RetrogeneDB ID: retro_ggor_836

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:114238178..114238787(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTF1
• Ensembl ID: ENSGGOG00000011920
• Aliases: None
• Description: None

Sequence

>retro_ggor_836
ATGTCAAAGCTGCCACCCAAACCGGTCAAACCAGGGTAAGATAAAGTCTTCAGAGCCCTCTATACTTTTGAACCCAGAAC
TCCAGATGAACTATGCTTTGAGAAAGGTGATATCATCTACGTTACTGACGTGAATGATGCAAATTGGTGGAAAGGCACCT
CCAAAGGCAGGACTGGACTAACTCCAAGCAACTATGTGGCCGAACAGGCAGAATCCATTGACAATCTATTGCATGAAGTA
GCAAAAAGAGGCAACTTGAGTTGGTTGCGAGAGTGTTTGGACAACGGAGTGGGTGTTAATGGCTTAGACAAGGCTGAAAG
CACTGCCTTAGACTAGGCTTGTCATGGGGATCTCAGAGATATAGTGGAAATGCTATTTACTCAATGGAGTATTTAACTGA
GCCAACAGAAAAAGTTGGGAGACACAGCTTTGCATGCTGCTGCCTGGAAGGGTTATGCAGATATTGTCCAGCTGCTTCTG
GCAAAAGGTGCCAGAACAGACTGAAGAAACAATGAGAAGAAGCTGGCTTTGGGCATGGCTACCAATGCCCACGCGTCTCT
CCTGAAAAAGAAACAGGAGACAGATGCAGTTCGAACACTAAGCAATGCT

Alignment

ORF - retro_ggor_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.8 %
• Parental protein coverage: 95.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKPPPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQA
          MSK.PPKPVKPG..KVFRALYTFEPRTPDEL.FE.GDIIY.TD..D.NWWKGTSKGRTGL.PSNYVAEQA
Retrocopy MSKLPPKPVKPG*DKVFRALYTFEPRTPDELCFEKGDIIYVTDVNDANWWKGTSKGRTGLTPSNYVAEQA

Parental  ESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQNKLG
          ESIDN.LHE.AKRGNLSWLRECLDN.VGVNGLDKA.STAL..ACHG...DIVEMLFTQ..I.L.QQ.KLG
Retrocopy ESIDNLLHEVAKRGNLSWLRECLDNGVGVNGLDKAESTALD*ACHGDLRDIVEMLFTQWSI*LSQQKKLG

Parental  DTALHAAAWKGYADIVQLLLAKGARTDLRNIEKKLAFDMATNAACASLLKKKQGTDAVRTLSNA
          DTALHAAAWKGYADIVQLLLAKGARTD.RN.EKKLA..MATNA..ASLLKKKQ.TDAVRTLSNA
Retrocopy DTALHAAAWKGYADIVQLLLAKGARTD*RNNEKKLALGMATNAH-ASLLKKKQETDAVRTLSNA

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	35.25 RPM
SRP007412_cerebellum	0.00 RPM	17.45 RPM
SRP007412_heart	0.00 RPM	8.38 RPM
SRP007412_kidney	0.00 RPM	32.59 RPM
SRP007412_liver	0.00 RPM	30.04 RPM
SRP007412_testis	0.00 RPM	21.13 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_836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_836 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1058
Pan troglodytes	retro_ptro_720
Pongo abelii	retro_pabe_883
Macaca mulatta	retro_mmul_836
Callithrix jacchus	retro_cjac_3249

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249,
Cavia porcellus	ENSCPOG00000007226	1 retrocopy	retro_cpor_1049,
Dipodomys ordii	ENSDORG00000002933	1 retrocopy	retro_dord_698,
Erinaceus europaeus	ENSEEUG00000008320	2 retrocopies	retro_eeur_545, retro_eeur_683,
Felis catus	ENSFCAG00000022374	1 retrocopy	retro_fcat_1869,
Homo sapiens	ENSG00000134996	1 retrocopy	retro_hsap_1058,
Gorilla gorilla	ENSGGOG00000011920	1 retrocopy	retro_ggor_836 ,
Macaca mulatta	ENSMMUG00000010401	1 retrocopy	retro_mmul_836,
Nomascus leucogenys	ENSNLEG00000001854	1 retrocopy	retro_nleu_2502,
Otolemur garnettii	ENSOGAG00000002603	1 retrocopy	retro_ogar_2962,
Pongo abelii	ENSPPYG00000019300	1 retrocopy	retro_pabe_883,
Pan troglodytes	ENSPTRG00000021031	1 retrocopy	retro_ptro_720,
Rattus norvegicus	ENSRNOG00000012156	2 retrocopies	retro_rnor_936, retro_rnor_937,
Sus scrofa	ENSSSCG00000005273	1 retrocopy	retro_sscr_979,
Tursiops truncatus	ENSTTRG00000003081	1 retrocopy	retro_ttru_492,