RetrogeneDB ID: retro_cpor_1166

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:8147074..8147836(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000027461
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSCPOG00000013303
• Aliases: None
• Description: None

Sequence

>retro_cpor_1166
GGTGTTTCATGGGACTCCCTCCCAGATGAGCTTCTCCTGGGGATTTTTTCTTGTTTGTGCCTCCCTGAGCTGCTGAGAGT
GTCTGGTGTCTGTAAGAGGTGGTACTGCCTTGCGTTTGACGAGTCCCTTTGGCAGACCCTAGACCTCACAGGTAGAAATC
TGCACCCAGATGTGACTGGTCGTTTGCTGTCTCGAGGAGTGATTGCCTTCCGCTGCCCACGATCATTTATGGACCAGCCA
TTGGTTGAACATTTCAGCCCTTTCCGCGTACAGCACATGGACCTGTCGAACTCCGTTATAAATGTGAATACCCTCCTTGG
CATTCTGTCTCGGTGCACCAAGTTGCAGAATCTAAGCCTGGAAGGCCTACAGCTTTCAGATCCCATTGTCAATAATCTTG
CACAGAACTCAAATTTAGTGCGACTAAACCTTTGTGGGTGTTCTGGATTTTCAGACTCTGCTCTAAAGACTTTGCTAAGC
AGCTGTTCCAGGCTGGATGAGCTGAATCTGTCTTGGTGCTTTGATTTCACTGAAAAGCATGTGCAAGTGGCTGTAACACA
TGTGTCAGAAACAGTCACCCAGCTGAATCTCAGTGGCTATAGAAAGAATCTCCAGAAGTCAGATGTCTCTACCTTAATTA
GAAGATGCCCCAACCTTGTCCATCTAGACTTAAGTGATAGTATCATGTTGAAGAATGATTGCTTTCCAGAATTTCTCCAG
CTCAACTACCTCCAACACTTGTCACTCAGTCGGTGCTATAAT

Alignment

ORF - retro_cpor_1166 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.61 %
• Parental protein coverage: 59.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVSWDSLPDELLLGIFSCLCLPELLRVSGVCKRWYCLAFDESLWQTLDLTGRNLHPDVTGRLLSRGVIAF
          GVSWDSLPDELLLGIFSCLCLPELLRVSGVCKRWYCLAFDESLWQTLDLTGRNLHPDVTGRLLSRGVIAF
Retrocopy GVSWDSLPDELLLGIFSCLCLPELLRVSGVCKRWYCLAFDESLWQTLDLTGRNLHPDVTGRLLSRGVIAF

Parental  RCPRSFMDQPLVEHFSPFRVQHMDLSNSVINVNTLLGILSRCTKLQNLSLEGLQLSDPIVNNLAQNSNLV
          RCPRSFMDQPLVEHFSPFRVQHMDLSNSVINVNTLLGILSRCTKLQNLSLEGLQLSDPIVNNLAQNSNLV
Retrocopy RCPRSFMDQPLVEHFSPFRVQHMDLSNSVINVNTLLGILSRCTKLQNLSLEGLQLSDPIVNNLAQNSNLV

Parental  RLNLCGCSGFSDSALKTLLSSCSRLDELNLSWCFDFTEKHVQVAVTHVSETVTQLNLSGYRKNLQKSDVS
          RLNLCGCSGFSDSALKTLLSSCSRLDELNLSWCFDFTEKHVQVAVTHVSETVTQLNLSGYRKNLQKSDVS
Retrocopy RLNLCGCSGFSDSALKTLLSSCSRLDELNLSWCFDFTEKHVQVAVTHVSETVTQLNLSGYRKNLQKSDVS

Parental  TLIRRCPNLVHLDLSDSIMLKNDCFPEFLQLNYLQHLSLSRCYD
          TLIRRCPNLVHLDLSDSIMLKNDCFPEFLQLNYLQHLSLSRCY.
Retrocopy TLIRRCPNLVHLDLSDSIMLKNDCFPEFLQLNYLQHLSLSRCYN

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	2.59 RPM
SRP017611_kidney	0.00 RPM	2.20 RPM
SRP017611_liver	0.04 RPM	2.92 RPM
SRP040447_lung	0.00 RPM	3.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1166 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1166 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166 ,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621,