RetrogeneDB ID: retro_ptro_1441

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:49204032..49204506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERP29
• Ensembl ID: ENSPTRG00000005468
• Aliases: None
• Description: None

Sequence

>retro_ptro_1441
GTGGCTGCCGCCGTGCCCCGCTCCGCGTCTCTCTCCCTGCTGCTTCCCCTTCTCCTGGGCTTCCTGCTCCTCTCCGCTCC
GCATGGCGGCAGCGGCCTGCACACCAAGCGCGCCCTTCCCCTGGATACGGTCACTTTCTACAAGGTCATTCCCAAAAGCA
GGTTCGTCTTGGTGAAGTTCAACACCCAGTACCGCTACGGTGAGAAGCAGGATGAGTTCAGGCGTCTTGCTGAAAACTCG
GCTTCCAGCGATGATCTCTTGGTGGCAGAGGTGGGGATCTCAGATTATGGTGACAAGCTGAACATGGAGCTGAGTGAGAA
ATACAAGCTGCTCAAAGAGAGCTACCCAGTCTTCTACCTCTCCCGGGAGGGGGACTTTGAGAACCCAGTCCCATGTACTG
GGGCAGTTAAGGTTGGAGCCATCCAGCGCTGGCTGAAGGGGCAAGGGGTCTAGCTAGCTGTGCCAGGTGGCCTG

Alignment

ORF - retro_ptro_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 60.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVPRAASLSPLLPLLLGFLLLSAPHGGSGLHTKGALPLDTVTFYKVIPKSKFVLVKFDTQYPYGEKQ
          .AAAVPR.ASLS.LLPLLLGFLLLSAPHGGSGLHTK.ALPLDTVTFYKVIPKS.FVLVKF.TQY.YGEKQ
Retrocopy VAAAVPRSASLSLLLPLLLGFLLLSAPHGGSGLHTKRALPLDTVTFYKVIPKSRFVLVKFNTQYRYGEKQ

Parental  DEFKRLAENSASSDDLLVAEVGISDYGDKLNMELSEKYKLDKESYPVFYLFRDGDFENPVPYTGAVKVGA
          DEF.RLAENSASSDDLLVAEVGISDYGDKLNMELSEKYKL.KESYPVFYL.R.GDFENPVP.TGAVKVGA
Retrocopy DEFRRLAENSASSDDLLVAEVGISDYGDKLNMELSEKYKLLKESYPVFYLSREGDFENPVPCTGAVKVGA

Parental  IQRWLKGQGVYLGMPGCL
          IQRWLKGQGV.L..PG.L
Retrocopy IQRWLKGQGV*LAVPGGL

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	0.04 RPM	62.36 RPM
SRP007412_cerebellum	0.04 RPM	70.94 RPM
SRP007412_heart	0.03 RPM	24.80 RPM
SRP007412_kidney	0.00 RPM	108.97 RPM
SRP007412_liver	0.03 RPM	138.33 RPM
SRP007412_testis	0.00 RPM	49.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1441 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1441 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2488

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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,