RetrogeneDB ID: retro_cpor_829

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:27555305..27555484(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C10ORF32
• Ensembl ID: ENSCPOG00000021622
• Aliases: None
• Description: None

Sequence

>retro_cpor_829
CAGCTACTAAGTCAGGCAGCTTGAAGCATGATCCTATAGGAAGACACTGTCTTACACTCCAAAGGTAGTCAAGGGAAATG
GCAACTGTAACAACACATCTTCAATACAAGCAAGAAGGTATTCAGATGGATACTGAATGGTCATCAGATCTGCAGGACTA
GTTGAACCATCTGTTGCAA

Alignment

ORF - retro_cpor_829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.66 %
• Parental protein coverage: 52.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELLGQAARNMVLQEDAILHSEDSL-RKMAIITTHLQYQQEAIQKNVEQSSDLQDQLKHLLK
          .LL.QAA..M.L.ED..LHS..S..R.MA..TTHLQY.QE.IQ...E.SSDLQD.L.HLL.
Retrocopy QLLSQAA*SMIL*EDTVLHSKGSQ<REMATVTTHLQYKQEGIQMDTEWSSDLQD*LNHLLQ

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
SRP017611_brain	0.00 RPM	3.85 RPM
SRP017611_kidney	0.00 RPM	4.50 RPM
SRP017611_liver	0.00 RPM	3.66 RPM
SRP040447_lung	0.00 RPM	6.51 RPM
SRP040447_skeletal_muscle	0.00 RPM	13.91 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_829 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_829 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021622	1 retrocopy	retro_cpor_829 ,
Loxodonta africana	ENSLAFG00000020646	4 retrocopies	retro_lafr_1177, retro_lafr_299, retro_lafr_608, retro_lafr_800,
Macropus eugenii	ENSMEUG00000013119	3 retrocopies	retro_meug_112, retro_meug_1350, retro_meug_231,
Procavia capensis	ENSPCAG00000000834	1 retrocopy	retro_pcap_87,