RetrogeneDB ID: retro_pabe_1434

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:16029452..16030754(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5D
• Ensembl ID: ENSPPYG00000016625
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', delta [Source:HGNC Symbol;Acc:9312]

Sequence

>retro_pabe_1434
AGAAAGACACGGCAAAATTCTTCAAGGTTTAGTGCAAGCAATAATAGAGAACTTCAAAAACTACCATCCTTAAAAGATGT
TCCTCCTGCTGATCAAGAGAAGCTTTTTATCCAGAAGTTATGTCAGTGTTGTGTCTTTTTTGACTTTGTTTCTGATCCAC
TAAGTGACCTAAAGTGGAAGGAAATAAAATGAGCTGCTTTAAGTGAAATGGTAGAACATATCACCCATAATTGGAACGTG
ATCACAGAGCTATTTACCCAGAAGTAGTCCATATGTTTGCAGTTAAGATGTTTTGAACATTACCACCTTCCTCCAATCCT
AGGGGAGCAGAATTTGACCCAGAGGAAGATGAACCAACGTTAGAAACAGCATGGCTTCATCTACAATTGTTTATGAATTT
TTCTTAAGATTTTTAGAGTCTCCGGATTTCCAACCTAATATAGCGAAGAAATATATTGATCAGAAGTTTGTATTGCAGCT
TTTAAAGCTCTTTGACAGTGAAGATCCTCGGGAGAGAGATTTTCTTAAAACCACCCTTCACAGAATCTATGGGAAATTCC
TAGGCTTGAGAGCTTACATCAGAAAACAGATAATATATTTTATAGGTTTATTTATGAAACAGATCATCATAACAGCATAG
GAGAGTTACTGGAAATATTGGGAAGTATAATTAATGGATTTGCCTTACCACTAAAAGAAGAACACAAGATTTTCTTATTG
AAGGTGTTACTACCTTTGAACAAAGTGAAATCTCTGAGTGTCTACCACCACCAGCTGGCATACTGTGGAGTGCAGTTTTT
AGAAAAGGATAGCACCCCTACAGAACCAGTGGTGATGGCACTTCTCAAATACTGGCCAAAGACTCACAGTCCAAAAGAAG
TAATGTTCTTAAATGAATTAGAAGCGATTTTAGATGTCATAGAACCATCAGAATTTGTGAAGACCATGGAGCCCCTCTTC
CAGCAGTTGGCCAAATGTGTCTCCAGCCCACAGTTCCAGGTGGCAGAGCGAGCTCTCTATTACTGGAATAATGAATACAT
CATGAGTTTAATCAGTGACAACGCAGCAAAGATTCTGCCCATCATGTTTCCTTCCTTGTACCACAACTCAAAGACCCATT
GGAACAAGATAATACATGGTTTGATATACAATGCCCTGAAGCTGTTCATGGAAATGAACCAAAAGCTATCTGATGACTGT
ACACAACAATTTAAGGCAGAGAAACTAAAAGAGAAGCTAAAAATGAAAGTACGGGAAGAAGCATGGGTTAAAATAGAAAA
TCTAGCCAAAGCCAATCCCCAG

Alignment

ORF - retro_pabe_1434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.59 %
• Parental protein coverage: 65.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KERRQSSSRFNLSKNRELQKLPALKDSPTQEREELFIQKLRQCCVLFDFVSDPLSDLKFKEVKRAGLNEM
          ...RQ.SSRF..S.NRELQKLP.LKD.P....E.LFIQKL.QCCV.FDFVSDPLSDLK.KE.K.A.L.EM
Retrocopy RKTRQNSSRFSASNNRELQKLPSLKDVPPADQEKLFIQKLCQCCVFFDFVSDPLSDLKWKEIK*AALSEM

Parental  VEYITHSRDVVTE-AIYPEAVTMFSVNLFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQL-VYEFFLRF
          VE.ITH...V.TE.AIYPE.V.MF.V..F.TLPPSSNP.GAEFDPEEDEPTLE.AW.HLQL.VYEFFLRF
Retrocopy VEHITHNWNVITE<AIYPEVVHMFAVKMF*TLPPSSNPRGAEFDPEEDEPTLETAWLHLQL<VYEFFLRF

Parental  LESPDFQPNIAKKYIDQKFVLALLDLFDSEDPRERDFLKTILHRIYGKFLGLRAYIRRQINHIFYRFIYE
          LESPDFQPNIAKKYIDQKFVL.LL.LFDSEDPRERDFLKT.LHRIYGKFLGLRAYIR.QI......F...
Retrocopy LESPDFQPNIAKKYIDQKFVLQLLKLFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQIIYFIGLFMKQ

Parental  -TEHHNGIAELLEILGSIINGFALPLKEEHKMFLIRVLLPLHKVKSLSVYHPQLAYCVVQFLEKESSLTE
          ...H...I.ELLEILGSIINGFALPLKEEHK.FL..VLLPL.KVKSLSVYH.QLAYC.VQFLEK.S..TE
Retrocopy <DHHNS-IGELLEILGSIINGFALPLKEEHKIFLLKVLLPLNKVKSLSVYHHQLAYCGVQFLEKDSTPTE

Parental  PVIVGLLKFWPKTHSPKEVMFLNELEEILDVIEPSEFSKVMEPLFRQLAKCVSSPHFQVAERALYYWNNE
          PV...LLK.WPKTHSPKEVMFLNELE.ILDVIEPSEF.K.MEPLF.QLAKCVSSP.FQVAERALYYWNNE
Retrocopy PVVMALLKYWPKTHSPKEVMFLNELEAILDVIEPSEFVKTMEPLFQQLAKCVSSPQFQVAERALYYWNNE

Parental  YIMSLISDNAARVLPIMFPALYRNSKSHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQYKAEKQKGRFRM
          YIMSLISDNAA..LPIMFP.LY.NSK.HWNK.IHGLIYNALKLFMEMNQKL.DDCTQQ.KAEK.K....M
Retrocopy YIMSLISDNAAKILPIMFPSLYHNSKTHWNKIIHGLIYNALKLFMEMNQKLSDDCTQQFKAEKLKEKLKM

Parental  KEREEMWQKIEELARLNPQ
          K.REE.W.KIE.LA..NPQ
Retrocopy KVREEAWVKIENLAKANPQ

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	0.11 RPM	27.20 RPM
SRP007412_cerebellum	0.24 RPM	13.62 RPM
SRP007412_heart	0.09 RPM	2.74 RPM
SRP007412_kidney	0.10 RPM	5.47 RPM
SRP007412_liver	0.09 RPM	2.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1434 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1434 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015445	1 retrocopy	retro_dnov_1333,
Monodelphis domestica	ENSMODG00000019007	1 retrocopy	retro_mdom_798,
Pongo abelii	ENSPPYG00000006152	3 retrocopies	retro_pabe_2322, retro_pabe_2414, retro_pabe_3101,
Pongo abelii	ENSPPYG00000016625	1 retrocopy	retro_pabe_1434 ,