RetrogeneDB ID: retro_ptro_1784

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:53218476..53219712(+)
• Located in intron of: ENSPTRG00000014996

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5C
• Ensembl ID: ENSPTRG00000006734
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', gamma [Source:HGNC Symbol;Acc:9311]

Sequence

>retro_ptro_1784
AAAGATGTTCCTCCTGCTGATCAAAAGAAGTTTTTTATCCAGAAGTTATGTCAGTGTTGCGTCCTTTTTGACTTTGTTTC
TGATCCACTAAGTGAACTAAAGTAGAAGGAATTAAAACGAGCTGCTTTAAGTGAAATGGTAGAATATATCACCCATAATT
GGAATGTGATCACAGAGCCTATTTACCCAGAAGTAGTCCATATGTTTGCAGTTAACATGTTTCGAATATTACCACCTTCC
TCCAATCCTACGGGAGCAGAATTTGACCCAGAGGAAGATGAACCAACGTTAGAAGCAGGCTGGCTTCATCTACACTTATT
TATGAATTTTTCTTAAGATTTTTAGAGTCTGCAGATTTCCAATCTAATATAGCGAAGAAATATATTGATCAGAAGTTTGT
ATTGCAGCTTTTAAAGCTCTTTGACAGTGAAGATCCTCAGGAGAGAGATTTTCTTAAAACCACCCTTCACAGAATCTATG
GGAAATTCCTAGGCTTGAGAGCTTACATCAGAAAACAGATAAATAATATATTTTATAGGTTTATTTATGAAACAGAGCAT
CATAATGGCATAGCAGAGTTACTGGAAATATTGGGAAGTATAATTAATGGATTTGCCTTACCACTAAAAGAAGAACACAA
GATTTTCTTATTGAAGGTGTTACTACCTTTGCACAAAGTGAAATCTCTTGAGCGTCTACCACCCCCAGCTGGCATACTGT
GGAGTGCAGTTTTTAGAAAAGGACAGCACCCCCACAGAACCAGTGGTGATGGCACTTCTCAAATGCTGGCCAAAGACTCA
CAGTCCAAAAGAAGTAATGTTCTTAAACAAATTAGAAGCGATTTTAGATGTCATTGAACCATCAGAATTTGTGAAGACCA
TGGAGCCCCTCTTCCGGCAGTTGGCGAAATGTGTCTCCAGCCCACACTTCCAGGTGGCAGAGCGAGCTCTCTATTACTGG
AATAATGAATACGTCATGAGTTTAATCAGTGACAATGCAGCGAAGATTCTGCCCATCATGTTTCCTTCCTTGTACCACAA
CTCAAAGACCCATTGGAACAAGATAATACATGGCTTGATATACAACGCCCTGAAGCTGTTCATAGAGATGAAACAAAAGC
TGTTTGATGACTGTACACAACAGTCCAAAGCAGAGAAACTAAAAGAGAAGCTAAAAATGGAAGTACGGGAAGAAGCATGG
GTTAAAATAGAAAATCTAGCCAAAGCCAATCCCCAG

Alignment

ORF - retro_ptro_1784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.03 %
• Parental protein coverage: 75.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITEPIYPEVVHMFA
          .DVPPADQ.K.FIQKL.QCCVLFDFVSDPLS.LK.KE.KRAALSEMVEYITHN.NVITEPIYPEVVHMFA
Retrocopy KDVPPADQKKFFIQKLCQCCVLFDFVSDPLSELK*KELKRAALSEMVEYITHNWNVITEPIYPEVVHMFA

Parental  VNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQL-VYEFFLRFLESPDFQPNIAKKYIDQKFVLQLLE
          VNMFR.LPPSSNPTGAEFDPEEDEPTLEA.W.HL.L..YEFFLRFLES.DFQ.NIAKKYIDQKFVLQLL.
Retrocopy VNMFRILPPSSNPTGAEFDPEEDEPTLEAGWLHLHL<IYEFFLRFLESADFQSNIAKKYIDQKFVLQLLK

Parental  LFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPL
          LFDSEDP.ERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPL
Retrocopy LFDSEDPQERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPL

Parental  KEEHKIFLLKVLLPLHKVKSL-SVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNEL
          KEEHKIFLLKVLLPLHKVKSL.SVYHPQLAYC.VQFLEKDST.TEPVVMALLK.WPKTHSPKEVMFLN.L
Retrocopy KEEHKIFLLKVLLPLHKVKSL>SVYHPQLAYCGVQFLEKDSTPTEPVVMALLKCWPKTHSPKEVMFLNKL

Parental  EEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNS
          E.ILDVIEPSEFVK.MEPLFRQLAKCVSSPHFQVAERALYYWNNEY.MSLISDNAAKILPIMFPSLY.NS
Retrocopy EAILDVIEPSEFVKTMEPLFRQLAKCVSSPHFQVAERALYYWNNEYVMSLISDNAAKILPIMFPSLYHNS

Parental  KTHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEKLKMKEREEAWVKIENLAKANPQ
          KTHWNK.IHGLIYNALKLF.EM.QKLFDDCTQQ.KAEKLKEKLKM..REEAWVKIENLAKANPQ
Retrocopy KTHWNKIIHGLIYNALKLFIEMKQKLFDDCTQQSKAEKLKEKLKMEVREEAWVKIENLAKANPQ

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	0.27 RPM	79.45 RPM
SRP007412_cerebellum	0.18 RPM	39.72 RPM
SRP007412_heart	0.23 RPM	67.79 RPM
SRP007412_kidney	0.18 RPM	52.28 RPM
SRP007412_liver	0.07 RPM	18.53 RPM
SRP007412_testis	1.48 RPM	130.99 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1784 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1784 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2649
Gorilla gorilla	retro_ggor_1850
Pongo abelii	retro_pabe_2322

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 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,
Pan troglodytes	ENSPTRG00000006734	1 retrocopy	retro_ptro_1784 ,