RetrogeneDB ID: retro_pabe_1393

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:45765479..45765710(-)
• Located in intron of: ENSPPYG00000007410

Retrocopy information

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

Parental gene information

• Parental gene symbol: C10orf57
• Ensembl ID: ENSPPYG00000002293
• Aliases: TMEM254, C10orf57
• Description: Transmembrane protein C10orf57 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R9A6]

Sequence

>retro_pabe_1393
GCCAGCAGTGCAGCTGCCACCTACTTCTGTCCAGCCAGACCCTTGCCCTTGCTGGTCACAGTCCTGGGGCTGGACTGCTT
CACATGGGTTGTCTTTTGGCCTTGGAGTATCCTTTATCAGAGCCTTGGGCCCCTGGACTCCTTCACTCAGTACTTGGTGG
GCCACCATCACACCCTCCTGTGCAGTGGGTATTGGCTTGCCTGGCTGAATCATGTGGGAGAGTCCTTGTAT

Alignment

ORF - retro_pabe_1393 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 62.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATAAGAAYFQRGSLFWFTVITLSFGYYTWVVFWPQSIPYQNLGPLGPFTQYLVDHHHTLLCNGYWLAWLI
          A..A.A.YF.........V..L.....TWVVFWP.SI.YQ.LGPL..FTQYLV.HHHTLLC.GYWLAWL.
Retrocopy ASSAAATYFCPARPLPLLVTVLGLDCFTWVVFWPWSILYQSLGPLDSFTQYLVGHHHTLLCSGYWLAWLN

Parental  HVGESLY
          HVGESLY
Retrocopy HVGESLY

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	12.00 RPM
SRP007412_cerebellum	0.12 RPM	7.17 RPM
SRP007412_heart	0.03 RPM	1.99 RPM
SRP007412_kidney	0.07 RPM	8.42 RPM
SRP007412_liver	0.06 RPM	10.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1393 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1393 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012986	4 retrocopies	retro_amel_1410, retro_amel_1554, retro_amel_1777, retro_amel_821,
Bos taurus	ENSBTAG00000001656	1 retrocopy	retro_btau_316,
Homo sapiens	ENSG00000133678	1 retrocopy	retro_hsap_1692,
Mustela putorius furo	ENSMPUG00000003613	2 retrocopies	retro_mputfur_400, retro_mputfur_407,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Nomascus leucogenys	ENSNLEG00000010657	1 retrocopy	retro_nleu_1337,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Pongo abelii	ENSPPYG00000002293	1 retrocopy	retro_pabe_1393 ,