RetrogeneDB ID: retro_cpor_367

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_133:1120013..1120257(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC42SE2
• Ensembl ID: ENSCPOG00000005142
• Aliases: None
• Description: None

Sequence

>retro_cpor_367
TTTCTTGTTTTTTTTAACTGTTGCATAGCAGAGCAGCCTCAGCCTAAAAAGTGGCGACAGACTGACCAAAATATGATCAG
AGAGCCAACAAACTTTGTATACATGGCTCTTTGTAGGCCTAAGAGAGATGTTCAGCAGAATGAATTCAGTTAGCTCCATT
TAGAACCAAATGCAGTCCAAGGGTTGCTATGGCAGAGGGATGGCTGCCAATATGCAATTGCAACTCATGTACACCAAGGC
AGGA

Alignment

ORF - retro_cpor_367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.22 %
• Parental protein coverage: 96.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FWLCFNCCIAEQPQPKRRRRIDRSMIGEPTNFVHTA-HVGSGDLFSGMNSVSLMQSKGGYGGGVGGGVQV
          F....NCCIAEQPQPK..R..D..MI.EPTNFV..A..VG....FS.MNSVS.........G..G.G...
Retrocopy FLXXXNCCIAEQPQPKKWRQTDQNMIREPTNFVYMA>FVGLREMFSRMNSVSSI*NQMQSKGCYGRGMAA

Parental  QVQMQLVDTKAG
          ..Q.QL..TKAG
Retrocopy NMQLQLMYTKAG

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	18.58 RPM
SRP017611_kidney	0.00 RPM	11.10 RPM
SRP017611_liver	0.00 RPM	3.18 RPM
SRP040447_lung	0.00 RPM	17.25 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_367 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_367 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008774	1 retrocopy	retro_chof_1622,
Cavia porcellus	ENSCPOG00000005142	1 retrocopy	retro_cpor_367 ,
Rattus norvegicus	ENSRNOG00000042449	2 retrocopies	retro_rnor_461, retro_rnor_696,