RetrogeneDB ID: retro_pabe_196

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:41049252..41049918(+)
• Located in intron of: ENSPPYG00000009980

Retrocopy information

• Ensembl ID: ENSPPYG00000009981
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CHMP2A
• Ensembl ID: ENSPPYG00000010511
• Aliases: None
• Description: charged multivesicular body protein 2A [Source:HGNC Symbol;Acc:30216]

Sequence

>retro_pabe_196
ATGGACCTGTTGTTTGGGCGCCAGAAGACGCCAGAGGAGCTACTGCGGCAGAACCAGAGGGCCCTGAACTGTGCCATGCG
GGAGCTGGACCGCGAGCGACAGAAATTAGAGACCCAGGAGAAGAAAATCATTGCAGACATCAAGAAGATGGCCAAGCAAG
GCCAGATGGATGCTGTTCGCATCATGGCAAAAGACTTGGTGTGCACCCGGCGCTATGTGTGCAAGTTTGTATTGATGCGG
GCCAACATCCAGGCTGTGTCCCTCAAGATCCAGACACTCAAGTCCAACAACTCAATGGCACAAGCCATGAAGGGTGTCAC
CAAGGCCATGGGCACCATGAACAGACTGCTGAAGTTGCCCCAGATCCAGAAGATCATGATGGAGTTTGAGCGGCAGGCAG
AGATCATGGATATGAAGGAGGAGATGATGAATGATGCCATTGATGACGCCATGGGTGATGAGGAAGATGAAGAGGAGAGT
GATGCTCTTGTGTCCCAGGTCCTGGATGAGCTGGGACTTAGCCTAACAGATGAGCTGTCAAACCTCCCCTCAACTGGGGG
CTCGCTTAGTGTGGCTGCTGGTGGGAAAAAAGCAGAGGCCACAGCCTCAGCCCTAGCTGATGCTGATGCAGACCTGGAGG
AACGGCTTAAGAACCTGCGGAGGGAC

Alignment

ORF - retro_pabe_196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVRIMAKDLVRTR
          MDLLFGR.KTPEELLRQNQRALN.AMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVRIMAKDLV.TR
Retrocopy MDLLFGRQKTPEELLRQNQRALNCAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVRIMAKDLVCTR

Parental  RYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKE
          RYV.KFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNR.LKLPQIQKIMMEFERQAEIMDMKE
Retrocopy RYVCKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRLLKLPQIQKIMMEFERQAEIMDMKE

Parental  EMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELSNLPSTGGSLSVAAGGKKAEATASALADADA
          EMMNDAIDDAMGDEEDEEESDA.VSQVLDELGLSLTDELSNLPSTGGSLSVAAGGKKAEATASALADADA
Retrocopy EMMNDAIDDAMGDEEDEEESDALVSQVLDELGLSLTDELSNLPSTGGSLSVAAGGKKAEATASALADADA

Parental  DLEERLKNLRRD
          DLEERLKNLRRD
Retrocopy DLEERLKNLRRD

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	0.61 RPM	40.80 RPM
SRP007412_cerebellum	0.85 RPM	28.21 RPM
SRP007412_heart	0.75 RPM	24.20 RPM
SRP007412_kidney	1.03 RPM	60.39 RPM
SRP007412_liver	0.92 RPM	36.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_196 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013531	1 retrocopy	retro_meug_1308,
Mus musculus	ENSMUSG00000033916	1 retrocopy	retro_mmus_1039,
Otolemur garnettii	ENSOGAG00000005628	2 retrocopies	retro_ogar_1870, retro_ogar_2753,
Pongo abelii	ENSPPYG00000010511	1 retrocopy	retro_pabe_196 ,