RetrogeneDB ID: retro_ggor_2363

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:89142953..89143270(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSGGOG00000003198
• Aliases: None
• Description: None

Sequence

>retro_ggor_2363
ATGATAAAATTTTTCCTCATGGTGAATAAACAAGGGCAGACTCGACTTTTTAAGTACTATGAACATGTGGATATTAATAA
GCGTACACTTCTGGAAACAGAAGTCATAAAGAGCTGTCTCTCTTCGATCCAATGAACAATGCTCTTTCATTGAATTATAA
GGATTTTAAGCTGATATATCGGCAGTATGCATCTCTCTTCGTTGTGGTTGGAGTTAATGACACTGAGAACAAGATGGCTA
TTTATGAATTCATTCATAACTTTGTGGAAGTTTTAGATGAGTATTTCAGCTGAGTAAGTGAATTAGATATAATGTTT

Alignment

ORF - retro_ggor_2363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• 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.MAIYEFIHNFVEVLDEYFS.VSELD..F
Retrocopy VGVNDTENKMAIYEFIHNFVEVLDEYFS*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	0.10 RPM	5.08 RPM
SRP007412_cerebellum	0.12 RPM	3.27 RPM
SRP007412_heart	0.00 RPM	0.69 RPM
SRP007412_kidney	0.08 RPM	1.27 RPM
SRP007412_liver	0.08 RPM	0.98 RPM
SRP007412_testis	0.00 RPM	3.32 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2363 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3496
Pan troglodytes	retro_ptro_2368
Pongo abelii	retro_pabe_2889
Macaca mulatta	retro_mmul_17

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 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,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,