RetrogeneDB ID: retro_pabe_2322

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:93969431..93970306(-)
• Located in intron of: ENSPPYG00000013810

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_2322
TTAAAAGATGTTCCTCCTGCTGATCAAAAGAAGCTTTTTATCCAGAAGTTGTGTCAGTGTTGCGTCCTTTTTGACTTTGT
TTCTGATCCACTAAGTGACCTAAAGTGGAAGGAATTAAAACGAGCTGCTTTAAGTGAAATGGTAGAATATATCACCCATA
ATTGGAATGTGATCACAGAGCCTGTTTACCCAGAAGTAGTCCATATGTTTGCAGTTAACATGTTTCGAACATTACCACCT
TCCTCCAATCCTACGGGAGCAGAATTTGACCCAGAGGAAGATGAACCAACGTTAGAAGCAGCCTGGCTTCATCTACACTT
GTTTATGAATTTTTCTTAAGATTTTTAGAGTCTCCAGATTTCCAATCTAATATAGCAAAGAAATATATTGATCAGAAGTT
TGTATTGCAGCTTTTAAAGCTCTTTGACAGTGAAGATCCTCGGGAGAGAGATTTTCTTAAAACCACCCTTCACAGAATCT
ATGGGAAATTCCTAGGCTTGAGAGCTTACATGAGAAAACAGATAAATAATATATTTTATAGGTTTATTTGTGAAACAGAG
CATCATAATGGCATAGCAGAGTTACTGGAAATATTGGGAAGTATAGTTAATGGCTTTGCCTTACCACTAAAAGAAGAACA
CAAGATTTTCTTATTGAAGGTGTTACTACCTTTGCACAAAGTGAAATCTCTGAGTGTCTACCACCCCCAGCTGGCATACT
GTGGAGTGCAGTTTTTAGAAAAGGACAGCACCCCCACAGAACCAGTGGTGATGGCACTTCTCAAATGCTGGCCAAAGACT
CACAGTCCAAAAGAAGAATTAGAAGCGATTTTAGATGTCATTGAACCATCAGAATTTGTGAAGACCATGGAGCCC

Alignment

ORF - retro_pabe_2322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 54.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITEPIYPEVVHMF
          ..DVPPADQ.KLFIQKL.QCCVLFDFVSDPLSDLKWKE.KRAALSEMVEYITHN.NVITEP.YPEVVHMF
Retrocopy LKDVPPADQKKLFIQKLCQCCVLFDFVSDPLSDLKWKELKRAALSEMVEYITHNWNVITEPVYPEVVHMF

Parental  AVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQL-VYEFFLRFLESPDFQPNIAKKYIDQKFVLQLL
          AVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAW.HL.L.VYEFFLRFLESPDFQ.NIAKKYIDQKFVLQLL
Retrocopy AVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWLHLHL<VYEFFLRFLESPDFQSNIAKKYIDQKFVLQLL

Parental  ELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALP
          .LFDSEDPRERDFLKTTLHRIYGKFLGLRAY.RKQINNIFYRFI.ETEHHNGIAELLEILGSI.NGFALP
Retrocopy KLFDSEDPRERDFLKTTLHRIYGKFLGLRAYMRKQINNIFYRFICETEHHNGIAELLEILGSIVNGFALP

Parental  LKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKE----VMF
          LKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYC.VQFLEKDST.TEPVVMALLK.WPKTHSPKE.......
Retrocopy LKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCGVQFLEKDSTPTEPVVMALLKCWPKTHSPKEELEAILD

Parental  LNELEEILDVIEP
          ..E..E.....EP
Retrocopy VIEPSEFVKTMEP

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	0.17 RPM	69.28 RPM
SRP007412_cerebellum	0.00 RPM	53.63 RPM
SRP007412_heart	0.00 RPM	52.38 RPM
SRP007412_kidney	0.00 RPM	51.61 RPM
SRP007412_liver	0.03 RPM	50.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2322 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2322 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2649
Pan troglodytes	retro_ptro_1784
Gorilla gorilla	retro_ggor_1850

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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,