RetrogeneDB ID: retro_ptro_82

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:33352559..33353051(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000005860
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000042329
• Aliases: None
• Description: None

Sequence

>retro_ptro_82
ATGACGGCCAGCGCACAGCCGCGCGGGCGGCGGCCAGGAGTCGGGGTCGGAGTCGTGGTGACCAGCTGCAAGCATCCGCG
TTGCGTCCTCCTGGGGAAGAGGAAAGGCTCGGTTGGAGCTGGCAGTTTCCAACTCCCTGGAGGTCATCTGGAGTTCGGTG
AAACCTGGGAAGAATGTGCTCAAAGGGAAACCTGGGAAGAAGCAGCTCTTCACCTGAAAAATGTTCACTTTGCCTCAGTT
GTGAATTCTTTCATTGAGAAGGAGAATTACCATTATGTTACTATATTAATGAAAGGAGAAGTGGATGTGACTCATGATTC
AGAACCAAAGAATGTAGAGCCTGAAAAAAATGAAAGTTGGGAGTGGGTTCCTTGGGAAGAACTACCTCCCCTGGACCAGC
TTTTCTGGGGACTGCGTTGTTTAAAAGAACAAGGCTATGATCCGTTTAAAGAAGATCTGAACCATCTGGTGGGATACAAA
GGAAATCATCTC

Alignment

ORF - retro_ptro_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MTASAQPRGRRPGVGVGVVVTSCKHPRCVLLGKRKGSVGAGSFQLPGGHLEFGETWEECAQRETWEEAAL
          MTASAQPRGRRPGVGVGVVVTSCKHPRCVLLGKRKGSVGAGSFQLPGGHLEFGETWEECAQRETWEEAAL
Retrocopy MTASAQPRGRRPGVGVGVVVTSCKHPRCVLLGKRKGSVGAGSFQLPGGHLEFGETWEECAQRETWEEAAL

Parental  HLKNVHFASVVNSFIEKENYHYVTILMKGEVDVTHDSEPKNVEPEKNESWEWVPWEELPPLDQLFWGLRC
          HLKNVHFASVVNSFIEKENYHYVTILMKGEVDVTHDSEPKNVEPEKNESWEWVPWEELPPLDQLFWGLRC
Retrocopy HLKNVHFASVVNSFIEKENYHYVTILMKGEVDVTHDSEPKNVEPEKNESWEWVPWEELPPLDQLFWGLRC

Parental  LKEQGYDPFKEDLNHLVGYKGNHL
          LKEQGYDPFKEDLNHLVGYKGNHL
Retrocopy LKEQGYDPFKEDLNHLVGYKGNHL

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	0.07 RPM	2.31 RPM
SRP007412_cerebellum	0.04 RPM	0.82 RPM
SRP007412_heart	0.03 RPM	1.57 RPM
SRP007412_kidney	0.03 RPM	2.96 RPM
SRP007412_liver	0.03 RPM	0.88 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_82 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_82 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_82 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019501	1 retrocopy	retro_btau_559,
Callithrix jacchus	ENSCJAG00000009274	1 retrocopy	retro_cjac_1497,
Homo sapiens	ENSG00000136159	2 retrocopies	retro_hsap_1822, retro_hsap_4063,
Gorilla gorilla	ENSGGOG00000008232	3 retrocopies	retro_ggor_2171, retro_ggor_2257, retro_ggor_2729,
Microcebus murinus	ENSMICG00000009583	1 retrocopy	retro_mmur_962,
Mus musculus	ENSMUSG00000033405	1 retrocopy	retro_mmus_1923,
Nomascus leucogenys	ENSNLEG00000002957	2 retrocopies	retro_nleu_2878, retro_nleu_563,
Pongo abelii	ENSPPYG00000005353	2 retrocopies	retro_pabe_1490, retro_pabe_3337,
Pan troglodytes	ENSPTRG00000042329	1 retrocopy	retro_ptro_82 ,
Tarsius syrichta	ENSTSYG00000006960	1 retrocopy	retro_tsyr_146,