RetrogeneDB ID: retro_ptro_56

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:38573218..38574037(+)
• Located in intron of: ENSPTRG00000014402

Retrocopy information

• Ensembl ID: ENSPTRG00000014403
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000010777
• Aliases: None
• Description: None

Sequence

>retro_ptro_56
TCGGTCGCAGCCCGCTCGGGCCCGTTCGCGCCCGTCCTGTCGGCCACGTCCCGCGGGGTGGCGGGCGCGCTGCGGCCCTT
GGTGCAGGCCACGGTGCCCGCCACCCCGGAGCAGCCTGTGTTGGACCTGAAGCGGCCCTTCCTCAGCCGGGAGTCACTGA
GCGGCCAGGCCGTGCACCGGCCTTTGGTCGCCTCCGTGGGCCTCAATGTCCCTGCTTCTGTTTGTTATTCCCACACAGAC
GTCAAGGTGCCTGACTTCTCTGAATACCGCCGCCTTGAAGTTTTAGATAGTACGAAGTCTTCAAGAGAAAGCAGCGAGGC
TAGGAAAGGTTTCTCCTATTTGGTAACTGGAGTAACTACTGTGGGTGTCGCATATGCTGCCAAGAATGCCGTCACCCAGT
TCGTTTCCAGCATGAGTGCTTCTGCTGATGTGTTGGCCCTGGCGAAAATCGAAATCAAGTTATCCGATATTCCAGAAGGC
AAGAACATGGCTTTCAAATGGAGAGGCAAACCCCTGTTTGTGCGTCATAAAACCCAGAAGGAAATTGAGCAGGAAGCTGC
AGTTGAATTATCACAGTTGAGGGACCCACAGCATGATCTAGATCGAGTAAAGAAACCTGAATGGGTTATCCTGATAGGTG
TTTGCACTCATCTTGGTTGTGTACCCATTGCAAATGCAGGAGATTTTGGTGGTTATTACTGCCCTTGCCATGGGTCACAC
TATGATGCATCTGGCAGGATCAGATTGGGTCCTGCTCCTCTCAACCTTGAAGTCCCCACGTATGAGTTCACCAGTGACGA
TATGGTGATTGTTGGTTAG

Alignment

ORF - retro_ptro_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 99.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVAARSGPFAPVLSATSRGVAGALRPLVHITVPATPEQRVLDLKRPFFSRETLSGQAVRRPMVASVGLNV
          SVAARSGPFAPVLSATSRGVAGALRPLV..TVPATPEQ.VLDLKRPF.SRE.LSGQAV.RP.VASVGLNV
Retrocopy SVAARSGPFAPVLSATSRGVAGALRPLVQATVPATPEQPVLDLKRPFLSRESLSGQAVHRPLVASVGLNV

Parental  PASVCYSHTDVKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVSSMSA
          PASVCYSHTDVKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVSSMSA
Retrocopy PASVCYSHTDVKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVSSMSA

Parental  SADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDPQHDLDRVKKPEWVI
          SADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRH.TQKEIEQEAAVELSQLRDPQHDLDRVKKPEWVI
Retrocopy SADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHKTQKEIEQEAAVELSQLRDPQHDLDRVKKPEWVI

Parental  LIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNLEVPTYEFTSDDMVIVG
          LIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNLEVPTYEFTSDDMVIVG
Retrocopy LIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNLEVPTYEFTSDDMVIVG

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	4.79 RPM	28.26 RPM
SRP007412_cerebellum	1.08 RPM	7.17 RPM
SRP007412_heart	3.12 RPM	23.67 RPM
SRP007412_kidney	6.41 RPM	33.87 RPM
SRP007412_liver	3.60 RPM	6.97 RPM
SRP007412_testis	0.84 RPM	8.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_56 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_56 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001887	1 retrocopy	retro_cjac_1458,
Gorilla gorilla	ENSGGOG00000012978	1 retrocopy	retro_ggor_2552,
Pan troglodytes	ENSPTRG00000010777	1 retrocopy	retro_ptro_56 ,