RetrogeneDB ID: retro_ggor_380

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:42384857..42385332(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSGGOG00000013978
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:G3RDM5]

Sequence

>retro_ggor_380
CATCTTCCTCTCACTGCCTTGGTGGATGGGCAGCTCTTCTGTCTCCATGGTGGTCTGTCACCATCTGTAGATACACTGCA
TCACATCAGAACACTGAATTGCCTACAGAAAATTCCCCATGAGGGTCCAATGGGTGACTTGCTATACTCAGATCCAGATG
ACCATGGTGGCTGGGGTATATCTCTTTGAGGAGATGGTTACACCTTTGGGCAAGATACTTCTGAGACATTTAATCATGCC
AATGGCCTCAGGTTGGTGTCTAGAGCTCACCAGCTGGTGATGGTGGGACATAACTGGTGTCATGACTGGAATGTAGTAGC
CATCTTCAGTACTCCAAACTATTGCTATCATTGTGGTAATCACACTGCAATCATGGAACTTGATAATACTCTAAAATACT
CTTTTTTTGCAGTATGACCCAGCACCTCACAGAGGCAAGCCACATGTTACTCATTGTACCCCAGATTACTTCCTG

Alignment

ORF - retro_ggor_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 51.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFG
          .LPLTALVDGQ.FCLHGGLSPS.DTL.HIR.L..LQ..PHEGPM.DLL.SDPDD.GGWGIS..G.GYTFG
Retrocopy HLPLTALVDGQLFCLHGGLSPSVDTLHHIRTLNCLQKIPHEGPMGDLLYSDPDDHGGWGISL*GDGYTFG

Parental  QDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYS-FLQFD
          QD.SETFNHANGL.LVSRAHQLVM.G.NWCHD.NVV.IFS.PNYCY.CGN..AIMELD.TLKYS.FLQ.D
Retrocopy QDTSETFNHANGLRLVSRAHQLVMVGHNWCHDWNVVAIFSTPNYCYHCGNHTAIMELDNTLKYS>FLQYD

Parental  PAPRRGEPHVTRRTPDYFL
          PAP.RG.PHVT..TPDYFL
Retrocopy PAPHRGKPHVTHCTPDYFL

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	117.92 RPM
SRP007412_cerebellum	0.00 RPM	98.02 RPM
SRP007412_heart	0.00 RPM	19.92 RPM
SRP007412_kidney	0.00 RPM	102.84 RPM
SRP007412_liver	0.00 RPM	51.04 RPM
SRP007412_testis	0.00 RPM	73.45 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_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_380 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_369

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012460	1 retrocopy	retro_cjac_985,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Homo sapiens	ENSG00000104695	1 retrocopy	retro_hsap_1631,
Gorilla gorilla	ENSGGOG00000013978	1 retrocopy	retro_ggor_380 ,
Macaca mulatta	ENSMMUG00000020819	1 retrocopy	retro_mmul_484,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Oryctolagus cuniculus	ENSOCUG00000005230	1 retrocopy	retro_ocun_1697,
Pongo abelii	ENSPPYG00000018491	1 retrocopy	retro_pabe_335,