RetrogeneDB ID: retro_pabe_2780

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:127219691..127220083(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf146
• Ensembl ID: ENSPPYG00000001156
• Aliases: None
• Description: chromosome 1 open reading frame 146 [Source:HGNC Symbol;Acc:24032]

Sequence

>retro_pabe_2780
GTTAGTATTAGCTCATTTCTTTAGTGTTATGAAGTTGTAGCTGCCCTAGAAAATTAAAGCCATAAGTTTTGGTAATCAAA
CAAATGGAAAATGGATCAATTATATTTCCTTTTTCTGTAGTTACATTTTAATTGATGGATGCTAAGGAATGCCTATGTTA
GCTGAAGCACTATTTCTAGCAAAATATGAGAAGTTCATAAAATATTCACTGAAATAACTTTTTGAATTTATCTGCTGCCC
TTTATGGACTTGAGAAATGGGAAATGTTGAGTATTCGGCAGAGATTTCTGAGTAGTAATTTACAAATAGTTTCAGTATAA
AACATAGTTAATGTTACTAATCTTGTACACACTATAGCTAAGACCACCCTATATAGAAATATGGATAGCATA

Alignment

ORF - retro_pabe_2780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.52 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IIISSSLKSYEVATALENRSHK-VRYSDSVENGSIIFSLSGVAFLLMDTKECL-LSTEEIFLAKIEKFI-
          ..ISS.L..YEV..ALEN.SHK.V......ENGSIIF..S.V.F.LMD.KECL....E..FLAK.EKFI.
Retrocopy VSISSFL*CYEVVAALEN*SHK<VLVIKQMENGSIIFPFSVVTF*LMDAKECL<MLAEALFLAKYEKFI>

Parental  NIHQNSFLVLSAALHGPEEWKLMFRIQQRFLGCNLRILPVHNTVNAINLMCTIAKTTSKPYIDSI
          NIH.N.FL.LSAAL.G.E.W..M..I.QRFL..NL.I..V.N.VN..NL..TIAKTT.....DSI
Retrocopy NIH*NNFLNLSAALYGLEKWE-MLSIRQRFLSSNLQIVSV*NIVNVTNLVHTIAKTTLYRNMDSI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.12 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2780 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2780 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3381
Pan troglodytes	retro_ptro_2298
Gorilla gorilla	retro_ggor_2289
Macaca mulatta	retro_mmul_2107
Callithrix jacchus	retro_cjac_1817

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027936	1 retrocopy	retro_btau_490,
Choloepus hoffmanni	ENSCHOG00000004012	1 retrocopy	retro_chof_2167,
Callithrix jacchus	ENSCJAG00000017547	1 retrocopy	retro_cjac_1817,
Erinaceus europaeus	ENSEEUG00000003083	1 retrocopy	retro_eeur_601,
Homo sapiens	ENSG00000203910	1 retrocopy	retro_hsap_3381,
Gorilla gorilla	ENSGGOG00000006653	1 retrocopy	retro_ggor_2289,
Macropus eugenii	ENSMEUG00000013311	1 retrocopy	retro_meug_143,
Myotis lucifugus	ENSMLUG00000016984	1 retrocopy	retro_mluc_1260,
Macaca mulatta	ENSMMUG00000010094	1 retrocopy	retro_mmul_2107,
Nomascus leucogenys	ENSNLEG00000010426	1 retrocopy	retro_nleu_970,
Pongo abelii	ENSPPYG00000001156	1 retrocopy	retro_pabe_2780 ,
Pan troglodytes	ENSPTRG00000030530	1 retrocopy	retro_ptro_2298,
Ictidomys tridecemlineatus	ENSSTOG00000012506	1 retrocopy	retro_itri_404,
Tursiops truncatus	ENSTTRG00000014426	1 retrocopy	retro_ttru_1727,