RetrogeneDB ID: retro_pabe_3456

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:23781403..23781760(-)
• Located in intron of: ENSPPYG00000019054

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSPPYG00000016613
• Aliases: None
• Description: 28S ribosomal protein S10, mitochondrial [Source:RefSeq peptide;Acc:NP_001124609]

Sequence

>retro_pabe_3456
CACGGTAAGGCTGTATTGGACAGTTAGGAATATTTTCCTGTGCTTGCTGCTAAAGAACTTGGTATCTCTATTAAAGTACA
CGAACCTCCAAAGAAAACAGAGCGATTTACTCTTCTCAAATCAGTGCATATTTACAAGAAGCACAGAGTTGAGTATGAAA
TGAGAACACTTCACAGATGTTTAGAGTTAGAACCTCTAACTGGAAGCACAGCAGACGTCTACTTGGAATATATTCAGCGA
AACTTACCTGAAGGGGTTGCCATGGAAGTGACAAAGACACAATTAGAACAGTTACCAGAACACGTCAAGGAGCCAGTCTG
GGAAACACTATCAGAAGAAGAAGAAGAAAGCAAGTCC

Alignment

ORF - retro_pabe_3456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLQSVHIYKKHRVQYEMRTLYRCLELEHLTGST
          H.KAVLDS.EYF.VLAAKELGISIKVHEPP.K.ERFTLL.SVHIYKKHRV.YEMRTL.RCLELE.LTGST
Retrocopy HGKAVLDS*EYFPVLAAKELGISIKVHEPPKKTERFTLLKSVHIYKKHRVEYEMRTLHRCLELEPLTGST

Parental  ADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS
          ADVYLEYIQRNLPEGVAMEVTKTQLEQLPEH.KEP.WETLSEE.EESKS
Retrocopy ADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHVKEPVWETLSEEEEESKS

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	9.40 RPM
SRP007412_cerebellum	0.00 RPM	6.08 RPM
SRP007412_heart	0.09 RPM	6.83 RPM
SRP007412_kidney	0.07 RPM	7.62 RPM
SRP007412_liver	0.09 RPM	7.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3456 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3456 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4157
Pan troglodytes	retro_ptro_2826

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456 ,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,