RPM
SRP007412_cerebellum	1.95 RPM	65.06 RPM
SRP007412_heart	1.23 RPM	27.57 RPM
SRP007412_kidney	2.78 RPM	63.84 RPM
SRP007412_liver	1.53 RPM	39.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1679 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1679 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2066
Pan troglodytes	retro_ptro_1379
Gorilla gorilla	retro_ggor_1487
Macaca mulatta	retro_mmul_1408

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018575	1 retrocopy	retro_cjac_1677,
Cavia porcellus	ENSCPOG00000012615	1 retrocopy	retro_cpor_707,
Echinops telfairi	ENSETEG00000007483	1 retrocopy	retro_etel_2061,
Macropus eugenii	ENSMEUG00000002060	1 retrocopy	retro_meug_1270,
Macaca mulatta	ENSMMUG00000032217	1 retrocopy	retro_mmul_1408,
Ochotona princeps	ENSOPRG00000001182	2 retrocopies	retro_opri_546, retro_opri_62,
Pongo abelii	ENSPPYG00000001711	1 retrocopy	retro_pabe_1679 ,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329,