RetrogeneDB ID: retro_ggor_2742

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:86277500..86278021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTA1
• Ensembl ID: ENSGGOG00000015524
• Aliases: None
• Description: None

Sequence

>retro_ggor_2742
ATGTTCATGATTGCTCTACTGTCCCCACCTCCTCCCCAGTTTAAGAGCATACAGCATCATATGAAAACAGCTCAGGAGCA
TGACAAGCCAGACCCCTCAGTGCTCTATTACTGTTGTTTCTATGCAATGCAAACCAGAATGAAGACTGATAGTAAAACTC
CTGAGAGTTGTACATTTTTATCAAAGCTAATGGATCAGTTAGAAATACTTATGAAACAGTTGGGTGATCATGAAGCTATT
AGGCAAGAAAATACTTAGTCCTGCCCATTTGGAGAACTATGCTTAGAAAATGTTTTTATACTCAGACAATGATCATGCTG
GGTGATTTCACAAGATGATCAAGCCCTTTTTATACTCCATAGTTTTAAATAGATGTCATAATAATATTAGGACAACTCAT
TGATGAAAATGTGAAACATAGAAAGCATGTAAGATGAAAGGCAAAATATATTCATATTTGTTTAAAGAATGGGGAGCTGC
CTCAACTAGTATCTGCTGGAATTGAAGAAGATAACAATATA

Alignment

ORF - retro_ggor_2742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.93 %
• Parental protein coverage: 57.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEAL
          M...A.L.P.P.QFKSIQHH..TAQEHDK.DP.V.YYC..YAMQT.MK.DSKTPE...FLSKLMDQLE.L
Retrocopy MFMIALLSPPPPQFKSIQHHMKTAQEHDKPDPSVLYYCCFYAMQTRMKTDSKTPESCTFLSKLMDQLEIL

Parental  KKQLGDNEAITQE-IVGCAHLENYALKMFLYADNEDRAGRFHKNMIK-SFYTASLLIDVITVFGELTDEN
          .KQLGD.EAI.QE.I...AHLENYA.KMFLY.DN.D.AG.FHK.MIK..FYT....IDVI...G.L.DEN
Retrocopy MKQLGDHEAIRQE>ILSPAHLENYA*KMFLYSDN-DHAG*FHK-MIK>PFYTP*F*IDVIIILGQLIDEN

Parental  VKHRKYARWKATYIHNCLKNGETPQAGPVGIEEDNDI
          VKHRK..R.KA.YIH.CLKNGE.PQ....GIEEDN.I
Retrocopy VKHRKHVR*KAKYIHICLKNGELPQLVSAGIEEDNNI

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	30.64 RPM
SRP007412_cerebellum	0.00 RPM	24.31 RPM
SRP007412_heart	0.00 RPM	3.88 RPM
SRP007412_kidney	0.04 RPM	20.24 RPM
SRP007412_liver	0.00 RPM	16.35 RPM
SRP007412_testis	0.00 RPM	19.58 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_2742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2742 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4088

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742 ,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864, retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825,