RetrogeneDB ID: retro_pabe_3108

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:146366787..146367089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HYPK
• Ensembl ID: ENSPPYG00000006424
• Aliases: None
• Description: huntingtin interacting protein K [Source:HGNC Symbol;Acc:18418]

Sequence

>retro_pabe_3108
CCGAGAAGCCAGGGAAACATGACTGACAGCGGTGCCGCGGACTTGGAGCAGGTCACCGACTATGCAGAGGAGAAGGAGAT
CAGAGTTCCAATCTGGAGACGGCCACGTCTGTGATTGGAGACAGAAGGTCCCGGGAGCAGAAAGCCAAACGGGAGGGGAA
GAAAGAACTGGCAATAGTCACTATCAAGAAGGAAGATCTGGAGCTGATAATGACCGAGATGGAGAGATCTCGAGCAGCAG
CGGAAGGCAGCTTGCGGGAACACATGAGCAACGTGGTAGAGGGGCTTATTGCTCTAACCAAC

Alignment

ORF - retro_pabe_3108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 78.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPEKPRKHDSGAADLERVTDYAEEKEI-QSSNLETAMSVIGDRRSREQKAKQEREKELAKVTIKKEDLEL
          P.......DSGAADLE.VTDYAEEKEI.QSSNLETA.SVIGDRRSREQKAK.E..KELA.VTIKKEDLEL
Retrocopy PRSQGNMTDSGAADLEQVTDYAEEKEI<QSSNLETATSVIGDRRSREQKAKREGKKELAIVTIKKEDLEL

Parental  IMTEMEISRAAAERSLREHMGNVVEALIALTN
          IMTEME.SRAAAE.SLREHM.NVVE.LIALTN
Retrocopy IMTEMERSRAAAEGSLREHMSNVVEGLIALTN

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	0.00 RPM	38.70 RPM
SRP007412_cerebellum	0.00 RPM	35.02 RPM
SRP007412_heart	0.00 RPM	50.75 RPM
SRP007412_kidney	0.00 RPM	72.46 RPM
SRP007412_liver	0.00 RPM	67.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3108 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3108 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3806
Pan troglodytes	retro_ptro_2582
Gorilla gorilla	retro_ggor_2557

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002541	2 retrocopies	retro_cjac_1352, retro_cjac_748,
Echinops telfairi	ENSETEG00000007464	3 retrocopies	retro_etel_1504, retro_etel_1616, retro_etel_1830,
Gorilla gorilla	ENSGGOG00000014809	1 retrocopy	retro_ggor_2557,
Macropus eugenii	ENSMEUG00000013059	1 retrocopy	retro_meug_1583,
Monodelphis domestica	ENSMODG00000017744	2 retrocopies	retro_mdom_26, retro_mdom_306,
Nomascus leucogenys	ENSNLEG00000005454	1 retrocopy	retro_nleu_2150,
Oryctolagus cuniculus	ENSOCUG00000001161	2 retrocopies	retro_ocun_1395, retro_ocun_967,
Otolemur garnettii	ENSOGAG00000010201	1 retrocopy	retro_ogar_1064,
Pongo abelii	ENSPPYG00000006424	1 retrocopy	retro_pabe_3108 ,
Pan troglodytes	ENSPTRG00000038721	1 retrocopy	retro_ptro_2582,
Rattus norvegicus	ENSRNOG00000015703	1 retrocopy	retro_rnor_2477,
Ictidomys tridecemlineatus	ENSSTOG00000006916	2 retrocopies	retro_itri_1861, retro_itri_1864,
Tursiops truncatus	ENSTTRG00000003726	1 retrocopy	retro_ttru_1499,