RetrogeneDB ID: retro_pabe_862

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:76611049..76611442(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF1
• Ensembl ID: ENSPPYG00000012270
• Aliases: None
• Description: polycomb group ring finger 1 [Source:HGNC Symbol;Acc:17615]

Sequence

>retro_pabe_862
TCCCGAGGTTTGGACCGGGTCACCCAGCCCAGTCGGGAAGAGCCAGCAGTGAGCAACCTTGGCCTCCGCTTCAGCAGCTT
TGACCACTCTAAAGTCCCCTACTATGGCTATGATGAGCAGCTGAGCCTGTGCCCGGAGTGGCTGAGTTCTGGCAAAGACA
AGAATAAAAGCATCCTGCAGAACAAATATGTCCGATGTTCTGTTAGAACTGAGGTATGCCATCTCTGGATGGTCCTGTGT
CATCACTTGATGCTAAATCCTCAGCATGTGCAGCTCCTTTTTGACAACGGAAGTTCTCCCTGATCACATGACAATGAAGC
AGCTATGGCTCTCTGCTGGTTCGACAAGCTATCCCCTTTGCTTTTACAATACAGTGTGAAAGAGCGGAGGAGG

Alignment

ORF - retro_pabe_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRGLDRVTQPSGEEPALSNLGLPFSSFDHSKAHYYRYDEQLNLCLERLSSGKDKNKSVLQNKYVRCSVRA
          SRGLDRVTQPS.EEPA.SNLGL.FSSFDHSK..YY.YDEQL.LC.E.LSSGKDKNKS.LQNKYVRCSVR.
Retrocopy SRGLDRVTQPSREEPAVSNLGLRFSSFDHSKVPYYGYDEQLSLCPEWLSSGKDKNKSILQNKYVRCSVRT

Parental  EVRHLRRVLCHRLMLNPQHVQLLFDN-EVLPDHMTMKQIWLSR-WFGKPSPLLLQYSVKEKRR
          EV.HL..VLCH.LMLNPQHVQLLFDN.EVLPDHMTMKQ.WLS..WF.K.SPLLLQYSVKE.RR
Retrocopy EVCHLWMVLCHHLMLNPQHVQLLFDN>EVLPDHMTMKQLWLSA<WFDKLSPLLLQYSVKERRR

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	14.26 RPM
SRP007412_cerebellum	0.00 RPM	11.55 RPM
SRP007412_heart	0.00 RPM	5.30 RPM
SRP007412_kidney	0.00 RPM	10.47 RPM
SRP007412_liver	0.00 RPM	7.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_862 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_862 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1029
Pan troglodytes	retro_ptro_704

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115289	1 retrocopy	retro_hsap_1029,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907,
Pongo abelii	ENSPPYG00000012270	1 retrocopy	retro_pabe_862 ,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704,
Sorex araneus	ENSSARG00000007319	1 retrocopy	retro_sara_448,
Sus scrofa	ENSSSCG00000008277	1 retrocopy	retro_sscr_1069,