RetrogeneDB ID: retro_cpor_282

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_116:360962..361784(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000008117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBXO25
• Ensembl ID: ENSCPOG00000008110
• Aliases: None
• Description: None

Sequence

>retro_cpor_282
AGAAATGACACAAATGCTCAAAGTTTTTATTGTGAAAAATGGATCTACGTCCATAAAGAAAGCACAAAAGAAAGGCATGC
TTATTGTACCTTGGGAGAAGCCTTTAACCGGCTAGACTTTTCAAGTGCGATTCAGGATATCCGAAGATTCACTTATGTGG
TCAAACTATTGCAGCTAATTGCAAAATCCCAGTTAACTTCATTGAGTGGTGTGGCACAGAAGAATTACTTCAGCATTTTG
GATAAAATCGTTCAAAAGATTCTTGATGACCACCAGAATCCTCGTTTGATCAAAGATCTTCTGCAAGACCTGAGCTCTAC
TCCATGTATTCTTATCAGAGGGGTAGGGAAGTCAGTGCTAGTCGGGAACATCAATATCTGGCTTTGCCGCTTAGAAACTG
TCCTTGGCTGGCAACAACAACTACAGAATCTTCAGATGACTAAGCACGTGAGCAGTGGCCTCACCCTCAGTGACCTGCCC
TTGCACATGCTGAGCAACGTCTGGTACCGCTTCTCGGATGGGTGGGACATCATTACTCCGGGCCAGGTGACACCCACTCT
GTACATGCTCAGTGAGGACAGGCAGCTGCCGAAGAAGCTGTGTCAGTACCACTTTGCTGAGCAACAGTTCTGTAGACATT
TGATCCTTTCACAAAAAGGTCATATCGAATGGAAGTTGATGTATTTTATACTTCAGAAATATTATCCAACTAAAGAACAG
TATGAAGACACCTTACATTTTTGTAGGCACTGCAGTATTCTTTTTTGGAAGGACTCAGGACATCCCTGCACTGCAGCTGA
CCCAGACAGCTGCTTCACGCCC

Alignment

ORF - retro_cpor_282 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 86.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNDTNAQSFYREKWIYVHKESTKERHGYCTLGEAFNRLDFSSAIQDIRRFTYVVKLLQLIAKSQLTSLSG
          .NDTNAQSFY.EKWIYVHKESTKERH.YCTLGEAFNRLDFSSAIQDIRRFTYVVKLLQLIAKSQLTSLSG
Retrocopy RNDTNAQSFYCEKWIYVHKESTKERHAYCTLGEAFNRLDFSSAIQDIRRFTYVVKLLQLIAKSQLTSLSG

Parental  VAQKNYFSILDKIVQKVLDDHQNPRLIKDLLQDLSSTLCILIRGVGKSVLVGNINIWICRLETVLGWQQQ
          VAQKNYFSILDKIVQK.LDDHQNPRLIKDLLQDLSST.CILIRGVGKSVLVGNINIW.CRLETVLGWQQQ
Retrocopy VAQKNYFSILDKIVQKILDDHQNPRLIKDLLQDLSSTPCILIRGVGKSVLVGNINIWLCRLETVLGWQQQ

Parental  LQNLQMTKHVNSGLTLSDLPLHMLSNILYRFSDGWDIITLGQVTPTLYMLSEDRQLWKKLCQYHFAEQQF
          LQNLQMTKHV.SGLTLSDLPLHMLSN..YRFSDGWDIIT.GQVTPTLYMLSEDRQL.KKLCQYHFAEQQF
Retrocopy LQNLQMTKHVSSGLTLSDLPLHMLSNVWYRFSDGWDIITPGQVTPTLYMLSEDRQLPKKLCQYHFAEQQF

Parental  CRHLILSEKGHIEWKLMYFILQKYYPTKEQYGDTLHFCRHCSILFWKDSGHPCTAADPDSCFTP
          CRHLILS.KGHIEWKLMYFILQKYYPTKEQY.DTLHFCRHCSILFWKDSGHPCTAADPDSCFTP
Retrocopy CRHLILSQKGHIEWKLMYFILQKYYPTKEQYEDTLHFCRHCSILFWKDSGHPCTAADPDSCFTP

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	1.09 RPM	14.95 RPM
SRP017611_kidney	0.84 RPM	24.08 RPM
SRP017611_liver	0.26 RPM	14.54 RPM
SRP040447_lung	0.28 RPM	13.01 RPM
SRP040447_skeletal_muscle	0.12 RPM	3.57 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_282 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_282 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007039	1 retrocopy	retro_btau_1712,
Cavia porcellus	ENSCPOG00000008110	1 retrocopy	retro_cpor_282 ,