RetrogeneDB ID: retro_cpor_512

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:414543..415103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005109
• Aliases: None
• Description: None

Sequence

>retro_cpor_512
AACAAGTAGGACAACGTGAATGCTGCAGTGCAGGAGCCCCTCTTGACTACTCTTTAAAAGCATCCATGTCACCCCAGAAC
TGGTTAGAGAGCAGCCAAGGACAGGGCTATGGCCACTGATGCTTTCAAAGTCAGGGAAGTCACTGGCCCAGGCCCCATGG
CTGAACAGCAATGTCCTCAGTGACCTGAAAGATTTTAACCAGGTGTTTTCACAGCTACTGGAGCACCCAGAGAACCTGGC
CTGAACGGACTAGTCTTTCAATAACCTGACTTTCACTGTAGCTGTCCTACTGATCTTCTTCAACCTGAGTGTCCTCTATC
TTCGTGGCAACAGCATTCAGCACCTGTAGGAGGTGAGCAAACTAGCTGTCCTCCGAGGGTGGCTCCAGAGACTGACACTC
CACAGGAACCCCATAGAGGAACAGAAAGGGTACAGCAGCATGTGCTGTGCAGTCTACCCCATATCACCATTTCAGCTTCT
GTGGGGTTACTGAAACAGAACATGCCACAGCTGAGGTTTGTAAACAGATGAACATCAAGTCCTACATCAAGGAGCATGCA

Alignment

ORF - retro_cpor_512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.64 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SKQDYMNTSVQEP-PLDYS-FKSISVIQDLISEEPRTGLRPLKHSKSGKSLTQSLWLNNNVLSDLRDFNP
          .K.D..N..VQEP.PLDYS.FKSI.V...L..E.PRTGL.PL..SKSGKSL.Q..WLN.NVLSDL.DFN.
Retrocopy NK*DNVNAAVQEP<PLDYS<FKSIHVTPELVREQPRTGLWPLMLSKSGKSLAQAPWLNSNVLSDLKDFNQ

Parental  VVSQLLEHPENLAWIDLSFNDLTSIDPVLTTFFNLSVLYLHGNSIQRLGEVNKLAVLPR-LRSLTLHGNP
          V.SQLLEHPENLA..D.SFN.LT....VL..FFNLSVLYL.GNSIQ.L.EV.KLAVL...L..LTLH.NP
Retrocopy VFSQLLEHPENLA*TD*SFNNLTFTVAVLLIFFNLSVLYLRGNSIQHL*EVSKLAVLRGWLQRLTLHRNP

Parental  IEEERGY-RQYVLCSLPRITT-FDFSGVTKTDRTTAEVWKRMNIKPRKTHIKENA
          IEE..GY..Q.VLCSLP.IT..F.F.GVT.T...TAEV.K.MNIK.....IKE.A
Retrocopy IEEQKGY<QQHVLCSLPHITI<FSFCGVTETEHATAEVCKQMNIK---SYIKEHA

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	0.06 RPM	5.06 RPM
SRP017611_kidney	0.00 RPM	13.50 RPM
SRP017611_liver	0.00 RPM	3.26 RPM
SRP040447_lung	0.00 RPM	9.13 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.44 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_512 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_512 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
Cavia porcellus	ENSCPOG00000005109	1 retrocopy	retro_cpor_512 ,
Sarcophilus harrisii	ENSSHAG00000002993	1 retrocopy	retro_shar_463,