RetrogeneDB ID: retro_pabe_2392

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:184485888..184486470(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF13
• Ensembl ID: ENSPPYG00000014202
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF13 precursor [Source:RefSeq peptide;Acc:NP_001125196]

Sequence

>retro_pabe_2392
ATGCTGCTCTCCATAGGGATGCTTATGCTTTCAGCCACACAAGTCTACAGCATCGTGGCTGTCCAGCTCTTTGCATTCTT
AAACCTACTGCCTGTAGAAGCAGACATTTTAGCATATAACTTTGGAAATACGTCTCAGACGTTTGATGACCTCCCTGAAA
GATTTGGTTATAGACTTCCAGCTGAAGGTTTAAAGGGTTTTTTGATTAACTCAAAACCAGAGAATGCCTGTGAACCCATA
GTGCCTCCACCAGTAAAAAACAATTCGTCTGGCACTTTCATTGTGTTAATTAGATGACTTGATTGTAATTTTGATATAAA
GGTTTTAAATGCACAGAGAGCAGAATACAAAGCAGCCATAGTTTACAATGTTGATTCTGATGACCTCATTAGCATTGGAT
CCAACGACATTGAGGTACTAAAGAAAATTAATGTTCTATCTGTCTTTATTGGCGAATCATCAGCTAATTCTCTGAAAGAT
GAATTCACATATGAAAAAGGGGGCCACCTTATTTTAGTTCTTGAATTTAGTCTTCCTTTGGAATGCTGCCTAATTTCCTT
CCTTGTCATAGTGGGCATCTGT

Alignment

ORF - retro_pabe_2392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.21 %
• Parental protein coverage: 50.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLSIGMLMLSATQVYTILTVQLFAFLNLLPVEADILAYNFENASQTFDDLPARFGYRLPAEGLKGFLIN
          MLLSIGMLMLSATQVY.I..VQLFAFLNLLPVEADILAYNF.N.SQTFDDLP.RFGYRLPAEGLKGFLIN
Retrocopy MLLSIGMLMLSATQVYSIVAVQLFAFLNLLPVEADILAYNFGNTSQTFDDLPERFGYRLPAEGLKGFLIN

Parental  SKPENACEPIVPPPVKDNSSGTFIVLIRRLDCNFDIKVLNAQRAGYKAAIVHNVDSDDLISMGSNDIEVL
          SKPENACEPIVPPPVK.NSSGTFIVLIR.LDCNFDIKVLNAQRA.YKAAIV.NVDSDDLIS.GSNDIEVL
Retrocopy SKPENACEPIVPPPVKNNSSGTFIVLIR*LDCNFDIKVLNAQRAEYKAAIVYNVDSDDLISIGSNDIEVL

Parental  KKIDIPSVFIGESSANSLKDEFTYEKGGHLILVPEFSLPLEYYLIPFLIIVGIC
          KKI...SVFIGESSANSLKDEFTYEKGGHLILV.EFSLPLE..LI.FL.IVGIC
Retrocopy KKINVLSVFIGESSANSLKDEFTYEKGGHLILVLEFSLPLECCLISFLVIVGIC

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	41.74 RPM
SRP007412_cerebellum	0.00 RPM	37.33 RPM
SRP007412_heart	0.00 RPM	18.60 RPM
SRP007412_kidney	0.00 RPM	54.49 RPM
SRP007412_liver	0.06 RPM	39.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2392 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2392 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010433	1 retrocopy	retro_amel_311,
Canis familiaris	ENSCAFG00000008370	1 retrocopy	retro_cfam_815,
Dasypus novemcinctus	ENSDNOG00000014687	1 retrocopy	retro_dnov_139,
Microcebus murinus	ENSMICG00000001221	1 retrocopy	retro_mmur_323,
Nomascus leucogenys	ENSNLEG00000003149	1 retrocopy	retro_nleu_627,
Pongo abelii	ENSPPYG00000014202	1 retrocopy	retro_pabe_2392 ,