RetrogeneDB ID: retro_ggor_2144

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:195387033..195387573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSGGOG00000008681
• Aliases: None
• Description: None

Sequence

>retro_ggor_2144
ATGTCTTTTCCGGGCGGAGGTCGTGGAGGCTTTGATCGAGGTGGTGGAGGTGGCGGTTTCAACCGCGGCAGCAGCAGCAG
CAACCGCTTCTGAGGTGGAGGCGGTGGAAATATCAGAGGTGGCGACAGGGGAGGATTTGGACGAGGGGGTGGCCACGGAG
GCTTTACCAAAGGCCAAGGCCAAGGACCTCCAGAATGTGTAGTCTTATTAGGAGAGTTCCTGCATCCCTGTGAAGGTGAC
ATAGTTTGTAAACGTACTGCAGATGAAAATAAGGTGTCTTATTTCAATGCTCCCGTTTACTTAGAAAACAAAGAACAAAT
TGGAAAAGCGGATGAAATATTTGGACAACTTAGAGATTTTTATTTTTCCGTTAACATGTCAGAAAACGGGAAGGCTTCAT
CCTTTAAAAAACTCTAGAAGTTTTATATAGACCCATATGAGCTGCTGCCACTGCAGAGGTTTTTACCTCGGCCTCCAGGT
GAGAAAGGACCTCCAAGACGTGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGC

Alignment

ORF - retro_ggor_2144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.24 %
• Parental protein coverage: 84.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFRGGGRGGFNRGGGGGGFNRG-GSSNHFRGGGGGGGGGNFRGGGRGGFGRGGGRGGFNKGQDQGPPER
          MSF.GGGRGGF.RGGGGGGFNRG..SSN.F.GGGGG....N.RGG.RGGFGRGGG.GGF.KGQ.QGPPE.
Retrocopy MSFPGGGRGGFDRGGGGGGFNRGSSSSNRF*GGGGG----NIRGGDRGGFGRGGGHGGFTKGQGQGPPEC

Parental  VVLLGEFMHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFK
          VVLLGEF.HPCE.DIVCK.T.DENKV.YFNAPVYLENKEQIGK.DEIFGQLRDFYFSV..SEN.KASSFK
Retrocopy VVLLGEFLHPCEGDIVCKRTADENKVSYFNAPVYLENKEQIGKADEIFGQLRDFYFSVNMSENGKASSFK

Parental  KLQKFYIDPYKLLPLQRFLPRPPGEKGPPRGGGRGGRGGGRGGG
          KL.KFYIDPY.LLPLQRFLPRPPGEKGPPR.GGRGGRGG.RGGG
Retrocopy KL*KFYIDPYELLPLQRFLPRPPGEKGPPRRGGRGGRGGRRGGG

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	6.76 RPM
SRP007412_cerebellum	0.00 RPM	6.38 RPM
SRP007412_heart	0.00 RPM	4.75 RPM
SRP007412_kidney	0.00 RPM	10.02 RPM
SRP007412_liver	0.00 RPM	8.94 RPM
SRP007412_testis	0.10 RPM	15.02 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_2144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2144 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3130

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144 ,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,