RetrogeneDB ID: retro_ggor_3016

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:54333462..54334158(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPIN
• Ensembl ID: ENSGGOG00000000061
• Aliases: None
• Description: None

Sequence

>retro_ggor_3016
TCAGGAAGTGGAGCACTTGTTCCTGTACCTCCAAAGAGAGCAGTTAAAAGAAATATATCCAAGCTGGATGCTCACAGATT
AATTTCAGAGAGAGGGCTTCCAGCCTTAAGGCATGTATTTGATAAGGCAAAATTCAAAGGTAAAAGTCATGAGGCTGAAG
ACTTAAAGATGCTAATCAGACACATGGAACACTGGGCATGTAGGCGATTCCCTAAACTGCAGTTTGAGGATTTTATTGAC
AGAGTTGAATACCTGAGAAATAAAAAGGAAATTCAGACCTGTTTAAAATGAATTCGACTTGATCTCCCTATTTTACATGA
ATGTGTTGTTAGCAATAATGAGGAAGTTGGGGAAAATAATGGACATTGTGTAACTGCTACTGAATTAGATCCCTTTCTGA
CAAACTCATCTGAAAGTGAGATGTTTGCTTCTGAGTCAAGTAGAAGCCTAACAGATGAGCAACAACAAAGGATTGAGAGA
AATAAACAACCGGCTTTGGAAAGAAGGCAGGCAAAGCTGCTGAGTAATAGTCCCTAGGAAATGATAATGTTAATGAATAC
ACCCAGGGTACAGACAATTGAAGAGGTTAATACTGATGAAGATCAAAAGGAGGAGTCAAATGGATTAAACAACGACATTC
TAGACAATCTATGTAATGATACTCCTGCCAATACTTTGAATGAAGAGAATGATTTA

Alignment

ORF - retro_ggor_3016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.74 %
• Parental protein coverage: 77.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGNGAPVPVPPKRTVKRNIPKLDAQRLISERGLPALRHVFDKAKFKGKGHEAEDLKMLIRHMEHWAHRLF
          SG.GA.VPVPPKR.VKRNI.KLDA.RLISERGLPALRHVFDKAKFKGK.HEAEDLKMLIRHMEHWA.R.F
Retrocopy SGSGALVPVPPKRAVKRNISKLDAHRLISERGLPALRHVFDKAKFKGKSHEAEDLKMLIRHMEHWACRRF

Parental  PKLQFEDFIDRVEYLGSKKEVQTCLKRIRLDVPILHEDFVSNNDEVAENNEHDVTSTELDPFLTNLSESE
          PKLQFEDFIDRVEYL..KKE.QTCLK.IRLD.PILHE..VSNN.EV.ENN.H.VT.TELDPFLTN.SESE
Retrocopy PKLQFEDFIDRVEYLRNKKEIQTCLK*IRLDLPILHECVVSNNEEVGENNGHCVTATELDPFLTNSSESE

Parental  MFASELSRSLTEEQQQRIERNKQLALERRQAKMLSNSQ-TLGND-MLMNTPRAHTVEEVNTDEDQKEESN
          MFASE.SRSLT...QQ............R....L......LGND.MLMNTPR..T.EEVNTDEDQKEESN
Retrocopy MFASESSRSLTD-EQQQRIERNKQPALERRQAKLLSNS<SLGND>MLMNTPRVQTIEEVNTDEDQKEESN

Parental  GLNEDILDNPCNDAIANTLNEEETL
          GLN.DILDN.CND..ANTLNEE..L
Retrocopy GLNNDILDNLCNDTPANTLNEENDL

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	4.17 RPM
SRP007412_cerebellum	0.00 RPM	7.53 RPM
SRP007412_heart	0.00 RPM	0.78 RPM
SRP007412_kidney	0.00 RPM	4.78 RPM
SRP007412_liver	0.00 RPM	3.96 RPM
SRP007412_testis	0.00 RPM	19.99 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_3016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016 ,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,