RetrogeneDB ID: retro_pabe_1829

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:49925463..49925937(-)
• Located in intron of: ENSPPYG00000011139

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERP29
• Ensembl ID: ENSPPYG00000004971
• Aliases: None
• Description: endoplasmic reticulum protein 29 [Source:HGNC Symbol;Acc:13799]

Sequence

>retro_pabe_1829
ATGGCTGCCGCTGTGCCCCGCTCCGCGTCTCTCTCCCCGCTGCTTCCCCTTCTCCTGGGCTTCCTGCTCCTCTCCGCTCC
GCATGGCGGCAGCGGCCTGCACACCAAGGGCACCCTTCCCCTGGATACGGTCACGTTCTGCAAGGTCATTCCCAAAAGCA
GGTTCGTCTTGGTGAAGGTCAACACCCAGTACCGCTACGGTGAGAAGCAGGATGAGTTCAGGCGTCTTGCTGAAAACTCG
GCTTCCAGCGATGATCTCTTGGTGGCAGAGGTGGGGATCTCAGATTATGGTGACAAGCTGAACATGGAGCCGAGTGAGAA
ATACAAGCTGCACAAAGAGAGCTACCCAGTCTTCTACCTCTCCCGGGAGGGGGACTTTGAGAACCCAGTCCCATGTACTG
GGGCAGTTAAGGTTGGAGCCATCCAGCGCTGGCTGAAGGGGCAAGGGGTCTACCTAGCTATGCCAGGTGGCCTG

Alignment

ORF - retro_pabe_1829 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.51 %
• Parental protein coverage: 60.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVPRAASLSPLLPLLLGFLLLSAPHGGSGLHTKGALPLDTVTFYKVIPKSKFVLVKFDTQYPYGEKQ
          MAAAVPR.ASLSPLLPLLLGFLLLSAPHGGSGLHTKG.LPLDTVTF.KVIPKS.FVLVK..TQY.YGEKQ
Retrocopy MAAAVPRSASLSPLLPLLLGFLLLSAPHGGSGLHTKGTLPLDTVTFCKVIPKSRFVLVKVNTQYRYGEKQ

Parental  DEFKRLAENSASSDDLLVAEVGISDYGDKLNMELSEKYKLDKESYPVFYLFRDGDFENPVPYTGAVKVGA
          DEF.RLAENSASSDDLLVAEVGISDYGDKLNME.SEKYKL.KESYPVFYL.R.GDFENPVP.TGAVKVGA
Retrocopy DEFRRLAENSASSDDLLVAEVGISDYGDKLNMEPSEKYKLHKESYPVFYLSREGDFENPVPCTGAVKVGA

Parental  IQRWLKGQGVYLGMPGCL
          IQRWLKGQGVYL.MPG.L
Retrocopy IQRWLKGQGVYLAMPGGL

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	0.06 RPM	54.02 RPM
SRP007412_cerebellum	0.00 RPM	44.26 RPM
SRP007412_heart	0.03 RPM	23.69 RPM
SRP007412_kidney	0.03 RPM	132.82 RPM
SRP007412_liver	0.00 RPM	72.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1829 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1829 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000089248	1 retrocopy	retro_hsap_2488,
Nomascus leucogenys	ENSNLEG00000000031	1 retrocopy	retro_nleu_276,
Pongo abelii	ENSPPYG00000004971	1 retrocopy	retro_pabe_1829 ,
Pan troglodytes	ENSPTRG00000005468	1 retrocopy	retro_ptro_1441,
Pteropus vampyrus	ENSPVAG00000012400	1 retrocopy	retro_pvam_388,