RetrogeneDB ID: retro_cpor_416

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_148:2454547..2455506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTX2
• Ensembl ID: ENSCPOG00000014083
• Aliases: None
• Description: deltex homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:15973]

Sequence

>retro_cpor_416
GTGGTAGTGGCTGTGTTGGAATGGCAGGATGGGCTGGGTACCTGGCATCCCTACAGTGCCACTGTGTGCAGCTACATTGA
GCAGCAGTTTGTCCAGCAGAAGGGTCAGCGCTTTGGGGTGGGCAGCCTGGCACACAGCATCCCCTTAGGCCAGGCTGACC
CCTCACTGGCCCCGTACATCATCGACCTCCCCAGCTGGACCCAGTTCCGCCAGGATACCGGCACCATGCGGGCTGTGCGT
AAACACCTGTTCTCCCAGCATTCGGCCCCAGGCCAGGGTATCATCTGGGAGTGGCTGGGCGATGATGGCTCCTGGACGGC
CTACGAAGCCAATGTCTGTGATTATCTGGAGCAGCACATGGCCAGGGGCATCCAGCTTGTGGACTTGGCTCCCCTGGGGT
ACAACTACACCGTCAACATGCCACCCACACGCAAACCAACAAAACTTCCAGTTTCTGCCGGAGTGTGCGGCGCCAAGTAG
GCCCAAATTATCCAGTGACCACCGTCATTGCTCCACCAGGCCACACAGGAGTCGCCTGCTCTTGCCAACAGTGCCTGCAT
GGCAGTGGAACTGGCCCTGTGTCAGGCCGCTACCGCCATTCCATGACCAACCTCCCTGCATAGCCCACACCCCAGGCCTC
CCACAGGACCACCGTTGTCTTTGGGGCCCACCAGGGCTTCGCCCCATACAACAAACCTTCACTCTCTGGGGCCAGATCTG
CACCGAGGCTCAACACCACCAACCCCTGGGCTGGGGCCCCTCCGGCCCTGGGGAACCAGCCCCTCTTCCACTCCAGCCTG
TCCCATGTGGGACCACAACTCCTGCCCCCTGGACCGTCCACTTCCAGCGGAGCCAGTGCCTCCCTCCACAGCGGTCCCTC
CAGCAGCCTTGGAAGTGTCCCCACCACTGTGCCCGTGCAGATGCCAAAGTCTAGCAGGGTCCAGCAAGCACTTGCAGGG

Alignment

ORF - retro_cpor_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.26 %
• Parental protein coverage: 51.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVVAVWEWQDGLGTWHPYSATVCSYIEQQFVQQKGQRFGVGSLAHSIPLGQADPSLAPYIIDLPSWTQFR
          VVVAV.EWQDGLGTWHPYSATVCSYIEQQFVQQKGQRFGVGSLAHSIPLGQADPSLAPYIIDLPSWTQFR
Retrocopy VVVAVLEWQDGLGTWHPYSATVCSYIEQQFVQQKGQRFGVGSLAHSIPLGQADPSLAPYIIDLPSWTQFR

Parental  QDTGTMRAVRRHLFSQHSAPGQGIIWEWLGDDGSWTAYEANVCDYLEQHMARGIQVVDLAPLGYNYTVN-
          QDTGTMRAVR.HLFSQHSAPGQGIIWEWLGDDGSWTAYEANVCDYLEQHMARGIQ.VDLAPLGYNYTVN.
Retrocopy QDTGTMRAVRKHLFSQHSAPGQGIIWEWLGDDGSWTAYEANVCDYLEQHMARGIQLVDLAPLGYNYTVN<

Parental  YATHTQTNKTSSFCRSVRRQVGPPYPVTTVIAPPGHTGVACSCQQCLHGSGTGPVSGRYRHSMTNLPAYP
          .ATHTQTNKTSSFCRSVRRQVGP.YPVTTVIAPPGHTGVACSCQQCLHGSGTGPVSGRYRHSMTNLPA.P
Retrocopy HATHTQTNKTSSFCRSVRRQVGPNYPVTTVIAPPGHTGVACSCQQCLHGSGTGPVSGRYRHSMTNLPA*P

Parental  TPQASHRTAVAFGAHQGFAPYNKPSLSGARSAPRLNTTNPWAGAPPALGNQPLFHSSLSHVGPQLLPPGP
          TPQASHRT.V.FGAHQGFAPYNKPSLSGARSAPRLNTTNPWAGAPPALGNQPLFHSSLSHVGPQLLPPGP
Retrocopy TPQASHRTTVVFGAHQGFAPYNKPSLSGARSAPRLNTTNPWAGAPPALGNQPLFHSSLSHVGPQLLPPGP

Parental  STSSGASASLPSGPSSSLGSIPTTVPVQMPKPSRVQQALAG
          STSSGASASL.SGPSSSLGS.PTTVPVQMPK.SRVQQALAG
Retrocopy STSSGASASLHSGPSSSLGSVPTTVPVQMPKSSRVQQALAG

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	3.57 RPM
SRP017611_kidney	0.00 RPM	7.22 RPM
SRP017611_liver	0.00 RPM	4.79 RPM
SRP040447_lung	0.00 RPM	29.16 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_416 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_416 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014083	2 retrocopies	retro_cpor_416 , retro_cpor_559,