RetrogeneDB ID: retro_cpor_446

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:8354799..8355000(+)
• Located in intron of: ENSCPOG00000012674

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHFM1
• Ensembl ID: ENSCPOG00000010402
• Aliases: None
• Description: None

Sequence

>retro_cpor_446
AAAACGCAGCCGGTAGATTTGGGTCTCCTCGAGGTGGATGATGAGTTTGAGGAGTTCCCTGCTGAAGACTGGGCTGGTTT
GGATGAAGATAAAGATGCTCATGTATGAGAAGATAACTGAAATGATGACAATGTAGAGGACAATCTCTCCAATCAGTTAC
CAGCTGAACTAGAGAAACGTAGTTATAATATGCAGACTTCA

Alignment

ORF - retro_cpor_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.6 %
• Parental protein coverage: 95.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYKMETS
          K.QPVDLGLLE.DDEFEEFPAEDWAGLDED.DAHV.EDN..DDNVED..SNQL.AELEK..Y.M.TS
Retrocopy KTQPVDLGLLEVDDEFEEFPAEDWAGLDEDKDAHV*EDN*NDDNVEDNLSNQLPAELEKRSYNMQTS

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	33.19 RPM
SRP017611_kidney	0.00 RPM	53.60 RPM
SRP017611_liver	0.00 RPM	70.91 RPM
SRP040447_lung	0.00 RPM	41.56 RPM
SRP040447_skeletal_muscle	0.00 RPM	71.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_446 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_446 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002179	1 retrocopy	retro_cfam_1174,
Cavia porcellus	ENSCPOG00000010402	1 retrocopy	retro_cpor_446 ,
Echinops telfairi	ENSETEG00000019778	1 retrocopy	retro_etel_961,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452, retro_ocun_77,