RetrogeneDB ID: retro_pabe_796

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:106577282..106577764(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSPPYG00000002430
• Aliases: None
• Description: transcription factor A, mitochondrial [Source:RefSeq peptide;Acc:NP_001124767]

Sequence

>retro_pabe_796
GGTCGCATGAGGGTTCTAGTTGTCACTGCGGGGGTTTTTCTGTGCCAGGAGGCTCTCTGAGATTGGGGCTCAGTCACTGC
CTCATTTGCCAGTGTGATGGCCTTCTTCGAAGCATGTGGGGCATGCTGTGTGCCCAGTGAAGGTCCAGAGTGGAGCTGTG
CACTGGCTGTGGAAGTTGACTGTGCTTACCTTTCAGTTTTGTGTATTTACTGAAATGGTTTTCATCCACCTTAGCTAGTT
ATCTGAAGAAACCTATGGTGTCTTACCTTCGATTTTTGAAAGAACAGCTACTCATATTTAAAGTTCAGAACCCAGATGCA
AAAAATTCAGAACTAATTAAAAGAATCGCTGAGCTATGGAGAGAACTTGCTGATTCAGAGAAAAAAAATATATGAATATG
TTTACAGGGCAGACTGGCAAGCATTCAGAGAAGAGATAAACAGAATTCAGGAACAGTAACTCCAAGTCAGATAATATCTT
TG

Alignment

ORF - retro_pabe_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 56.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSQAVPVVIAGVVYCQEALRDWGRVTASSAGAMAF-LRSMWGVLSALGRSGAELCTGCGSRLRSPFSFVY
          G...V.VV.AGV..CQEAL.DWG.VTAS.A..MAF.LRSMWG.L.A..RS..ELCTGCGS.L..PFSFVY
Retrocopy GRMRVLVVTAGVFLCQEAL*DWGSVTASFASVMAF<LRSMWGMLCAQ*RSRVELCTGCGS*LCLPFSFVY

Parental  LPRWFSSVLASCPKKPISSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSK-KKIYQDAYRAE
          L..WFSS.LAS..KKP..SYLRF.KEQL.IFK.QNPDAK..ELI.RIA..WREL.DS.....Y...YRA.
Retrocopy LLKWFSSTLASYLKKPMVSYLRFLKEQLLIFKVQNPDAKNSELIKRIAELWRELADSE>XXXYEYVYRAD

Parental  WQVYKEEISRFKEQ-LTPSQIMSL
          WQ...EEI.R..EQ..TPSQI.SL
Retrocopy WQAFREEINRIQEQ<VTPSQIISL

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	5.42 RPM
SRP007412_cerebellum	0.00 RPM	7.42 RPM
SRP007412_heart	0.00 RPM	5.69 RPM
SRP007412_kidney	0.00 RPM	6.73 RPM
SRP007412_liver	0.03 RPM	5.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_796 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_796 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796 ,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,