RetrogeneDB ID: retro_ptro_3012

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391667.1:108355..108955(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSRC1
• Ensembl ID: ENSPTRG00000001045
• Aliases: None
• Description: proline/serine-rich coiled-coil 1 [Source:HGNC Symbol;Acc:24472]

Sequence

>retro_ptro_3012
ATGGAGGATTTGGAGGAAGATATAAGGTTTATTGTGGATGAGATCTTGGACTTTGGGGGGCTGTCACCATCTGACAGCCG
TGAGGAGGAAGACATAACAGTGTTGGTGACTCCAGAGAAACCATTTCGACAGGGCCTCTCCCACCGAAGTGACCCAAATG
CAGTGGCACCTGCCCCCCAGGGTGTGAGGCTCAGCCTAGGCCCCCTCAGCCCAGAGAAGCTGGAGGAGATCCTCGATGAG
GCCAACCGGCTGGCCGCTCAGCTGGAGCAGTGTGCCCTGCAGGATCGGGAGAGTGCAGGCGAGGGCCTGGGGCCTCGCCG
AGTGAAGCCCAGTCCTCGGCGGGAGACCTTTGTGCTGAAGGACAGTCCTGTCCGAGACCTGCTGCCCACTGTGAACTCTT
TGACGCGGAGCACCCCCTCCCCAAGCAGCCTGACGCCTCGACTCCGGAGCAATGATAGGAAGGGGTCGGTCAGGGCTCTC
CGGGCTACATCTGGAAAGAGGCCCTCCAACATGAAGAGGGAGTCACCCAATTGCAATCTGTTCCCTGCATCCAAAAGCCC
AGCATCTTCTCCTCTTACCCGATTGACTCCCCCAGTCCGG

Alignment

ORF - retro_ptro_3012 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97. %
• Parental protein coverage: 60.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDLEEDVRFIVDETLDFGGLSPSDSREEEDITVLVTPEKPLRRGLSHRSDPNAVAPAPQGVRLSLGPLS
          MEDLEED.RFIVDE.LDFGGLSPSDSREEEDITVLVTPEKP.R.GLSHRSDPNAVAPAPQGVRLSLGPLS
Retrocopy MEDLEEDIRFIVDEILDFGGLSPSDSREEEDITVLVTPEKPFRQGLSHRSDPNAVAPAPQGVRLSLGPLS

Parental  PEKLEEILDEANRLAAQLEQCALQDRESAGEGLGPRRVKPSPRRETFVLKDSPVRDLLPTVNSLTRSTPS
          PEKLEEILDEANRLAAQLEQCALQDRESAGEGLGPRRVKPSPRRETFVLKDSPVRDLLPTVNSLTRSTPS
Retrocopy PEKLEEILDEANRLAAQLEQCALQDRESAGEGLGPRRVKPSPRRETFVLKDSPVRDLLPTVNSLTRSTPS

Parental  PSSLTPRLRSNDRKGSVRALRATSGKRPSNMKRESPTCNLFPASKSPASSPLTRSTPPVR
          PSSLTPRLRSNDRKGSVRALRATSGKRPSNMKRESP.CNLFPASKSPASSPLTR.TPPVR
Retrocopy PSSLTPRLRSNDRKGSVRALRATSGKRPSNMKRESPNCNLFPASKSPASSPLTRLTPPVR

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	35.44 RPM
SRP007412_cerebellum	0.04 RPM	4.66 RPM
SRP007412_heart	0.09 RPM	0.41 RPM
SRP007412_kidney	3.37 RPM	1.18 RPM
SRP007412_liver	1.57 RPM	0.98 RPM
SRP007412_testis	0.11 RPM	3.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3012 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000001045	1 retrocopy	retro_ptro_3012 ,
Rattus norvegicus	ENSRNOG00000020013	1 retrocopy	retro_rnor_442,