RetrogeneDB ID: retro_cpor_846

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:8045083..8045451(-)
• Located in intron of: ENSCPOG00000011890

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000001818
• Aliases: None
• Description: None

Sequence

>retro_cpor_846
CTGTCCCACCTGCTCAAAATACACCAGGCCACACAGAACAAGCGCAAAGAGCTGCAGGGAAATGTGGCATCAAGAAGCCA
TCACCGCAGTGACCTGTCTGACAGAAGCTTTGGGGGACCAGCTCTATGAGGATGTGGCCCAGGCCTACATGAACCAAAGG
AAGCTGGACCACAAAGTGAAGACCCAGAAGGGCCAAGTTGCTCGGTTTGCCTAGACAACAGGCAGTAGATCGGGATGGTG
GAGAACTTCACCGAAACACTCCAGAAAATCAGCCTATGAGGAGAATCAGGCTTGGAGCAATAAGCTGGACATGCCACCAT
TGCCGGCACCCGTGAGCAGTCTACAAAGGGCAGCAGCAGTCTGTCCCT

Alignment

ORF - retro_cpor_846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 98.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LSRLLKEHQAKQNERKELQ-EKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
          LS.LLK.HQA.QN.RKELQ.E....EAITA.TCLTEAL.D.L...VAQAYMNQRKLDH.VKT...Q.A.F
Retrocopy LSHLLKIHQATQNKRKELQ>EMWHQEAITAVTCLTEALGDQLYEDVAQAYMNQRKLDHKVKTQKGQVARF

Parental  AKQTG-QWIGMVENFNQALKEI-GDVENWARSIELDM-RTIATALEY-VYKGQLQSAP
          A..TG.Q.IGMVENF...L..I....EN.A.S..LDM..TIA...E..VYKGQ.QS.P
Retrocopy A*TTG<Q*IGMVENFTETLQKI>AYEENQAWSNKLDM<ATIAGTREQ<VYKGQQQSVP

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	0.58 RPM	13.86 RPM
SRP017611_kidney	0.31 RPM	32.24 RPM
SRP017611_liver	0.17 RPM	17.89 RPM
SRP040447_lung	0.08 RPM	27.01 RPM
SRP040447_skeletal_muscle	0.05 RPM	31.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_846 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_846 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260, retro_cpor_846 ,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467,