RetrogeneDB ID: retro_cpor_1163

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_51:6128340..6128739(-)
• Located in intron of: ENSCPOG00000011466

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIVA1
• Ensembl ID: ENSCPOG00000024811
• Aliases: None
• Description: None

Sequence

>retro_cpor_1163
AAGCAGCTGCTTTTCCATGGGGCCCAGGCCTGCAGAGACCATGTGTGGGGTGAAAGCTGTGCCACTGTCCACCTGCCAGA
GTCCCTGAAGCCTGGCCCTACAGACACACCTCGAGCTGCAAGAGGCCAGCTGCTGATTGGACCTGATGGCTGACTGATCA
GGAGCAGTGTCCAGGCCTCCAAAGCTGACCTGTCCAGGGCAGCATTTCGCGCCTGCTCATCATGCGTGCGAGCAGTGGAT
GGGAAGGTGGTCTGCAGCCAGTGCGAGGAGGCCCTGTGTGGGCAGTGTATGCGCACCTGCTGAGGCTGTGGTGCTGTGGC
CTGTTCCCTGTGTGGCCTTGTAGACTGCAGTGATGTGTGTGAGAAGGCACTGTGTGGCAGCTGCGCCATGTTCGACGCC

Alignment

ORF - retro_cpor_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.48 %
• Parental protein coverage: 76.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQLLFHGAQACRDHVWGESCAIVHLPESPKPGPTETPRAARGQLLIGPDGQLIRSSAQASKADLSRAASR
          KQLLFHGAQACRDHVWGESCA.VHLPES.KPGPT.TPRAARGQLLIGPDG.LIRSS.QASKADLSRAA.R
Retrocopy KQLLFHGAQACRDHVWGESCATVHLPESLKPGPTDTPRAARGQLLIGPDG*LIRSSVQASKADLSRAAFR

Parental  ACSSCVRAVDGKVVCSQCERALCGQCTRTCWGCGAVACSLCGLVDCSDVCEKALCSSCAMFDA
          ACSSCVRAVDGKVVCSQCE.ALCGQC.RTC.GCGAVACSLCGLVDCSDVCEKALC.SCAMFDA
Retrocopy ACSSCVRAVDGKVVCSQCEEALCGQCMRTC*GCGAVACSLCGLVDCSDVCEKALCGSCAMFDA

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	9.09 RPM
SRP017611_kidney	0.00 RPM	17.59 RPM
SRP017611_liver	0.00 RPM	9.27 RPM
SRP040447_lung	0.00 RPM	26.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	44.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1163 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1163 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024811	1 retrocopy	retro_cpor_1163 ,
Dasypus novemcinctus	ENSDNOG00000005703	2 retrocopies	retro_dnov_1591, retro_dnov_2683,
Mus musculus	ENSMUSG00000064326	1 retrocopy	retro_mmus_2288,
Otolemur garnettii	ENSOGAG00000016881	1 retrocopy	retro_ogar_3280,