RetrogeneDB ID: retro_pabe_1167

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:45119092..45119397(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDA1
• Ensembl ID: ENSPPYG00000009710
• Aliases: None
• Description: DET1- and DDB1-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RD86]

Sequence

>retro_pabe_1167
ATGGCAGATTTTTTGAAAGGACTGCCTGTCTACAACAAAAGCAATTTTAGTCGATTTCACGGGGACTCCGTGTGCAAAGC
CTCGAACCAATGGCCCTCAGTCTACCTGCCCACCCGAGAGTACCCGTCTGAACAGATCATCGTGACCGAAAAGACAAACA
TCCTCCTGCGCTACCAGCATCAGCAATGGACAAAAAGAACGCTGCCAAGAAGAAAGACCAGGAGCAAGTGGAGCTGGAAG
GCGAGACCTCGGCGCCCCTCCGCAAGGTGGCGCTGACCCACAGCCCAGAGATGCACGAGGACACT

Alignment

ORF - retro_pabe_1167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQW-DKKNAA
          MADFLKGLPVYNKSNFSRFH.DSVCKASN..PSVYLPTREYPSEQIIVTEKTNILLRY.HQQW.DKKNAA
Retrocopy MADFLKGLPVYNKSNFSRFHGDSVCKASNQWPSVYLPTREYPSEQIIVTEKTNILLRYQHQQW<DKKNAA

Parental  KKRDQEQVELEGESSAPPRKVARTDSPDMHEDT
          KK.DQEQVELEGE.SAP.RKVA.T.SP.MHEDT
Retrocopy KKKDQEQVELEGETSAPLRKVALTHSPEMHEDT

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	26.15 RPM
SRP007412_cerebellum	0.00 RPM	5.23 RPM
SRP007412_heart	0.00 RPM	5.18 RPM
SRP007412_kidney	0.03 RPM	8.88 RPM
SRP007412_liver	0.06 RPM	5.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1167 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1167 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1409
Pan troglodytes	retro_ptro_966
Gorilla gorilla	retro_ggor_1093
Macaca mulatta	retro_mmul_2248

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017068	3 retrocopies	retro_btau_1152, retro_btau_536, retro_btau_74,
Canis familiaris	ENSCAFG00000031251	3 retrocopies	retro_cfam_1089, retro_cfam_2033, retro_cfam_475,
Cavia porcellus	ENSCPOG00000006944	1 retrocopy	retro_cpor_435,
Felis catus	ENSFCAG00000001001	1 retrocopy	retro_fcat_487,
Homo sapiens	ENSG00000130311	1 retrocopy	retro_hsap_1409,
Gorilla gorilla	ENSGGOG00000005802	1 retrocopy	retro_ggor_1093,
Microcebus murinus	ENSMICG00000001763	1 retrocopy	retro_mmur_1162,
Myotis lucifugus	ENSMLUG00000003990	1 retrocopy	retro_mluc_1014,
Macaca mulatta	ENSMMUG00000016231	1 retrocopy	retro_mmul_2248,
Nomascus leucogenys	ENSNLEG00000005738	2 retrocopies	retro_nleu_1427, retro_nleu_1428,
Otolemur garnettii	ENSOGAG00000003701	1 retrocopy	retro_ogar_2375,
Pongo abelii	ENSPPYG00000009710	2 retrocopies	retro_pabe_1167 , retro_pabe_1214,
Pan troglodytes	ENSPTRG00000010668	1 retrocopy	retro_ptro_966,
Rattus norvegicus	ENSRNOG00000039417	1 retrocopy	retro_rnor_1511,