RetrogeneDB ID: retro_pabe_3131

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:39155165..39155464(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000017583
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS23
• Ensembl ID: ENSPPYG00000025941
• Aliases: None
• Description: mitochondrial ribosomal protein S23 [Source:HGNC Symbol;Acc:14509]

Sequence

>retro_pabe_3131
ATTGGAGCAAAATCCTATTCAGCCTACAAATCTGGTCAAAAGCTTTTGATCTGTTCAATCCAGGCTTCAAGCCTACCTGT
CAATGCTTTGTGAAGTATATTGAGCTGCAGAAACTTAAAGAAACAGATGAAGAGAAGTTATTTGTAGAAACAAGGAAAGC
TTTATTGGCAGAAAGTGTCATTTTAAGATGAGTAGGAGAAGCAAGGACTCAACAGGAAGGTAGTCACATTTCCTGGAAAT
CTGAACACATGATTGTCAGACCCCAAACTGCGTTGAAAGAAAACCAGCCTCAGAAAGAA

Alignment

ORF - retro_pabe_3131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRAKFYSVYGSGQR-AFDLFNPNFKSTCQRFVEKYAVLQKLGETDEEKLFVETGKALLAEGVILRRVGEA
          I.AK.YS.Y.SGQ..AFDLFNP.FK.TCQ.FV.KY..LQKL.ETDEEKLFVET.KALLAE.VILR.VGEA
Retrocopy IGAKSYSAYKSGQK<AFDLFNPGFKPTCQCFV-KYIELQKLKETDEEKLFVETRKALLAESVILR*VGEA

Parental  RTQHGGSHVSWKSEHLNVRPQTALEENETQKE
          RTQ..GSH.SWKSEH..VRPQTAL.EN..QKE
Retrocopy RTQQEGSHISWKSEHMIVRPQTALKENQPQKE

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	0.17 RPM	22.23 RPM
SRP007412_cerebellum	0.00 RPM	19.82 RPM
SRP007412_heart	0.03 RPM	8.88 RPM
SRP007412_kidney	0.07 RPM	16.11 RPM
SRP007412_liver	0.06 RPM	10.71 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3131 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3131 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3727
Pan troglodytes	retro_ptro_2523
Macaca mulatta	retro_mmul_1691

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014008	1 retrocopy	retro_cjac_3047,
Cavia porcellus	ENSCPOG00000008761	1 retrocopy	retro_cpor_1175,
Felis catus	ENSFCAG00000005711	1 retrocopy	retro_fcat_963,
Homo sapiens	ENSG00000181610	1 retrocopy	retro_hsap_3727,
Macaca mulatta	ENSMMUG00000001913	1 retrocopy	retro_mmul_1691,
Mustela putorius furo	ENSMPUG00000015372	1 retrocopy	retro_mputfur_1274,
Nomascus leucogenys	ENSNLEG00000008072	1 retrocopy	retro_nleu_1972,
Pongo abelii	ENSPPYG00000025941	1 retrocopy	retro_pabe_3131 ,
Pan troglodytes	ENSPTRG00000009440	1 retrocopy	retro_ptro_2523,
Tarsius syrichta	ENSTSYG00000009862	1 retrocopy	retro_tsyr_2077,