RetrogeneDB ID: retro_cpor_1167

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:8222445..8222839(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000027616
• Aliases: None
• Description: None

Sequence

>retro_cpor_1167
AGGCTGCTGTGTCTAGTCTGTTTGGCATTACAGATCATCCACACGAGAAACAGCTATCACGCAGAGAAACATACAGGTGG
TAGAGAAGTCAGCAATGTCGCCACCCCAGAGCTGAGGCCCACAGCGCTCCCTAGAGCCCTGGATCATTTCAGGGCGGGAG
AAAAAGAAGCAGCAATGGCTGGAGACATCAGCCTGTGATCCCGGACCCCAGGGCCCACGGAGCGCATGCGCTGCAGCCGC
ACTGTTGCAGGAACCAGGTTACCTGCCTGCTAGCGGCCTCTGCGTGTGCCCAGCGCACTTTACAGGCTGCTACTATGAGC
GCAATCAGAGGCGCACAGACTGCAGTGCCTTGGGGCACTGAGCCTGGACCATCTGAGGCTGCCGCCTCTGCAGA

Alignment

ORF - retro_cpor_1167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.4 %
• Parental protein coverage: 77.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLLCLVSLALQLVHTGNSSHGEKHKGGREVSNVATPELRPTALPRALDH-FRAGNA-SCQGWRPRRATPH
          RLLCLV.LALQ..HT.NS.H.EKH.GGREVSNVATPELRPTALPRALDH.F..G...S..GWR.....P.
Retrocopy RLLCLVCLALQIIHTRNSYHAEKHTGGREVSNVATPELRPTALPRALDH<FQGGRKRSSNGWRHQPVIPD

Parental  PRAHGARAPPPRCCRNGGTCVLGS-FCVCPAHFTGRYCEHDQRRSDCSALSNGAWTIRGCRLCR
          PRAHGA.A..P.CCRN..TC.L....CVCPAHFTG.Y.E..QRR.DCSAL...AWTI.GCRLCR
Retrocopy PRAHGAHALQPHCCRNQVTCLLAA<LCVCPAHFTGCYYERNQRRTDCSALGH*AWTI*GCRLCR

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	1.73 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.08 RPM
SRP040447_skeletal_muscle	0.01 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1167 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1167 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	ENSCPOG00000027616	1 retrocopy	retro_cpor_1167 ,