RetrogeneDB ID: retro_pabe_3268

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:76309026..76309307(+)
• Located in intron of: ENSPPYG00000029711

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGS10
• Ensembl ID: ENSPPYG00000002702
• Aliases: None
• Description: regulator of G-protein signaling 10 [Source:HGNC Symbol;Acc:9992]

Sequence

>retro_pabe_3268
AGGAAATTTTTTAAAAAGATATTCAATGAAGAAAATATTTTGTTTTGGCTAGCATGTAAAGATTTCTTTTTTTAATGCAA
GATAAGCAGATGCAGGAAAAGGCAAAGGAGGTCTACATGACCTTTCTTTCCAGTAAGGCCTCGTCACAAGTCAAAAAGAG
GCAGTCTTCACTCAACGAAAAGATCCTGGAAGAACCACATCCTCTGATGTTCCAGGAACTCCAGGACTGGATTTTCAATC
TCACGAAGTACAACAGCTACAGTAGCTGCTTAAAGTTTGAC

Alignment

ORF - retro_pabe_3268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 75.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QEFLKKEFSEENVLFWLACED-FKKMQDKTQMQEKAKEIYMTFLSSKASSQVNVEGQSRLNEKILEEPHP
          ..F.KK.F.EEN.LFWLAC.D.F.......QMQEKAKE.YMTFLSSKASSQV....QS.LNEKILEEPHP
Retrocopy RKFFKKIFNEENILFWLACKD<FLFLMQDKQMQEKAKEVYMTFLSSKASSQVK-KRQSSLNEKILEEPHP

Parental  LMFQKLQDQIFNLMKYDSYSRFLKSD
          LMFQ.LQD.IFNL.KY.SYS..LK.D
Retrocopy LMFQELQDWIFNLTKYNSYSSCLKFD

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	1.94 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.00 RPM	2.12 RPM
SRP007412_liver	0.00 RPM	1.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3268 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3268 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2669
Macaca mulatta	retro_mmul_2295

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000008414	1 retrocopy	retro_ggor_2669,
Macaca mulatta	ENSMMUG00000021610	1 retrocopy	retro_mmul_2295,
Nomascus leucogenys	ENSNLEG00000016735	1 retrocopy	retro_nleu_2034,
Procavia capensis	ENSPCAG00000003150	1 retrocopy	retro_pcap_59,
Pongo abelii	ENSPPYG00000002702	1 retrocopy	retro_pabe_3268 ,