RetrogeneDB ID: retro_cpor_559

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_197:17973..18980(+)
• 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_559
ATGGCCATGGCTCCAGGCCCTTCCCTGGCTCAGGTGTACCCCAGCCCTGTGGTAGTGGCTGTGTTGGAATGGCAGGATGG
GCTGGGTACCTGGCATCCCTACAGTGCCACTGTGTGCAGCTACATTGAGCAGCAGTTTGTCCAGCAGAAGGGTCAGCGCT
TTGGGGTGGGCAGCCTGGCACACAGCATCCCCTTAGGCCAGGCTGACCCCTCACTGGCCCCGTACATCATCGACCTCCCC
AGCTGGACCCAGTTCCGCCAGGATACCGGCACCATGCGGGCTGTGCGTAAACACCTGTTCTCCCAGCATTCGGCCCCAGG
CCAGGGTATCATCTGGGAGTGGCTGGGCGATGATGGCTCCTGGACGGCCTACGAAGCCAATGTCTGTGATTATCTGGAGC
AGCACATGGCCAGGGGCATCCAGCTTGTGGACTTGGCTCCCCTGGGGTACAACTACACCGTCAACATGCCACCCACACGC
AAACCAACAAAACTTCCAGTTTCTGCCGGAGTGTGCGGCGCCAAGTAGGCCCAAATTATCCAGTGACCACCGTCATTGCT
CCACCAGGCCACACAGGAGTCGCCTGCTCTTGCCAACAGTGCCTGCATGGCAGTGGAACTGGCCCTGTGTCAGGCCGCTA
CCGCCATTCCATGACCAACCTCCCTGCATAGCCCACACCCCAGGCCTCCCACAGGACCACCGTTGTCTTTGGGGCCCACC
AGGGCTTCGCCCCATACAACAAACCTTCACTCTCTGGGGCCAGATCTGCACCGAGGCTCAACACCACCAACCCCTGGGCT
GGGGCCCCTCCGGCCCTGGGGAACCAGCCCCTCTTCCACTCCAGCCTGTCCCATGTGGGACCACAACTCCTGCCCCCTGG
ACCGTCCACTTCCAGCGGAGCCAGTGCCTCCCTCCCCAGCGGTCCCTCCAGCAGCCTTGGAAGTGTCCCCACCACTGTGC
CCGTGCAGATGCCAAAGCCTAGCAGGGTCCAGCAAGCACTTGCAGGG

Alignment

ORF - retro_cpor_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.03 %
• Parental protein coverage: 54.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMAPGPSLAQVYPSPVVVAVWEWQDGLGTWHPYSATVCSYIEQQFVQQKGQRFGVGSLAHSIPLGQADP
          MAMAPGPSLAQVYPSPVVVAV.EWQDGLGTWHPYSATVCSYIEQQFVQQKGQRFGVGSLAHSIPLGQADP
Retrocopy MAMAPGPSLAQVYPSPVVVAVLEWQDGLGTWHPYSATVCSYIEQQFVQQKGQRFGVGSLAHSIPLGQADP

Parental  SLAPYIIDLPSWTQFRQDTGTMRAVRRHLFSQHSAPGQGIIWEWLGDDGSWTAYEANVCDYLEQHMARGI
          SLAPYIIDLPSWTQFRQDTGTMRAVR.HLFSQHSAPGQGIIWEWLGDDGSWTAYEANVCDYLEQHMARGI
Retrocopy SLAPYIIDLPSWTQFRQDTGTMRAVRKHLFSQHSAPGQGIIWEWLGDDGSWTAYEANVCDYLEQHMARGI

Parental  QVVDLAPLGYNYTVN-YATHTQTNKTSSFCRSVRRQVGPPYPVTTVIAPPGHTGVACSCQQCLHGSGTGP
          Q.VDLAPLGYNYTVN..ATHTQTNKTSSFCRSVRRQVGP.YPVTTVIAPPGHTGVACSCQQCLHGSGTGP
Retrocopy QLVDLAPLGYNYTVN<HATHTQTNKTSSFCRSVRRQVGPNYPVTTVIAPPGHTGVACSCQQCLHGSGTGP

Parental  VSGRYRHSMTNLPAYPTPQASHRTAVAFGAHQGFAPYNKPSLSGARSAPRLNTTNPWAGAPPALGNQPLF
          VSGRYRHSMTNLPA.PTPQASHRT.V.FGAHQGFAPYNKPSLSGARSAPRLNTTNPWAGAPPALGNQPLF
Retrocopy VSGRYRHSMTNLPA*PTPQASHRTTVVFGAHQGFAPYNKPSLSGARSAPRLNTTNPWAGAPPALGNQPLF

Parental  HSSLSHVGPQLLPPGPSTSSGASASLPSGPSSSLGSIPTTVPVQMPKPSRVQQALAG
          HSSLSHVGPQLLPPGPSTSSGASASLPSGPSSSLGS.PTTVPVQMPKPSRVQQALAG
Retrocopy HSSLSHVGPQLLPPGPSTSSGASASLPSGPSSSLGSVPTTVPVQMPKPSRVQQALAG

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	0.04 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_559 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_559 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 2 retrocopies.

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