RetrogeneDB ID: retro_ptro_1793

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:73381146..73381602(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042114
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCDC137
• Ensembl ID: ENSPTRG00000009767
• Aliases: None
• Description: coiled-coil domain containing 137 [Source:HGNC Symbol;Acc:33451]

Sequence

>retro_ptro_1793
ATGGCACAAGCTGGAGGTGGGGCAGCGGTGCCCAGGGCGCCGGCGGGTCCTGGGAGTCCCCGGCGGGAGCAGCAGCCAGC
AGCAAGTGCAGCTGCTGGGGAAGCAGCGCCCAGCCCTGTGGTCCAGGATTCACAACAAAGAGGAGAAAGTGAATTGCAAG
CCCAAAACCCAGGACAAACAGGAGATCCCTTTCCGGCTCCGGGAGATTATGAGGAGCCGCTGGGAGATGAAAAATCCGAC
CGGTAACAAGAAGAGGAAGAAAGCGGCCCAGGTGGCCCCAGAAAGACACTGGAAAGGGAAGCAAAGGGAGTGGAGCCCGA
CATTGCCGTCCCCAAGTTCAAGCAGAGGAAGGGGGAGTCCGACTAGGCCTATATCCAGCACATGCTATTCCTCAGCAAGA
ACCAGGCCACCCAGCAGCCAGAGGTCCAGGCAGCTCCCAAGGAGAAGTCTGAGCTG

Alignment

ORF - retro_ptro_1793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.88 %
• Parental protein coverage: 84.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGAGRGGAVSRVQAGPGSPRRAR-GRQQVQPLGKQRPAPWPGLRSKEKKKVNCKPKNQDEQEIPFRLRE
          MA.AG.G.AV.R..AGPGSPRR.....QQVQ.LGKQRPA.W.....KE.K.VNCKPK.QD.QEIPFRLRE
Retrocopy MAQAGGGAAVPRAPAGPGSPRREQ>SQQQVQLLGKQRPALWSRIHNKEEK-VNCKPKTQDKQEIPFRLRE

Parental  IMRSRQEMKNPISNKKRKKAAQVT-FRKTLEKEAKGEEPDIAVPKFKQRKGESDGAYIQRMPFQKRRLDK
          IMRSR.EMKNP..NKKRKKAAQV...RKTLE.EAKG.EPDIAVPKFKQRKGESD.AYIQ.M.F.......
Retrocopy IMRSRWEMKNPTGNKKRKKAAQVA<PRKTLEREAKGVEPDIAVPKFKQRKGESD*AYIQHMLFLSK--NQ

Parental  VRRKKEEKAADRLEQEL
          .....E..AA.....EL
Retrocopy ATQQPEVQAAPKEKSEL

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	3.04 RPM
SRP007412_cerebellum	0.00 RPM	5.48 RPM
SRP007412_heart	0.00 RPM	1.31 RPM
SRP007412_kidney	0.03 RPM	3.50 RPM
SRP007412_liver	0.00 RPM	3.86 RPM
SRP007412_testis	0.00 RPM	3.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1793 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1793 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793 ,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,