RetrogeneDB ID: retro_ggor_1019

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:1103671..1104135(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB7
• Ensembl ID: ENSGGOG00000012164
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:G3R8Z6]

Sequence

>retro_ggor_1019
TCCAACTTGGAGCTCCACTCCATCTCTAGTGGTCATCTTCCTGAGTTGTCATGGCCAATCAGATGCTGAAGCAAATGCTT
TTAAAGAATCAAGTTTACATTGGTGCAGCCCTAGTTTTAAGGAGATTGAGAGTTTTTACTGGACCTCACCTCTACAGCAT
CTATCCTCATGAATCAACTGATAACTTGCCTCATCACCATGGATCCTTGGCAGCAAAGGCTGTATTTGAAGATATTCTAG
GCCAGATATGGGGGAAGAGGAAGCAAAGAAGATGGTAAGTGAAGCCACTGCAGCTGGCTTCTTCAACAACCTGGGCTCTG
GAAGCCACATTGATCTCAGCATTATAGGCAAGAGCAAGGTAGATTTTCTTGGCCCATTCACAGTGCCCAAAAAGAAGGGG
ACTAGATTTGGCAGGTACAGGTGTGAGAAAAGGGACCACTGCAGTCCTCACCAAAGAAGCCACT

Alignment

ORF - retro_ggor_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNLELHSLSTGRLPR-VVTANRMLKQMLFRYQGYIGAALVLGGVDV-TGPHLYSIYPHGSTDKLPYVTMG
          SNLELHS.S.G.LP..VV.AN.MLKQML...Q.YIGAALVL....V.TGPHLYSIYPH.STD.LP.....
Retrocopy SNLELHSISSGHLPE<VVMANQMLKQMLLKNQVYIGAALVLRRLRVFTGPHLYSIYPHESTDNLPH---H

Parental  SGSLAAMAVFEDKF-RPEMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDFLRPYTVPNKKGT
          .GSLAA.AVFED...RP.M.EEEAK..VSEA.AAG.FN.LGSGS.IDL..I.K.K.DFL.P.TVP.KKGT
Retrocopy HGSLAAKAVFEDIL<RPDMGEEEAKKMVSEATAAGFFNNLGSGSHIDLSIIGKSKVDFLGPFTVPKKKGT

Parental  RLGRYRCEK-GTTAVLTEKIT
          R.GRYRCEK.GTTAVLT...T
Retrocopy RFGRYRCEK>GTTAVLTKEAT

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	128.04 RPM
SRP007412_cerebellum	0.00 RPM	70.33 RPM
SRP007412_heart	0.00 RPM	71.23 RPM
SRP007412_kidney	0.00 RPM	142.46 RPM
SRP007412_liver	0.00 RPM	99.31 RPM
SRP007412_testis	0.00 RPM	220.46 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_1019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1019 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1303

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019 ,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,