RetrogeneDB ID: retro_pabe_335

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:189141974..189142449(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSPPYG00000018491
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_pabe_335
CATCTTCCTCTCACTGCCTTGGTGGATGGGCAGCTCTTCCGTCTCCATGGTGGCCTGTCGCCATCTGTAGATACACTGTA
TCACATCAGAACACTGAATTGCCTACAGAAAATTCCCCATGAAGGTCCAATGGGTGACTTACTATACTGAGATCCAGATG
ACCATGGTGGCTGGGGTATATCTCTTTGAGGAGATGGTTACACCTTTGGGCAAGATACTTCTGAGACATTTAATCATGCC
AATGGCCTCCGGTTGGTGTCTAGAGCTCACCAGCTGGTGATGGTGGGACATAACTGGTGTCAAGACTGGAATGTAGTAGC
CATCTTCAGTACTCCAAACTATTGCTATCGTTGTGGTAATCACGCTGCAATCATGGAACTTGATAATACTCTAAAATACT
CTTTTTTTGCAGTTTGACCCAGCACCTCACAGAGGCAAGCCACATGTTACTCATTGTACCCCAGATTACTTCCTG

Alignment

ORF - retro_pabe_335 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: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFG
          .LPLTALVDGQ.F.LHGGLSPS.DTL.HIR.L..LQ..PHEGPM.DLL..DPDD.GGWGIS..G.GYTFG
Retrocopy HLPLTALVDGQLFRLHGGLSPSVDTLYHIRTLNCLQKIPHEGPMGDLLY*DPDDHGGWGISL*GDGYTFG

Parental  QDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYS-FLQFD
          QD.SETFNHANGL.LVSRAHQLVM.G.NWC.D.NVV.IFS.PNYCYRCGN.AAIMELD.TLKYS.FLQFD
Retrocopy QDTSETFNHANGLRLVSRAHQLVMVGHNWCQDWNVVAIFSTPNYCYRCGNHAAIMELDNTLKYS>FLQFD

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	80.50 RPM
SRP007412_cerebellum	0.00 RPM	103.73 RPM
SRP007412_heart	0.00 RPM	57.44 RPM
SRP007412_kidney	0.00 RPM	65.37 RPM
SRP007412_liver	0.00 RPM	28.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_335 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_335 has 0 orthologous retrocopies within eutheria group .

---

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 ,