RetrogeneDB ID: retro_pabe_2071

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:83112805..83113234(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC8
• Ensembl ID: ENSPPYG00000005287
• Aliases: None
• Description: exosome component 8 [Source:HGNC Symbol;Acc:17035]

Sequence

>retro_pabe_2071
GCTGGGTTCAAAACCACGGAACCTCTGGTATATTACAGATTTCTGAAAGAGATCTGCCTTCCTGATGAAAGAGAACTTGG
TGAATTCAGAACCACAACTGTCAACACAGGTTCAATTAGTACTGCAGTCGGTTCTCCTTTAGTGAAGCTGGGAAATACTA
CAGAAATGTGTAAGGTTAAAGCAGAGTTTACAGCACCATCCACAGATGCTTCCATAAAGGATCTGTGGCTCCCACTGGGG
CTCTGCCACCCTTGTGTTCCATTGAGATTTCAGTCTGGACCTCCTGGAGAAGAGACCCAAGCTGCTAGCCAGATCACTGA
AGATATCACTGAAAATTCACAGATAATTCAGAAAGGGAATTTAAGCATTTCTCCAGGAAGGCGTGCTTGAATTCTATGCT
ATGATCCATTTGCCTCTCTCATTTGCCTA

Alignment

ORF - retro_pabe_2071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.12 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNVGSISTADGSALVKLGNTTVICGVKAEFAAPPTD
          AGFKT.EPL.YYR.FLKE.C.PD.RELGEFRTTTVN.GSISTA.GS.LVKLGNTT..C.VKAEF.AP.TD
Retrocopy AGFKTTEPLVYYR-FLKEICLPDERELGEFRTTTVNTGSISTAVGSPLVKLGNTTEMCKVKAEFTAPSTD

Parental  AP-DTGYVVPNVDLPPLCS-SRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVL----Y
          A....G.V.P...LPPLCS..RF.SGPPGEE.Q.ASQ...D..ENSQIIQK..L.ISPG.....L.....
Retrocopy AS<HKGSVAPTGALPPLCS>LRFQSGPPGEETQAASQITEDITENSQIIQKGNLSISPGRRA*ILCYDPF

Parental  CDLICL
          ..LICL
Retrocopy ASLICL

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	5.97 RPM
SRP007412_cerebellum	0.12 RPM	12.28 RPM
SRP007412_heart	0.00 RPM	8.58 RPM
SRP007412_kidney	0.00 RPM	9.58 RPM
SRP007412_liver	0.00 RPM	8.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2071 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2071 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2071 has 0 orthologous retrocopies within eutheria group .

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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,