RetrogeneDB ID: retro_pabe_1163

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:38841055..38841494(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIPPLY3
• Ensembl ID: ENSPPYG00000011408
• Aliases: None
• Description: ripply3 homolog (zebrafish) [Source:HGNC Symbol;Acc:3047]

Sequence

>retro_pabe_1163
TGGAGACCTATGATCCTGACACCTGCAGATGCTGAGCTGACCAGAACTGGAAGCCAGTTTAAACTCGGGGGAGATCAAGA
AACTTTTGGATTAAAGGAAGTCTTCAGGTTTCAGCATCCTGTAAGACTTTACTTACCCTTTTTGAAATGTCAAGAATATT
TTCAGTGTTCTGGGGAATAAGTGCTGGTCTGTTTTCCAGTGCAAGCCGTGATATACTTCTATAACGATGAGTCTGATTCA
GATGATGAAGAGCAAGAGGAAGAAACCAGCTCTTCCATTTTCTGTGCCAGGAGGCGGAAGGTCTGGAGGAAACTGTCCTG
GGGGAAAGGGCAGAGACAGGATCATAAACTGAGGATGGCAATCTGAAAGAAGGGGTGGCCTCTGTGTGGAGGACCAGCTC
CCCTGAGGTGAGTCCTCAAGGGGCAGGGAGTGCTCCTCA

Alignment

ORF - retro_pabe_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.58 %
• Parental protein coverage: 78.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WRPWIQTPGDAELTRTGRPLEPRADQHAFGSKGAFGFQHPVRVYLPMSKRQEYLQSSGEQVLASFPVQAT
          WRP.I.TP.DAELTRTG.......DQ..FG.K..F.FQHPVR.YLP..K.QEY.Q.SGE.VL..FPVQA.
Retrocopy WRPMILTPADAELTRTGSQFKLGGDQETFGLKEVFRFQHPVRLYLPFLKCQEYFQCSGE*VLVCFPVQAV

Parental  IDFYDDESTESASEAEEPEEGTPP-LHPLLQEVGGLQE-NCPGGKGRDQGSNRGQRSSGGGDPWGEGLLP
          I.FY.DES....S..EE.EE.T....H.L.QE..GL.E.NCPGGKGRD...N.G..S...G....E..LP
Retrocopy IYFYNDESD---SDDEEQEEETSS<FHFLCQEAEGLEE<NCPGGKGRDRIIN*GWQSERRGGLCVEDQLP

Parental  HSVSSRGGKCSS
          ...SSRG..CSS
Retrocopy *GESSRGRECSS

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	0.17 RPM
SRP007412_cerebellum	0.00 RPM	0.73 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.93 RPM
SRP007412_liver	0.00 RPM	0.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1163 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1163 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1407
Pan troglodytes	retro_ptro_964
Gorilla gorilla	retro_ggor_1091

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036019	1 retrocopy	retro_btau_1393,
Homo sapiens	ENSG00000183145	1 retrocopy	retro_hsap_1407,
Gorilla gorilla	ENSGGOG00000006091	1 retrocopy	retro_ggor_1091,
Nomascus leucogenys	ENSNLEG00000004521	1 retrocopy	retro_nleu_1423,
Pongo abelii	ENSPPYG00000011408	1 retrocopy	retro_pabe_1163 ,
Pan troglodytes	ENSPTRG00000013896	1 retrocopy	retro_ptro_964,