RetrogeneDB ID: retro_cpor_1402

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:39412304..39412643(+)
• Located in intron of: ENSCPOG00000003196

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSDE1
• Ensembl ID: ENSCPOG00000000538
• Aliases: None
• Description: Cold shock domain-containing protein E1 [Source:UniProtKB/Swiss-Prot;Acc:P29174]

Sequence

>retro_cpor_1402
TTTGGCTTCATTAATGATGAAGCAGGAGATAGCAAGCTCTTTTTCCATGTGAAAGAAGTTCAGGATGACATTGAGCTACA
GGCAGGAGACAAGGTGGAGTTCTCAGTGATTCTTAAGCAGCACACTGGCAAGTACAGTGCCTGTAATGTTTGGCAAGTCT
GCAAGGGTCCCAAGGCTGTTGCAGTCCCTCGATCTGATTGATTGGTCAACCGCTTGAAGATCATCATCCTCGATGATGCC
AGTGCTGCTCGCCTAATGGTTGTTTGTCATCAAAGGGGACCAGATAACTCAGTGGGATTTGGTGCAGAAAGAAAGATACC
TCAAGCTGGTGTCATTGAC

Alignment

ORF - retro_cpor_1402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRVCEGPKAVAAPRPDRLV
          FGFIN.E.GDS.KLFFHVKEVQD.IELQAGD.VEFSVIL.Q.TGK.SACNVW.VC.GPKAVA.PR.D.LV
Retrocopy FGFINDEAGDS-KLFFHVKEVQDDIELQAGDKVEFSVILKQHTGKYSACNVWQVCKGPKAVAVPRSD*LV

Parental  NRLKNITLDDASAPRLMVLRQPRGPDNSMGFGAERKIRQAGVID
          NRLK.I.LDDASA.RLMV....RGPDNS.GFGAERKI.QAGVID
Retrocopy NRLKIIILDDASAARLMVVCHQRGPDNSVGFGAERKIPQAGVID

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	0.23 RPM	50.50 RPM
SRP017611_kidney	0.10 RPM	91.18 RPM
SRP017611_liver	0.00 RPM	35.78 RPM
SRP040447_lung	0.03 RPM	103.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	181.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1402 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1402 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017129	1 retrocopy	retro_amel_1392,
Cavia porcellus	ENSCPOG00000000538	2 retrocopies	retro_cpor_1402 , retro_cpor_513,
Myotis lucifugus	ENSMLUG00000005681	1 retrocopy	retro_mluc_1011,
Mus musculus	ENSMUSG00000068823	1 retrocopy	retro_mmus_1757,
Rattus norvegicus	ENSRNOG00000030302	1 retrocopy	retro_rnor_1429,