RetrogeneDB ID: retro_pabe_2414

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3_random:256568..257442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5C
• Ensembl ID: ENSPPYG00000006152
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', gamma [Source:HGNC Symbol;Acc:9311]

Sequence

>retro_pabe_2414
TTAAAAGATGTTCCTCCTGCTGATCAAGAGAAGCTTTTTATCCAGAAGTTATGTCAGTGTTGCGTCTTTTTTGACTTTGT
TTCTGATCCACTAAGTGACCTAAAGTGGAAGGAAATAAAACGAGCTGCTTTAAGTGAAATGGTAGAACATATCACCCATA
ATTGGAATGTGATCACAGAGCTATTTACCCAGAAGTAGTCCATATGTTTGCAGTTAACATGTTTCGAACATTACCACCTT
CCTCCAATCCTACGGGAGCAGAATTTGACCCAGAGGAAGATGAACCAACGTTAGAAGCAGCCTGGCTTCATCTACAATTG
TTTATGAATTTTTCTTAAGATTTTTAGAGTCTCCAGATTTCCAATCTAATATAGCAAAGAAATATATTGATCAGAAGTTT
GTATTGCAGCTTTTAAAGCTCTTTGACAGTGAAGATCCTCGGGAGAGAGATTTTCTTAAAACCACCCTTCACAGAATCTA
TGGGAAATTCCTAGGCTTGAGAGCTTACATGAGAAAACAGATAAATAATATATTTTATAGGTTTATTTGTGAAACAGAGC
ATCATAATGGCATAGCAGAGTTACTGGAAATATTGGGAAGTATAGTTAATGGATTTGCCTTACCACTAAAAGAAGAACAC
AAGATTTTCTTATTGAAGGTGTTACTACCTTTGCACAAAGTGAAATCTCTGAGTGTCTACCACCCCCAGCTGGCATACTG
TGGAGTGCAGTTTTTAGAAAAGGACAGCACCCCCACAGAACCAGTGGTGATGGCACTTCTCAAATGCTGGCCAAAGACTC
ACAGTCCAAAAGAAGAATTAGAAGCGATTTTAGATGTCATTGAACCATCAGAATTTGTGAAGACCATGGAGCCC

Alignment

ORF - retro_pabe_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.1 %
• Parental protein coverage: 54.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITE-PIYPEVVHM
          ..DVPPADQEKLFIQKL.QCCV.FDFVSDPLSDLKWKE.KRAALSEMVE.ITHN.NVITE..IYPEVVHM
Retrocopy LKDVPPADQEKLFIQKLCQCCVFFDFVSDPLSDLKWKEIKRAALSEMVEHITHNWNVITE<AIYPEVVHM

Parental  FAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQL-VYEFFLRFLESPDFQPNIAKKYIDQKFVLQL
          FAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAW.HLQL.VYEFFLRFLESPDFQ.NIAKKYIDQKFVLQL
Retrocopy FAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWLHLQL<VYEFFLRFLESPDFQSNIAKKYIDQKFVLQL

Parental  LELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFAL
          L.LFDSEDPRERDFLKTTLHRIYGKFLGLRAY.RKQINNIFYRFI.ETEHHNGIAELLEILGSI.NGFAL
Retrocopy LKLFDSEDPRERDFLKTTLHRIYGKFLGLRAYMRKQINNIFYRFICETEHHNGIAELLEILGSIVNGFAL

Parental  PLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKE----VM
          PLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYC.VQFLEKDST.TEPVVMALLK.WPKTHSPKE......
Retrocopy PLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCGVQFLEKDSTPTEPVVMALLKCWPKTHSPKEELEAIL

Parental  FLNELEEILDVIEP
          ...E..E.....EP
Retrocopy DVIEPSEFVKTMEP

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	0.33 RPM	69.28 RPM
SRP007412_cerebellum	0.00 RPM	53.63 RPM
SRP007412_heart	0.06 RPM	52.38 RPM
SRP007412_kidney	0.20 RPM	51.61 RPM
SRP007412_liver	0.24 RPM	50.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2414 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000078304	2 retrocopies	retro_hsap_2649, retro_hsap_3796,
Nomascus leucogenys	ENSNLEG00000015727	2 retrocopies	retro_nleu_1125, retro_nleu_655,
Otolemur garnettii	ENSOGAG00000006274	1 retrocopy	retro_ogar_1944,
Pongo abelii	ENSPPYG00000006152	3 retrocopies	retro_pabe_2322, retro_pabe_2414 , retro_pabe_3101,
Pongo abelii	ENSPPYG00000016625	1 retrocopy	retro_pabe_1434,
Pan troglodytes	ENSPTRG00000006734	1 retrocopy	retro_ptro_1784,