RetrogeneDB ID: retro_cpor_931

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:23628160..23628552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAPA
• Ensembl ID: ENSCPOG00000006042
• Aliases: None
• Description: None

Sequence

>retro_cpor_931
CCCGAGGAATTAATGGATTCTAAATTGAGATTGTGTTTAAAATGCCAAATGAAAATAAGTTGAACAATATGGCACCTAGC
AAAGCTGTTCCACTGAGTGCCTCTAAACAAGATGAACCCACGCCCAAACGGCACAGTGTTTCACTCAATGATACTGAGCC
ATGGAAGCTTATGGAAGAGTTTAAAAGACTTCAGAGAGAAATGAGGAAACTGTCAAAAGGAAAATCTACACCTGAGGGAG
GAAGGCTTAAGGCTCTGAAAGGTGGCACATCCAAGAGAAGCCTGGCTGGGCCTCTGCGTCCTTCAGAGACAAACGTCACC
AGTCCTCTCCCCTCACTCCTTGTTGTGATTGCAACCATCTTCACTGGGTTCTTTCTAGGGAAGTTCATCTTG

Alignment

ORF - retro_cpor_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 58.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PDELMDSKLRC-VFEMPNENDKLNDMEPSKAVPLNASKQDGPMPKPHSVSLNDTETRKLMEECKRLQGEM
          P.ELMDSKLR..VF.MPNEN.KLN.M.PSKAVPL.ASKQD.P.PK.HSVSLNDTE..KLMEE.KRLQ.EM
Retrocopy PEELMDSKLRL<VFKMPNEN-KLNNMAPSKAVPLSASKQDEPTPKRHSVSLNDTEPWKLMEEFKRLQREM

Parental  MKLSE-ENRHLKEEGLRLRKVAH-SEKSGSASAASFRD-NVTSPLPSLLVVIAAIFIGFFLGKFIL
          .KLS..EN.HL.EEGLRL.KVAH..EK.G.ASA.SFRD.NVTSPLPSLLVVIA.IF.GFFLGKFIL
Retrocopy RKLSK>ENLHLREEGLRL*KVAH>QEKPGWASA-SFRD>NVTSPLPSLLVVIATIFTGFFLGKFIL

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	1.27 RPM	55.50 RPM
SRP017611_kidney	1.05 RPM	55.38 RPM
SRP017611_liver	1.09 RPM	60.89 RPM
SRP040447_lung	0.86 RPM	48.70 RPM
SRP040447_skeletal_muscle	0.76 RPM	61.12 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_931 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_931 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006042	2 retrocopies	retro_cpor_783, retro_cpor_931 ,
Myotis lucifugus	ENSMLUG00000008965	1 retrocopy	retro_mluc_542,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57,
Mus musculus	ENSMUSG00000024091	1 retrocopy	retro_mmus_1774,
Rattus norvegicus	ENSRNOG00000014765	1 retrocopy	retro_rnor_266,