RetrogeneDB ID: retro_ptro_2368

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:89699367..89699684(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSPTRG00000006239
• Aliases: None
• Description: adaptor-related protein complex 4, sigma 1 subunit [Source:HGNC Symbol;Acc:575]

Sequence

>retro_ptro_2368
ATGATAAAATTTTTCCTCATGGTGAATAAACAAGGGCAGACTCGACTTTTTAAGTACTATGAACATGTGGATATTAATAA
GCGTACACTTCTGGAAACAGAAGTCATAAAGAGCTGTCTCTCCTCGATCCAATGAACAATGCTCTTTCATTGAATTATAA
GGATTTTAAGCTGATATATCGGCAGTATGCATCTCTCTTCGTTGTGGTTGGAGTTAATGACACTGAGAACAAGGTGGCTA
TTTATGAATTCATTCATAACTTTGTGGAAGTTTTAGATGAGTATTTCAGCTGAGTAAGTGAATTAGATATAATGTTT

Alignment

ORF - retro_ptro_2368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.65 %
• Parental protein coverage: 66.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIKFFLMVNKQGQTRLSKYYEHVDINKRTLLETEVIKSCLS-RSNEQCSFIE-YKDFKLIYRQYAALFIV
          MIKFFLMVNKQGQTRL.KYYEHVDINKRTLLETEVIKSCLS.RSNEQCSFIE.YKDFKLIYRQYA.LF.V
Retrocopy MIKFFLMVNKQGQTRLFKYYEHVDINKRTLLETEVIKSCLS>RSNEQCSFIE>YKDFKLIYRQYASLFVV

Parental  VGVNDTENEMAIYEFIHNFVEVLDEYFSRVSELDVSF
          VGVNDTEN..AIYEFIHNFVEVLDEYFS.VSELD..F
Retrocopy VGVNDTENKVAIYEFIHNFVEVLDEYFS*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	0.05 RPM	4.77 RPM
SRP007412_cerebellum	0.11 RPM	4.30 RPM
SRP007412_heart	0.06 RPM	1.57 RPM
SRP007412_kidney	0.03 RPM	2.46 RPM
SRP007412_liver	0.00 RPM	0.59 RPM
SRP007412_testis	1.16 RPM	13.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2368 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2368 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3496
Gorilla gorilla	retro_ggor_2363
Pongo abelii	retro_pabe_2889
Macaca mulatta	retro_mmul_17

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Parental genes homology:

Parental genes homology involve 14 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,
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,
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 ,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Pan troglodytes	ENSPTRG00000019520	3 retrocopies	retro_ptro_1234, retro_ptro_24, retro_ptro_2554,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,