RetrogeneDB ID: retro_pabe_2599

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4_random:8291664..8292268(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSPPYG00000012825
• Aliases: None
• Description: speckle-type POZ protein-like [Source:HGNC Symbol;Acc:27934]

Sequence

>retro_pabe_2599
ATGTTTCAGGAGCCCGCCCCACCTCTATCTAGATGTATGTCTTCTTGTCCCATAACAGAAAGCTAGTGTTATACACAGAT
CAAAGTAGTAAAATGTTCGACACGTAGACCATTAATAACTTCAGTTTTTGTCAAGAGGAAATGGGTGAGGTGTTAAAAAG
TTCCACATTTTCGCCTGGCCCAGTGACAAAATGAAATGGTGCCTGAGGGTAAACCCAAAGGGATTAGATAATGAAAGTAA
AGACTACTTGTCCTTATATTTGCTTTTAGTCAGATGCTCCAAAAGTGAAGTGTGAGCAAAATTCAAATTTTCCCTTCTGA
ATGCTAAAAGGGAAGAAACAAAAGCAATGGAAAGCCAAAGAGCATATCAATTTGTGCAAGGGAAGGACAGCGATTTTTAA
AAATTCATTAGAAGGAACCTTTTGCTTGACGAAGCTAATGGTCTTTTACCAGATGACAAGCTTACATTATTTTGTGAGGT
GAGTATGGTCCAAAATGCAGTAAACAAATCAGGACATACTAATACAAACACTTTGAAGGTGGCTGAGTGTCGGCTAGGAG
AAGATTTAGGTAATCTCTGGGAAAACACAAGATTTACAGACTGC

Alignment

ORF - retro_pabe_2599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSREPTPPLPGDMSTGPIAESWCYTQVKVV-KFSYMWTINNFSFCREEMGEVLKSSTFSSGP-SDKMKWC
          M..EP.PPL...MS..PI.ES.CYTQ.KVV.K.....TINNFSFC.EEMGEVLKSSTFS.GP.SDKMKWC
Retrocopy MFQEPAPPLSRCMSSCPITES*CYTQIKVV<KMFDT*TINNFSFCQEEMGEVLKSSTFSPGP<SDKMKWC

Parental  LRVNPKGLDDESKDYLSLYLLLVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFIR
          LRVNPKGLD.ESKDYLSLYLLLV.C.KSEV.AKFKFSLLNAKREETKAMESQRAY.FVQGKD..F.KFIR
Retrocopy LRVNPKGLDNESKDYLSLYLLLVRCSKSEV*AKFKFSLLNAKREETKAMESQRAYQFVQGKDSDF*KFIR

Parental  RDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDC
          R..LLDEANGLLPDDKLTLFCEVS.VQ..VN.SGHTNTNTLKV.ECRL.EDLGNLWENTRFTDC
Retrocopy RNLLLDEANGLLPDDKLTLFCEVSMVQNAVNKSGHTNTNTLKVAECRLGEDLGNLWENTRFTDC

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	12.00 RPM
SRP007412_cerebellum	0.00 RPM	22.74 RPM
SRP007412_heart	0.00 RPM	7.29 RPM
SRP007412_kidney	0.00 RPM	13.39 RPM
SRP007412_liver	0.00 RPM	7.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2599 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2599 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599 ,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,