RetrogeneDB ID: retro_ptro_2740

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:35147890..35148430(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000031009
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF5
• Ensembl ID: ENSPTRG00000018010
• Aliases: None
• Description: ring finger protein 5, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10068]

Sequence

>retro_ptro_2740
ATGGCAGCAGCGGAGGAGGAGGACGGGGGCCCCGAAGGGCCAAATCGCGAGCGGGGCGGGGCGGGCGCGACCTTCGAATG
TAATATATGTTTGGAGACTGCTCGGGAAGCTGTGGTCAGTGTGTGTGGCCACCTGTACTGTTGGCCATGTCTTCATCAGT
GGCTGGAGACACGGCCAGAACGGCAAGAGTGTCCAGTATGTAAAGCTGGGATCAGCAGAGAGAAGGTTGTCCCGCTTTAT
GGGCGAGGGAGCCAGAAGCCCCAGGATCCCAGATTAAAAACTCCACCCCGCCCCCAGGGCCAGAGACCAGCTCCAGAGAG
CAGAGCGGGATTCCAGCCATTTGGTGATACCGGGGGCTTCCACTTCTCATTTGGTGTTGGTGCTTTTCCCTTTGGCTTTT
TCACCATCGTCTTCAATGCCCATGAGCCTTTCCGCCGGGGTACAGGTGTGGATCTGGGACAGGGTCACCCGGCCTCCAGC
TGACAGGATTCCCTCTTCCTGTTTCTCGCCATCTTCTTCTTTTTTTGGCTGCTCAGTATT

Alignment

ORF - retro_ptro_2740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAG
          MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAG
Retrocopy MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAG

Parental  ISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFTTVFNA
          ISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESR.GFQPFGDTGGFHFSFGVGAFPFGFFT.VFNA
Retrocopy ISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRAGFQPFGDTGGFHFSFGVGAFPFGFFTIVFNA

Parental  HEPFRRGTGVDLGQGHPASSWQDSLFLFLAIFFFFWLLSI
          HEPFRRGTGVDLGQGHPASS.QDSLFLFLAIFFFFWLLSI
Retrocopy HEPFRRGTGVDLGQGHPASS*QDSLFLFLAIFFFFWLLSI

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	2.41 RPM	26.40 RPM
SRP007412_cerebellum	1.54 RPM	21.54 RPM
SRP007412_heart	1.72 RPM	18.42 RPM
SRP007412_kidney	3.32 RPM	46.34 RPM
SRP007412_liver	2.09 RPM	28.12 RPM
SRP007412_testis	0.11 RPM	6.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2740 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2740 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4046

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000016417	1 retrocopy	retro_ocun_1241,
Otolemur garnettii	ENSOGAG00000031466	1 retrocopy	retro_ogar_1951,
Oreochromis niloticus	ENSONIG00000013523	1 retrocopy	retro_onil_48,
Ochotona princeps	ENSOPRG00000004366	2 retrocopies	retro_opri_166, retro_opri_667,
Pan troglodytes	ENSPTRG00000018010	1 retrocopy	retro_ptro_2740 ,
Ictidomys tridecemlineatus	ENSSTOG00000024478	1 retrocopy	retro_itri_480,
Tupaia belangeri	ENSTBEG00000016320	1 retrocopy	retro_tbel_2183,