RetrogeneDB ID: retro_pabe_1295

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:52239344..52240066(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSPPYG00000000851
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_pabe_1295
ATGCTGAGGAGCTGCACCGGGTGCCTCCACATGCTGTGGGCTCTTTGCCGGCCACTGCCAGTAGGCTGGCGCCTGCCAGG
TAGTGGACTGCGACCCACGCTGAGATCATTTTCTTCTGAGGAAGTCATTCTTAAGGACTATTCTGTCCCCAACCCCAGCT
GGAACAAGGACCTAAGACTGCTCTTTGACCAGTTTATGAAGAAATGTGAAGACGGCTCCTTGGAAACGTTTGCCTTCATA
TAAATGTACACCTACTGAAAAGATTCAAGACTTCAAAACCTGTTTTCTTGATCCAAAGCTTATGAAAGAAGAACAAGTGT
CACAGGCCCAGCTCTTCACCAGAAGCTTTGATGATGGCCTGGGCTTTGAATACGTGATGTTCTACAATGACATTGAGAAA
AGGATGGTTTGCTTATTTCAAGGAGGCCCTTATCTGGAAGAACCACCTGGATTTATTCATGGAGGTGCCATTGCAACCAT
GATTGATGCTACTGTTGGTTTGTGTGCAATGATGGCTGGGGGAATCGTCATTACTGCCAGTCTCAACATCAATTATAAAA
GACCTATCCCTCTTTGTTCTGTTGTTATGATAAATAGCCAACTTGATAAAGTTGAAGAAAAGAAATTTTGTTTCCTGTAT
TGTTCAGAGTGTTGATGAGAAGACCCTATACTCAGAGGTGACAAGCTTATTTATAAAGCTGAATCCTGCTTAAAGTCTGA
CA

Alignment

ORF - retro_pabe_1295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLRSCAARFRTLGALCRP-PVGRRLPGSEPRPALRSFSSEEVILKDYSVPNTSWNKDLRLLFDQFMKKCE
          MLRSC......L.ALCRP.PVG.RLPGS..RP.LRSFSSEEVILKDYSVPN.SWNKDLRLLFDQFMKKCE
Retrocopy MLRSCTGCLHMLWALCRPLPVGWRLPGSGLRPTLRSFSSEEVILKDYSVPNPSWNKDLRLLFDQFMKKCE

Parental  DGS-WKRLPSYKRTPTERIQDFKTRFLDPKLMKEEQMSQAQLFTRSFDDGLGFEYVMFYNDVEKRMVCLF
          DGS.WKRLPSYK.TPTE.IQDFKT.FLDPKLMKEEQ.SQAQLFTRSFDDGLGFEYVMFYND.EKRMVCLF
Retrocopy DGS>WKRLPSYKCTPTEKIQDFKTCFLDPKLMKEEQVSQAQLFTRSFDDGLGFEYVMFYNDIEKRMVCLF

Parental  QGGPYLEGPPGFIHGGAIATMIDATVGMCAMMAGGIVMTANLNINYKRPIPLCSVVMINSQLD-KVEGRK
          QGGPYLE.PPGFIHGGAIATMIDATVG.CAMMAGGIV.TA.LNINYKRPIPLCSVVMINSQLD.K...R.
Retrocopy QGGPYLEEPPGFIHGGAIATMIDATVGLCAMMAGGIVITASLNINYKRPIPLCSVVMINSQLD>KLKKRN

Parental  FFVSCNVQSVDEKTLYSEATSLFIKLNPAKSLT
          F.VSC.VQSVDEKTLYSE.TSLFIKLNPA.SLT
Retrocopy F-VSCIVQSVDEKTLYSEVTSLFIKLNPA*SLT

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	0.50 RPM	5.09 RPM
SRP007412_cerebellum	0.36 RPM	4.38 RPM
SRP007412_heart	0.24 RPM	5.00 RPM
SRP007412_kidney	0.30 RPM	5.20 RPM
SRP007412_liver	0.06 RPM	2.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1295 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1295 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1569
Pan troglodytes	retro_ptro_1056
Gorilla gorilla	retro_ggor_1195

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295 ,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,