RetrogeneDB ID: retro_cpor_847

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:9033587..9034238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC4H2
• Ensembl ID: ENSCPOG00000019721
• Aliases: None
• Description: None

Sequence

>retro_cpor_847
ATGTGCAAACTGGAAAGCATTAAAGAGATCAGGAACAAAACTCTGCAGATGGAGATGATCAAGGCTCGACTGAAGGCTGA
ATTTGAGGCACTTGAGTCAGAGGAACGGCACCTGAAAGAATACAAGCAGGAGATGGACCTCCTGTTACAGGAGAAGATGG
CCCATGTGGAGGAACTCCGACTTATCCACGCTGACATCAATGTGATGGAAAACACCATTAAACAGTCTGAAAATGACCTT
AACAAGCTGCTAGAGTCTACAAGGCGACTGCATGAGGAGTATAAGCCTCTGAAGGAACATGTGGATGCTCTACATATGAC
TTTGGGCTTGCAGAGGCTTCCTGACTTGTGTGAAGAGGAGGAGAAGCTCTCTTTGGATTACTTTGAGAAACAGAAAGCAG
AATGGCAGACAGAGCCTCAGGAGCCCCCTATCCCTGAGTCCTTGGCTGCTGCAGCTGCTGTTGCCCAACAACTCCAAGTG
GCTAGATAGCAGGACACTCGACAGACAGCCACCTTCAGGCAGCAGCCTCCACCTATGAAGGCCTGTTTGTCATGCCACCA
GCAAATTCACCGGAATGCACCCATATGCCCTCTGTGCAAAGCCAAAAGTCGGTCCCGGAACCCCAAGAAGCCCAAACGGA
AGCAGGATGAA

Alignment

ORF - retro_cpor_847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ICFLESISYLKNKTLQMEKIKARLKAEFEALESEERHLKEYKQEMDLLLQEKMAHVEELRLIHADINVME
          .C.LESI....NKTLQME.IKARLKAEFEALESEERHLKEYKQEMDLLLQEKMAHVEELRLIHADINVME
Retrocopy MCKLESIKEIRNKTLQMEMIKARLKAEFEALESEERHLKEYKQEMDLLLQEKMAHVEELRLIHADINVME

Parental  NTIKQSENDLNKLLESTRRLHEEYKPLKEHVDALRMTLGLQRLPDLCEEEEKLSLDYFEKQKAEWQTEPQ
          NTIKQSENDLNKLLESTRRLHEEYKPLKEHVDAL.MTLGLQRLPDLCEEEEKLSLDYFEKQKAEWQTEPQ
Retrocopy NTIKQSENDLNKLLESTRRLHEEYKPLKEHVDALHMTLGLQRLPDLCEEEEKLSLDYFEKQKAEWQTEPQ

Parental  EPPIPESLAAAAAAAQQLQVARKQDTRQTATFRQQPPPMKACLSCHQQIHRNAPICPLCKAKSRSRNPKK
          EPPIPESLAAAAA.AQQLQVAR.QDTRQTATFRQQPPPMKACLSCHQQIHRNAPICPLCKAKSRSRNPKK
Retrocopy EPPIPESLAAAAAVAQQLQVAR*QDTRQTATFRQQPPPMKACLSCHQQIHRNAPICPLCKAKSRSRNPKK

Parental  PKRKQDE
          PKRKQDE
Retrocopy PKRKQDE

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	0.06 RPM	5.64 RPM
SRP017611_kidney	0.00 RPM	4.19 RPM
SRP017611_liver	0.26 RPM	2.96 RPM
SRP040447_lung	0.00 RPM	4.16 RPM
SRP040447_skeletal_muscle	0.01 RPM	1.19 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_847 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_847 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000019721	1 retrocopy	retro_cpor_847 ,