RetrogeneDB ID: retro_pabe_3216

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:1903559..1903835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000020009
• Aliases: None
• Description: None

Sequence

>retro_pabe_3216
TGGTGTAAACCTGGGGCCTGGATGTCCATTTGAGGCCTGATGTACACCTCAAGTCCAGTGTCCACCTGTGGCCTGATGTC
AACTTGGAAGCTGATATCCACCTGGGGACTGATGTTCTCCTGGGTCCTGATATCCAACTGGGATCAGATGTTCACCTAAG
GCCTGGAGTTAATCTGGGGCCTGATGGTCACCAGGGTCCCAGGTGTCCACCTAGGGCTTAGTGTCCAACTAGGGCCTGAT
GTCCACCTGGAGTCTAGTATCCACCTTGGCCCTGAT

Alignment

ORF - retro_pabe_3216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.04 %
• Parental protein coverage: 61.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WCPPCGLMYSWVLVSSWGLVFTWGLMSTLRL-GIHQGTSVQLGPDIHLGPGVNLKHGINLGPG-YLPGSW
          WC.P...M....L......V.T.GLMST..L..IH.GT.V.LGPDI.LG..V.L..G.NLGP....PGS.
Retrocopy WCKPGAWMSI*GLMYTSSPVSTCGLMSTWKL<DIHLGTDVLLGPDIQLGSDVHLRPGVNLGPD<WSPGSQ

Parental  IFIVDLVSTWGLMSTLGL-GIYLGPD
          .....LVS..GLMST..L..I.LGPD
Retrocopy VST*GLVSN*GLMSTWSL<SIHLGPD

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	0.06 RPM	0.00 RPM
SRP007412_cerebellum	0.24 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3216 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000025403	2 retrocopies	retro_ggor_1605, retro_ggor_78,
Pongo abelii	ENSPPYG00000020009	1 retrocopy	retro_pabe_3216 ,