RetrogeneDB ID: retro_ptro_343

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:132667220..132668060(-)
• Located in intron of: ENSPTRG00000001383

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSPTRG00000010926
• Aliases: None
• Description: Pan troglodytes proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 (PSMD8), mRNA. [Source:RefSeq mRNA;Acc:NM_001251986]

Sequence

>retro_ptro_343
GTGAACAGTGCAGCCGGCGCCTTGAGCTCCGGGCCCCTGGCGCCTAGGGCCCTGTCCTGCAGGCTGAGGACGGCAAGTAC
AAGCAACTCAAGGGCGAGTGGAACCGTAAAAGCCCCAATCTTAGCAAGTGCAGGGAAGAGCTGGGCTGCCTCAAGCTAGT
TCTTCTGGAGCTCAACTTCTTGCCAACCACAGGGACCAAGCTGACCAAACAGCAGCTCATTCTGGCCCGTGACATACTGA
AGATCGGGGCCAGTGGAGCATCCTATGCAAGGACATCCCCTCCTTCCAGCGCCACATGACCCAGCTCAAATGCTGCTACT
TTGATTACAAGGAACAGCTTCCCCAGTCAGCCTACATGCACCAGCTCTTGGGCCTCAATCTCCTCTTCCTGCTGTCCCAG
AAGTGGGTGGCTGAGTTCCACATGGAGCTGGAGTGGCTGCCTGCCAAGGACATCCAGACCAATGTCTACACCAAAAACCT
TGTGTCCCTGGAGCAATACCTAATGGAGGGCAGCTACAACAAAGTGTTCCTGGCCAAGGGTAACATCCTCGCCAAGAGCT
ACACCGTCTTCATCGACATCCTGCTTGACACTATCAGGGATGAGATGGCCGGGTGCATCAAGAAAGCCTATGAGAAAATC
CCTTTTACCAAGGCCACCAGATCCTCTTCTTCAACACACCCAAAAAGATGACCGACTACACCAAGAAGTGAGGGTGGGTC
CCGGGCCCCAACAACTAATATAGTTTTGCCGGCCAGCAGCAGGAGCCAGAAGACACTACCATTCCCTCCACAGAACTGGC
CAAACAGGTCACCGAGTATGCCCGGCAGCTGGAGATGATC

Alignment

ORF - retro_ptro_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 80.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VNGAAGFSSSGPAATS-GAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLT
          VN.AAG..SSGP.A...G.VLQA..G.Y.QLKGEWNRKSPNLSKC.EELG.LKLVLLELNFLPTTGTKLT
Retrocopy VNSAAGALSSGPLAPR<GPVLQAEDGKYKQLKGEWNRKSPNLSKCREELGCLKLVLLELNFLPTTGTKLT

Parental  KQQLILARDILEIGA-QWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRVA
          KQQLILARDIL.IGA.QWSIL.KDIPSF.R.M.QLKC.YFDYKEQLP.SAYMHQLLGLNLLFLLSQ..VA
Retrocopy KQQLILARDILKIGA<QWSILCKDIPSFQRHMTQLKCCYFDYKEQLPQSAYMHQLLGLNLLFLLSQKWVA

Parental  EFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIE
          EFH.ELE.LPAKDIQTNVY.K..VSLEQYLMEGSYNKVFLAKGNI.A.SYT.FIDILLDTIRDE.AGCI.
Retrocopy EFHMELEWLPAKDIQTNVYTKNLVSLEQYLMEGSYNKVFLAKGNILAKSYTVFIDILLDTIRDEMAGCIK

Parental  KAYEKILFTEATR-ILFFNTPKKMTDYAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQ
          KAYEKI.FT.ATR.ILFFNTPKKMTDY.KK.GWV.GPNN.YSFA.QQQ.PEDTTIPSTELAKQV.EYARQ
Retrocopy KAYEKIPFTKATR<ILFFNTPKKMTDYTKK*GWVPGPNN*YSFAGQQQEPEDTTIPSTELAKQVTEYARQ

Parental  LEMI
          LEMI
Retrocopy LEMI

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	0.00 RPM	78.27 RPM
SRP007412_cerebellum	0.00 RPM	62.73 RPM
SRP007412_heart	0.03 RPM	70.42 RPM
SRP007412_kidney	0.03 RPM	80.42 RPM
SRP007412_liver	0.13 RPM	76.73 RPM
SRP007412_testis	0.11 RPM	59.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_343 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_343 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000099341	1 retrocopy	retro_hsap_456,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Nomascus leucogenys	ENSNLEG00000016876	1 retrocopy	retro_nleu_878,
Pongo abelii	ENSPPYG00000009931	1 retrocopy	retro_pabe_277,
Pan troglodytes	ENSPTRG00000010926	1 retrocopy	retro_ptro_343 ,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,