RetrogeneDB ID: retro_ptro_641

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:107778592..107779319(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSPTRG00000002519
• Aliases: None
• Description: Pan troglodytes transcription factor A, mitochondrial (TFAM), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001194942]

Sequence

>retro_ptro_641
CTTCGAAGCATGTGGGGCATGCTGAGTGCCCAGTGAAGGTCCAGAGTGGAGCTGTGCACTGGCTGTGGAAGTTGACTGTG
CTTACCTTTCAGTTTTGTGTATTTACTGAAATGGTTTTCATCCACCTTAGCTAGTTATCTGAAGAAATCTATGGTGTCTT
ACCTTCGATTTTTGAAAGAACAGCTACTCATATTTAAAGTTCAGAACCCAGATACAAAAAATTCAGAACTAATTAAAAGA
ATCACTGAGCTATGGAGAGAACTTGCTGATTCAGAGAAAAAAATATATGAAGATGCTAACAGGGCAGTCTGGCAGGCATT
CAGAGAAGAGATAAACAGAATTCAGGAACAGCTAACTCCAAGTCAGATAATATCTTTGGAAAAGAAATCATGCAAAAACT
TTAAAAAAAGAAAGCGTTAATAAAAAAGAGAAATCTAATAATGCTTGGAAAACCAAAAAGATCTTGCTCAGCTTACAACA
TTTTTGTATCTGAAATCTTCCAAGAAGCTAAGGATGGTTCATCACAGGCAAAGCTGAAGACTGTAAATGAAAACTGGAAA
AATCTGTCTAGTTCTCAAAACAAGTATACATTCAGCTTGCTAAAGATGATAAAATTCATTATGATAATGAAATGAAGTCT
TGGGAAGAACAAATGATTGAAGTTGGACAAAATGATTTTATACATTTTGAAATGAAGCAACCACCAAAATTTGGCAATGA
GGAGTGT

Alignment

ORF - retro_ptro_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRSMWGVLSALGRSGAELCTGCGSRLRSPFSFVYLPRWFSSVLASCPKKPVSSYLRFSKEQLPIFKAQNP
          LRSMWG.LSA..RS..ELCTGCGS.L..PFSFVYL..WFSS.LAS..KK...SYLRF.KEQL.IFK.QNP
Retrocopy LRSMWGMLSAQ*RSRVELCTGCGS*LCLPFSFVYLLKWFSSTLASYLKKSMVSYLRFLKEQLLIFKVQNP

Parental  DAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLE-KEIMDKHLKRKA
          D.K..ELI.RI...WREL.DS.KKIY.DA.RA.WQ...EEI.R..EQLTPSQI.SLE.KEIM........
Retrocopy DTKNSELIKRITELWRELADSEKKIYEDANRAVWQAFREEINRIQEQLTPSQIISLE<KEIMXXXXXXXX

Parental  MTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSE-KELYIQHAKEDETRY
          ......L..LGKPKR..SAYN..V.E.FQEAK..S.Q.KLKTV.ENWKNLS.S..K..YIQ.AK.D...Y
Retrocopy XXXXXXLIMLGKPKRSCSAYNIFVSEIFQEAKDGSSQAKLKTVNENWKNLSSSQ<KQVYIQLAKDDKIHY

Parental  HNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEEC
          .NEMKSWEEQMIEVG..D......K...K.G.EEC
Retrocopy DNEMKSWEEQMIEVGQNDFIHFEMKQPPKFGNEEC

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	4.47 RPM
SRP007412_cerebellum	0.00 RPM	9.89 RPM
SRP007412_heart	0.00 RPM	11.45 RPM
SRP007412_kidney	0.00 RPM	11.64 RPM
SRP007412_liver	0.00 RPM	9.46 RPM
SRP007412_testis	0.00 RPM	189.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_641 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_641 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_745

---

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,