RetrogeneDB ID: retro_ggor_745

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:107641293..107642018(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSGGOG00000004948
• Aliases: None
• Description: None

Sequence

>retro_ggor_745
CTTCGAAGCATGTGGGGCATGCTGAGTGCCCAGTGAAGGTCCAGAGTGGAGCTGTGCACTGGTTGTGGAAGTTGACTGTG
CTTACCTTTCAGTTCTGTGTATTTACTGAAATGGTTTTCATCCACCTTAGCTAGTTATCTGAAGAAACCTATGGTGTCTT
ACCTTTGATTTTTGAAAGAACAGATACTCATATTTAAAGTTCAGAACCCAGATGCAAAAAATTCAGAACTAATTAAAAGA
GTCACTGAGCTATGGAGAGAACTTGCTGATTCAGAGAAAAAATATATGAAGATGCTAACACGGCAGTCTGGCAGGCATTC
AGAGAAGAGATAAACAGAATTCAGAACAGCTAACTCCAAGTCAGATAATATCTTTGGAAAAGAAATCATGCAAAAACTTT
AAAAAAAGAAAGCGTTAATAAAAAAGAGAAAGCTAATAATGCTTGGAAAACCTAAAATATCTTGCTCAGCTTACAACATT
TTTGTATCTGAAAGCTTCCAAGAAGCTAAGGATGGTTCATCACAGGCAAAGCTGAAGACTGTAAATGAAAACTGGAAAAA
TCTATCTAGTTCTCAAAACAAGTATACATTCAGCTTGCTAAAGATGATAAAATTCATTATGATAATGAAATGAAGTCTTG
GGAAGAACAAATGATTGAAGTTGGACAAAATGATTTTATACATCTTGAAATGAAGCAACCACCAAAATTTGGCAATGAGG
AGTGT

Alignment

ORF - retro_ggor_745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.13 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LRSMWGVLSALGRSGAELCTGCGSRLRSPFSFVYLPRWFSSVLASCPKKPVSSYLRFSKEQLPIFKAQNP
          LRSMWG.LSA..RS..ELCTGCGS.L..PFS.VYL..WFSS.LAS..KKP..SYL.F.KEQ..IFK.QNP
Retrocopy LRSMWGMLSAQ*RSRVELCTGCGS*LCLPFSSVYLLKWFSSTLASYLKKPMVSYL*FLKEQILIFKVQNP

Parental  DAKTTELIRRIAQRWRELPDSKK-KIYQDAYRAEWQVYKEEISRFK-EQLTPSQIMSLE-KEIMDKHLKR
          DAK..ELI.R....WREL.DS.K.KIY.DA..A.WQ...EEI.R...EQLTPSQI.SLE.KEIM......
Retrocopy DAKNSELIKRVTELWRELADSEK<KIYEDANTAVWQAFREEINRIQ<EQLTPSQIISLE<KEIMXXXXXX

Parental  KAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSE-KELYIQHAKEDET
          ........L..LGKPK...SAYN..V.E.FQEAK..S.Q.KLKTV.ENWKNLS.S..K..YIQ.AK.D..
Retrocopy XXXXXXXXLIMLGKPKISCSAYNIFVSESFQEAKDGSSQAKLKTVNENWKNLSSSQ<KQVYIQLAKDDKI

Parental  RYHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEEC
          .Y.NEMKSWEEQMIEVG..D......K...K.G.EEC
Retrocopy HYDNEMKSWEEQMIEVGQNDFIHLEMKQPPKFGNEEC

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	6.81 RPM
SRP007412_cerebellum	0.00 RPM	6.89 RPM
SRP007412_heart	0.00 RPM	2.41 RPM
SRP007412_kidney	0.00 RPM	13.25 RPM
SRP007412_liver	0.00 RPM	9.10 RPM
SRP007412_testis	0.00 RPM	53.46 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_745 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_641

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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,