RetrogeneDB ID: retro_cpor_368

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_133:2981495..2981735(+)
• Located in intron of: ENSCPOG00000010338

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSCPOG00000015389
• Aliases: None
• Description: None

Sequence

>retro_cpor_368
ATGAGTCTGCGGAAGCAAACTCCTAGTGACTTCTTAAAGCAAATCATCGGAAGGCCAGTTGTGGTCAAATTAAATTCTGG
AGTGGATTATCGAGGGGTCCTGGCTTGCCTGGATGGCTATATGAATATAGCCCTAGAGCAGACCGAAAAGTATGTAAACG
GACAACTCAAGAATAAGTATGGGAATGCGTGTATCTGAGGAAACAATGTATTATACATAAGTACACAGAAGAGAAGGATG

Alignment

ORF - retro_cpor_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNV
          MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTE.YVNGQLKNKYG.A.I.GNNV
Retrocopy MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEKYVNGQLKNKYGNACI*GNNV

Parental  LYISTQKRRM
          LYISTQKRRM
Retrocopy LYISTQKRRM

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	0.29 RPM	6.73 RPM
SRP017611_kidney	0.52 RPM	8.27 RPM
SRP017611_liver	0.22 RPM	4.61 RPM
SRP040447_lung	0.18 RPM	10.37 RPM
SRP040447_skeletal_muscle	0.07 RPM	7.50 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_368 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_368 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 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368 ,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,