RetrogeneDB ID: retro_pabe_2979

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:92880903..92881277(-)
• Located in intron of: None

Retrocopy information

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

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_2979
GTCCGTGTCGGTGACGGAGTCTGTGGCAAGACATGCTTGCTCATTGTCTTCAGCAAGGACCAGTTCCCAGAGGGGTGCGC
ACCCTCAGGGTTTCAGAACTATGTGGCCCATATTGAGGATGGGAAACGCGTAGAGCTGACTTTGTGGGACACAGCCAGGC
AGGAAGATTAGGATCGCCTGAGGTCCCTCTTTTACTCAGACACTGATGTTATGTGTTCTCCGTTGACAATCCTGATAGTC
TAGAAAACATCTCAGAGAAATGGAGCCCAGAAGTCAAGCATTTCTGTCCCAACGTGCCCACCGGCCTGGTTGGGAACAAG
AAGGATCTTCGGAATGATGTGCACACAAGGTGGGAGCTAGCCAAGATGAAGCAG

Alignment

ORF - retro_pabe_2979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.74 %
• Parental protein coverage: 75.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTD
          V.VGDG.CGKTCLLIVFSKDQFPE...P..F.NY.A.IE.DGK.VEL.LWDTA.QED.DRLR.L.Y.DTD
Retrocopy VRVGDGVCGKTCLLIVFSKDQFPEGCAPSGFQNYVAHIE-DGKRVELTLWDTARQED*DRLRSLFYSDTD

Parental  VILMC-FSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQ
          V..MC.FS.D.PDSLENI.EKW.PEVKHFCPNVP..LVGNKKDLR.D.HTR.ELAKMKQ
Retrocopy V--MC<FSVDNPDSLENISEKWSPEVKHFCPNVPTGLVGNKKDLRNDVHTRWELAKMKQ

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	6.69 RPM
SRP007412_cerebellum	0.00 RPM	2.19 RPM
SRP007412_heart	0.00 RPM	6.62 RPM
SRP007412_kidney	0.00 RPM	23.87 RPM
SRP007412_liver	0.00 RPM	12.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2979 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2979 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3632
Pan troglodytes	retro_ptro_2456
Gorilla gorilla	retro_ggor_2450

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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,