RetrogeneDB ID: retro_ptro_1527

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:11367283..11367826(+)
• Located in intron of: ENSPTRG00000011658

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000042169
• Aliases: None
• Description: None

Sequence

>retro_ptro_1527
ATGGCGGAGGAAGACAGCGATCAAAAGGCCGAACGCCTCAGAGAAGAGCTTGTGGCCTCTGTGGAGTCCCTGCTGGGCCC
TGTGGGGCTTAGAGCTGCGGGCGACGGCACAGGCGGTGCTGGCAGCTGCAGCGGCGGCGGCGGGATCAGCTGTCGGGGTT
ATTGCTGACGCTTCTGTCAGGTGGTTGAAGATTACGTTGGAAGATGGCAGGTCCCTTTGCCACAGCTTCAGGTTCTTCAG
ACTGTACTTTGTTGTTTTACAACAGCCAGTGCATCATTCCCAGATGAATGTGAGCACGTACAACACGTTTTGAGTAGCCT
TGCTGTGAGTTTCTTCGAGTTGCTGCTGTTCTTTGGAAGAGGTGAGTTTTATGAAGAGCCCTTAAAGGATATTCTTGGAT
CATTCCAGGAATACCAGAATCACCTCCGCAGATATGGAAATGTGAATCTGGAACTGGTGACTCGAATCATTAGAGATGGC
GGCCCATGGGAAGATCCAGTGTTGCAAGCTGTCCTTAAAGCTCAGCCAGCATCTCAGGAGATA

Alignment

ORF - retro_ptro_1527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 51.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEEESDQEAERLGEELVAIVESPLGPVGLRAAGDGRGGAGSGNCGSGVGISSRDYCRRFCQVVEDYAGR
          MAEE.SDQ.AERL.EELVA.VES.LGPVGLRAAGDG.GGAGS..C..G.GIS.R.YC.RFCQVVEDY.GR
Retrocopy MAEEDSDQKAERLREELVASVESLLGPVGLRAAGDGTGGAGS--CSGGGGISCRGYC*RFCQVVEDYVGR

Parental  WQVPLPQLQVLQTALCCFTTASASFPDECEHVQYVLSSLAVSFFELLLFFGRDEFYEEPLKDILGSFQEC
          WQVPLPQLQVLQT.LCCFTTASASFPDECEHVQ.VLSSLAVSFFELLLFFGR.EFYEEPLKDILGSFQE.
Retrocopy WQVPLPQLQVLQTVLCCFTTASASFPDECEHVQHVLSSLAVSFFELLLFFGRGEFYEEPLKDILGSFQEY

Parental  QNHLRRYGNVNLELVTRIIRDGGPWEDPVLQAVLKAQPASQEI
          QNHLRRYGNVNLELVTRIIRDGGPWEDPVLQAVLKAQPASQEI
Retrocopy QNHLRRYGNVNLELVTRIIRDGGPWEDPVLQAVLKAQPASQEI

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	0.09 RPM	0.97 RPM
SRP007412_cerebellum	0.07 RPM	2.87 RPM
SRP007412_heart	0.03 RPM	1.72 RPM
SRP007412_kidney	0.03 RPM	1.67 RPM
SRP007412_liver	0.00 RPM	1.44 RPM
SRP007412_testis	0.21 RPM	3.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1527 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1527 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2075

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000229729	1 retrocopy	retro_hsap_2075,
Nomascus leucogenys	ENSNLEG00000011752	1 retrocopy	retro_nleu_2375,
Pan troglodytes	ENSPTRG00000042169	1 retrocopy	retro_ptro_1527 ,