RetrogeneDB ID: retro_ptro_2429

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:44338871..44339302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC8
• Ensembl ID: ENSPTRG00000005790
• Aliases: None
• Description: exosome component 8 [Source:HGNC Symbol;Acc:17035]

Sequence

>retro_ptro_2429
ATGGTAGCTGGGTTCAAAACCACGGAACCTCTGGTAATTACAGGAGATTTCTGAAAGAGATCTGCCTTGCTGATGAAAGA
GAACTTGGTGAATTCAGAACCACAACTGTCAACACAGGTTCAATTAGTACTGCAGTCGGTTCTCCTTTAGTGAAGCTGGG
AAATATTACAGTAATGTGTAAGGTTAAAGCAGAGTTTGCAGCACCGTCCACAGATGCTTCCATAAAGGATCTGTGGCTCC
CACTGGGGCTCTGCCACCCTTGTGTTCCATTGAGATTTCAGTCTGGACCTCCTGGAGAAGGGACCCAAGCCACTAGCCAG
ATCACTGAAGATATCACTGAAAATTCACAGATAATTCAGAAAAGGAATTTATGCATTTCTCCAGGAAAGCGTGCTTGAAT
TCTATGCTATGATCTCATTCGCCTCTCTCAT

Alignment

ORF - retro_ptro_2429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.03 %
• Parental protein coverage: 52.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAGFKTVEPLEY-YRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAP
          M.AGFKT.EPL...YRRFLKE.C..D.RELGEFRTTTVN.GSISTA.GS.LVKLGN.TV.C.VKAEFAAP
Retrocopy MVAGFKTTEPLVI<YRRFLKEICLADERELGEFRTTTVNTGSISTAVGSPLVKLGNITVMCKVKAEFAAP

Parental  PTDAP-DKGYVVPNVDLPPLCS-SRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYC
          .TDA...KG.V.P...LPPLCS..RF.SGPPGE..Q..SQ...D..ENSQIIQK..LCISPGK....L..
Retrocopy STDAS<HKGSVAPTGALPPLCS>LRFQSGPPGEGTQATSQITEDITENSQIIQKRNLCISPGKRA*ILCY

Parental  DLICLDY
          DLI.L..
Retrocopy DLIRLSH

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	4.68 RPM
SRP007412_cerebellum	0.00 RPM	8.82 RPM
SRP007412_heart	0.00 RPM	8.95 RPM
SRP007412_kidney	0.00 RPM	7.79 RPM
SRP007412_liver	0.00 RPM	10.34 RPM
SRP007412_testis	0.00 RPM	54.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2429 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2429 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3585
Gorilla gorilla	retro_ggor_2418

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000120699	1 retrocopy	retro_hsap_3585,
Gorilla gorilla	ENSGGOG00000011902	1 retrocopy	retro_ggor_2418,
Nomascus leucogenys	ENSNLEG00000001745	1 retrocopy	retro_nleu_1684,
Otolemur garnettii	ENSOGAG00000002745	2 retrocopies	retro_ogar_1154, retro_ogar_423,
Pongo abelii	ENSPPYG00000005287	1 retrocopy	retro_pabe_2071,
Pan troglodytes	ENSPTRG00000005790	1 retrocopy	retro_ptro_2429 ,
Pteropus vampyrus	ENSPVAG00000014610	1 retrocopy	retro_pvam_275,
Tupaia belangeri	ENSTBEG00000012040	9 retrocopies	retro_tbel_1492, retro_tbel_1680, retro_tbel_2932, retro_tbel_349, retro_tbel_3712, retro_tbel_4030, retro_tbel_419, retro_tbel_4649, retro_tbel_527,