RetrogeneDB ID: retro_ptro_966

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:43775985..43776183(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000038961
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDA1
• Ensembl ID: ENSPTRG00000010668
• Aliases: None
• Description: DET1 and DDB1 associated 1 [Source:UniProtKB/TrEMBL;Acc:K7CQT7]

Sequence

>retro_ptro_966
ATGGCAGATTTTTTGAAAGGACTGCCTGTCTACAACAAAAGCAATTTTAGTCGATTTCACGGGGACTCCGTGTGCAAAGC
CTCGAACCAACGGCCCTCAGTCTACCTGCCCACCCGAGAGTACCCGTCTGAACAGATCATCGTGACCGAAAAGACAAACA
TCCTCCTGCGCTACCTGCATCAGCAATGGACAAAAAGA

Alignment

ORF - retro_ptro_966 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKK
          MADFLKGLPVYNKSNFSRFH.DSVCKASN.RPSVYLPTREYPSEQIIVTEKTNILLRYLHQQW.K.
Retrocopy MADFLKGLPVYNKSNFSRFHGDSVCKASNQRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWTKR

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	1.04 RPM	7.67 RPM
SRP007412_cerebellum	0.90 RPM	7.96 RPM
SRP007412_heart	0.96 RPM	6.38 RPM
SRP007412_kidney	1.02 RPM	5.41 RPM
SRP007412_liver	1.31 RPM	10.41 RPM
SRP007412_testis	3.58 RPM	18.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_966 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_966 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_966 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1409
Gorilla gorilla	retro_ggor_1093
Pongo abelii	retro_pabe_1167
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,