RetrogeneDB ID: retro_cpor_435

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:31027999..31028295(-)
• Located in intron of: ENSCPOG00000013559

Retrocopy information

• Ensembl ID: ENSCPOG00000021433
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDA1
• Ensembl ID: ENSCPOG00000006944
• Aliases: None
• Description: None

Sequence

>retro_cpor_435
AACTTTCTGAAAGGGTTGCCTGTCTACAGCAAAGGCAGTTTTAGTGGATTCCATGCCACCTCTGTGTACAAGGCTCCGAA
CCAATGCCCCTGCGTCTACCTGCCCATCTGGGAGTACCTGCCAGAACAGATCATTGTGACAGAGAAGACAAACATCCTCC
TATGCTACCTACATCAACAATGGGACAAAAATGCTGCCAAGCGAGGGACCAGGAGCAGGTGGAGCTAGAGGGTGAGAGCT
CAATGCCATGCCTGATGATACTGCAGCTGGACAGCCCCAACATGCACGAGGACACC

Alignment

ORF - retro_cpor_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.28 %
• Parental protein coverage: 98.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKK-
          .FLKGLPVY.K..FS.FHA.SV.KA.N..P.VYLP..EY..EQIIVTEKTNILL.YLHQQWD.KNAAK..
Retrocopy NFLKGLPVYSKGSFSGFHATSVYKAPNQCPCVYLPIWEYLPEQIIVTEKTNILLCYLHQQWD-KNAAKR<

Parental  RDQEQVELEGESSAPPRKVARTDSPDMHEDT
          RDQEQVELEGESS.P.......DSP.MHEDT
Retrocopy RDQEQVELEGESSMPCLMILQLDSPNMHEDT

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	17.14 RPM
SRP017611_kidney	0.00 RPM	10.15 RPM
SRP017611_liver	0.00 RPM	5.57 RPM
SRP040447_lung	0.00 RPM	20.88 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_435 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_435 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 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017068	3 retrocopies	retro_btau_1152, retro_btau_536, retro_btau_74,
Canis familiaris	ENSCAFG00000031251	3 retrocopies	retro_cfam_1089, retro_cfam_2033, retro_cfam_475,
Cavia porcellus	ENSCPOG00000006944	1 retrocopy	retro_cpor_435 ,
Felis catus	ENSFCAG00000001001	1 retrocopy	retro_fcat_487,
Homo sapiens	ENSG00000130311	1 retrocopy	retro_hsap_1409,
Gorilla gorilla	ENSGGOG00000005802	1 retrocopy	retro_ggor_1093,
Microcebus murinus	ENSMICG00000001763	1 retrocopy	retro_mmur_1162,
Myotis lucifugus	ENSMLUG00000003990	1 retrocopy	retro_mluc_1014,
Macaca mulatta	ENSMMUG00000016231	1 retrocopy	retro_mmul_2248,
Nomascus leucogenys	ENSNLEG00000005738	2 retrocopies	retro_nleu_1427, retro_nleu_1428,
Otolemur garnettii	ENSOGAG00000003701	1 retrocopy	retro_ogar_2375,
Pongo abelii	ENSPPYG00000009710	2 retrocopies	retro_pabe_1167, retro_pabe_1214,
Pan troglodytes	ENSPTRG00000010668	1 retrocopy	retro_ptro_966,
Rattus norvegicus	ENSRNOG00000039417	1 retrocopy	retro_rnor_1511,