RetrogeneDB ID: retro_pabe_2889

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:90002220..90002536(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSPPYG00000005723
• Aliases: None
• Description: adaptor-related protein complex 4, sigma 1 subunit [Source:HGNC Symbol;Acc:575]

Sequence

>retro_pabe_2889
ATGATAAAATTTTTCCTCATGGTGAATAAACAAGGGCAGACTCGACTTTTTAAGTACTATGAACATGTGGATATTAATAA
GCGTACACTTCTGGAAACAGAAGTCATAAAGAGCTGTCTCTCCTCGATCCAATGAACAATGCTCTTTCATTGAATATAAG
GATTTTAAGCTGGTATATCGGCAGTATGCAGCTCTCTTCGTTGTGGTTGGAGTTAATGACACTGAGAACAAGATGGCTAT
TTATGAATTTATTCATAACTTTGTGGAAGTTTTAGATGAGTGTTTCAGCTGAGTAAGTGAATTAGATATAATGTTT

Alignment

ORF - retro_pabe_2889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.51 %
• Parental protein coverage: 66.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIKFFLMVNKQGQTRLSKYYEHVDINKRTLLETEVIKSCLS-RSNEQCSFIEYKDFKLIYRQYAALFIVV
          MIKFFLMVNKQGQTRL.KYYEHVDINKRTLLETEVIKSCLS.RSNEQCSFIEYKDFKL.YRQYAALF.VV
Retrocopy MIKFFLMVNKQGQTRLFKYYEHVDINKRTLLETEVIKSCLS>RSNEQCSFIEYKDFKLVYRQYAALFVVV

Parental  GVNDTENEMAIYEFIHNFVEVLDEYFSRVSELDVSF
          GVNDTEN.MAIYEFIHNFVEVLDE.FS.VSELD..F
Retrocopy GVNDTENKMAIYEFIHNFVEVLDECFS*VSELDIMF

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	0.50 RPM	3.43 RPM
SRP007412_cerebellum	0.85 RPM	1.82 RPM
SRP007412_heart	0.24 RPM	0.78 RPM
SRP007412_kidney	0.03 RPM	0.40 RPM
SRP007412_liver	0.06 RPM	0.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2889 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2889 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3496
Pan troglodytes	retro_ptro_2368
Gorilla gorilla	retro_ggor_2363
Macaca mulatta	retro_mmul_17

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013301	4 retrocopies	retro_chof_2345, retro_chof_2677, retro_chof_393, retro_chof_820,
Callithrix jacchus	ENSCJAG00000005786	1 retrocopy	retro_cjac_2742,
Dipodomys ordii	ENSDORG00000009468	1 retrocopy	retro_dord_595,
Erinaceus europaeus	ENSEEUG00000013009	1 retrocopy	retro_eeur_301,
Homo sapiens	ENSG00000100478	1 retrocopy	retro_hsap_3496,
Gorilla gorilla	ENSGGOG00000003198	1 retrocopy	retro_ggor_2363,
Myotis lucifugus	ENSMLUG00000011671	1 retrocopy	retro_mluc_1841,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Nomascus leucogenys	ENSNLEG00000015901	1 retrocopy	retro_nleu_788,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889 ,
Pan troglodytes	ENSPTRG00000006239	1 retrocopy	retro_ptro_2368,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455,
Rattus norvegicus	ENSRNOG00000005765	1 retrocopy	retro_rnor_2200,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,