RetrogeneDB ID: retro_cpor_771

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:18312901..18313388(+)
• Located in intron of: ENSCPOG00000008918

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSCPOG00000000880
• Aliases: None
• Description: None

Sequence

>retro_cpor_771
CCCTCTCACCTTAACTATGTTGGACTGAGCTGCTTTTATTTGGCTGTAAAATCTATAGAAGAGGAAACAGATGTCTCATT
GACAATTGACTTGATCCAAGTAAGTCAGTGTAGGTTCACGATTTGAGACTTGATGAGAATGGAAAAGATTGTATTAGAGA
TGCATTGGAAAGTCAAAGGTACCATTGCCTTTCAATTTCTATAATTCTGTTATTCACTCAAACAAGAGAACTTGCCATTT
GAAAGAAAAATAGCCTAAATTTTGAAAGACTAGAAGCTTCCCTTAAGGAATGGCACTGTAGGATCACATTTTCTAAAGCA
AAACTTTCTGTGTTGGCCTTACTTATCGTTGCATTGGAGATACAAGCACAGAAGTGTGTAGAGTTAACAGGAGTAGAATG
TCTCCAGAAATGTTCTAGGTAAATGGCAGAGGTCTGACCTGGCAAGAGCTTGTATACAAGTATTTAACTGAATAATCATC
AAACAAG

Alignment

ORF - retro_cpor_771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.4 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQFLQL
          P.HL..VGLSCFYLAVKSIEEE..V.L..DLI..SQ.RFT..DLMRMEKIVLE...WKVK.T.AFQFL..
Retrocopy PSHLNYVGLSCFYLAVKSIEEETDVSLTIDLIQVSQCRFTI*DLMRMEKIVLE-MHWKVKGTIAFQFL*F

Parental  YYSLIQESLPFER-KNNLNFERLEAQLKACHCRIMFSKAKPSVLALSIIALEIQAQKCVELTDGIECLQK
          .YSL.QE.LPFER.KN.LNFERLEA.LK..HCRI.FSKAK.SVLAL.I.ALEIQAQKCVELT.G.ECLQK
Retrocopy CYSLKQENLPFER<KNSLNFERLEASLKEWHCRITFSKAKLSVLALLIVALEIQAQKCVELT-GVECLQK

Parental  HSK-INGRDLTFWQELVSKCLTEYSSNK
          .S...NGR.LT.WQELV.K.LTE.SSNK
Retrocopy CSR<VNGRGLT-WQELVYKYLTE*SSNK

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	0.17 RPM	17.95 RPM
SRP017611_kidney	0.00 RPM	26.90 RPM
SRP017611_liver	0.00 RPM	21.59 RPM
SRP040447_lung	0.03 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.01 RPM	158.66 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_771 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_771 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771 ,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,