RetrogeneDB ID: retro_ggor_3060

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:128191044..128191360(-)
• Located in intron of: ENSGGOG00000007569

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL4A
• Ensembl ID: ENSGGOG00000005285
• Aliases: None
• Description: None

Sequence

>retro_ggor_3060
GACCGAGGCGTCATCATTTGGTTTGGACATAATTGGGACCCTACTTTTATGAATATGAATGAGTTCTGTATTGTATAGCT
GAAAAGGTTAAAAATGTTGTAGTTATTTATCTTGATATTACAGAAGTACTTTACTTCAACAAAAATGTATGAGTTTATAT
GATCTATGTATTGTCATATTTTTATTTGGGAACAAGCACATCATGATTTTGACTTGATTACTGGCAACAACAAGATTAAC
TGGGCCACAGAAGGACAAACAGGAGATGGTCAACATAATAGAGACTGTGTATTGAGGTCCCCGCAAAGAACGAGGT

Alignment

ORF - retro_ggor_3060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.3 %
• Parental protein coverage: 74.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DRVVVIRFGHDWDPTCMKMDE-VLYSIAEKVKNFAVIYLVDITEVPDFNK-MYE-LYDPCTVMFFFRNKH
          DR.V.I.FGH.WDPT.M.M.E.VLY.IAEKVKN..VIYL.DITEV..FNK.MYE.LYD.C.V.F.F.NKH
Retrocopy DRGVIIWFGHNWDPTFMNMNE<VLYCIAEKVKNVVVIYL-DITEVLYFNK>MYE>LYDLCIVIFLFGNKH

Parental  IMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRG
          IMI...............DKQEMV.IIETVY.G.RK.RG
Retrocopy IMILT*LLATTRLTGPQKDKQEMVNIIETVY*GPRKERG

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	0.05 RPM	45.27 RPM
SRP007412_cerebellum	0.00 RPM	24.43 RPM
SRP007412_heart	0.00 RPM	28.74 RPM
SRP007412_kidney	0.04 RPM	41.62 RPM
SRP007412_liver	0.00 RPM	24.43 RPM
SRP007412_testis	0.00 RPM	34.60 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_3060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3060 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4900
Macaca mulatta	retro_mmul_2636

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060 ,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,