RetrogeneDB ID: retro_pabe_2013

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:91917674..91918003(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000012616
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHOC
• Ensembl ID: ENSPPYG00000010686
• Aliases: None
• Description: ras homolog family member C [Source:HGNC Symbol;Acc:669]

Sequence

>retro_pabe_2013
AAAGACGAGTTCCCGGAAGTGTTACGTACCCACGGTCTTCGAGACTATGTGCGACATCGGAGGTGGACGGCAAGCAGGTG
GAGCTGGCGCTGTGGGACACCGCGGGCCAGGAGGACTACGACCGCCTGCGGCCGCTCTCCTACCCGGACACCGACGTCAT
CCTCATGTGTTTCTCGGTGGACAGCCCGGACTCGCTGGAGAACATCCCCGAGAAGTGGGTCCCCGAGGTGAAGCACTTCT
GTCCCAACGTGCCCATCATCCTGGTGGCCAACAAAAAAGACCTGCGCAGCGACGAGCATGTCCGCACAGAGCTGGCCCGC
ATGAAGCAG

Alignment

ORF - retro_pabe_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 65.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDQFPEV-YVPTVFENYIADI-EVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLEN
          KD.FPEV.YVPTVFE....DI.EVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFS.DSPDSLEN
Retrocopy KDEFPEV>YVPTVFET-MCDI>EVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSVDSPDSLEN

Parental  IPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQ
          IPEKW.PEVKHFCPNVPIILV.NKKDLR.DEH.R.ELA.MKQ
Retrocopy IPEKWVPEVKHFCPNVPIILVANKKDLRSDEHVRTELARMKQ

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	29.08 RPM	6.69 RPM
SRP007412_cerebellum	14.71 RPM	2.19 RPM
SRP007412_heart	14.66 RPM	6.62 RPM
SRP007412_kidney	24.40 RPM	23.87 RPM
SRP007412_liver	23.96 RPM	12.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2013 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2013 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_178

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004807	1 retrocopy	retro_meug_37,
Pongo abelii	ENSPPYG00000010686	2 retrocopies	retro_pabe_2013 , retro_pabe_2979,
Tetraodon nigroviridis	ENSTNIG00000015041	1 retrocopy	retro_tnig_2,