RetrogeneDB ID: retro_pabe_2540

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:103181859..103182060(-)
• Located in intron of: ENSPPYG00000014944

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBCA
• Ensembl ID: ENSPPYG00000015579
• Aliases: None
• Description: tubulin folding cofactor A [Source:HGNC Symbol;Acc:11579]

Sequence

>retro_pabe_2540
AGAGCTGAAGATGGTGAAAATGATGCCATTAAAAAGCAGGCAGAAATTCTGTGAGAATCCCAGGTGATAAGCCTTGTTTG
CCAGCACAGGTTGGAAGCCGCATATACCGTTCTTTGGCAGATGTTAGAAAGTGAAAAAGACTTGGAAGAAGCTGAGGAAT
ATAAAGAACATTTAGTACTGCATTCAGTGAAGTTAGAAGCC

Alignment

ORF - retro_pabe_2540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAEDGENYDIKKQAEILQESRMMIPDCQRRLEAAYLDLQQILESEKDLEETEEYKEARLVLDSVKLEA
          RAEDGEN..IKKQAEIL.ES......CQ.RLEAAY..L.Q.LESEKDLEE.EEYKE..LVL.SVKLEA
Retrocopy RAEDGENDAIKKQAEIL*ESQVISLVCQHRLEAAYTVLWQMLESEKDLEEAEEYKE-HLVLHSVKLEA

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	33.67 RPM
SRP007412_cerebellum	0.00 RPM	31.37 RPM
SRP007412_heart	0.12 RPM	22.34 RPM
SRP007412_kidney	0.03 RPM	48.53 RPM
SRP007412_liver	0.03 RPM	26.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2540 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2540 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3065
Pan troglodytes	retro_ptro_2067

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Cavia porcellus	ENSCPOG00000012187	1 retrocopy	retro_cpor_930,
Echinops telfairi	ENSETEG00000016572	1 retrocopy	retro_etel_93,
Homo sapiens	ENSG00000171530	3 retrocopies	retro_hsap_3065, retro_hsap_346, retro_hsap_4667,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Mus musculus	ENSMUSG00000042043	3 retrocopies	retro_mmus_1486, retro_mmus_2839, retro_mmus_2970,
Otolemur garnettii	ENSOGAG00000010198	1 retrocopy	retro_ogar_3193,
Ochotona princeps	ENSOPRG00000002460	4 retrocopies	retro_opri_550, retro_opri_727, retro_opri_879, retro_opri_91,
Pongo abelii	ENSPPYG00000015579	2 retrocopies	retro_pabe_2540 , retro_pabe_350,
Pan troglodytes	ENSPTRG00000017013	2 retrocopies	retro_ptro_2067, retro_ptro_274,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Sorex araneus	ENSSARG00000009943	1 retrocopy	retro_sara_699,