RetrogeneDB ID: retro_cpor_1438

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_83:5313227..5313643(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000021255
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C20ORF20
• Ensembl ID: ENSCPOG00000020272
• Aliases: None
• Description: None

Sequence

>retro_cpor_1438
ATCCGGGACAAGCTCAGCCAGAACATCGGGCGGCAGGCTCCATCCAAGGTCATGTGGGGCCATCTGAGCACCACGTATGA
CATGCAGACGCTGCCTGAGTCTGAGATTCTTCCCTTCCCCAGTCCAGAAGGGAACTTCATCCTTCCTGAAGAGGTCATTC
AAGAGGTCCAGGAAGGAAAAGTAATCACTGAAGGGGAGATGAAGGAAGATGTGGACCAGCGCAGCGGGGCTGATGATGTT
TTCCCGTCTTCAGGGAGCTCGGGCAAAGCAACAGAAAATCGAGCAAAGACAAGGAGAAGAACTCTTCAGACTTGGAGTGC
AAAGAAGGGGCGGATAAGCGGGAGCGCAGCCGGGTCACCCACACAGTGCTCACAGCAAACAGTAGCCCTCCAGCGCCAGC
GCCGCCCAGACACCGG

Alignment

ORF - retro_cpor_1438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 70.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRDKFSQNIGRQVPSKVIWDHLSTMYDMQALHESEILPFPNPERNFVLPEEIIQEVREGKVIIEEEMKEE
          IRDK.SQNIGRQ.PSKV.W.HLST.YDMQ.L.ESEILPFP.PE.NF.LPEE.IQEV.EGKVI.E.EMKE.
Retrocopy IRDKLSQNIGRQAPSKVMWGHLSTTYDMQTLPESEILPFPSPEGNFILPEEVIQEVQEGKVITEGEMKED

Parental  MKEDVDPHSGADDVFSSSGSLGKATE-KSSKDKEKNSSDLGCKEGADKRKRSRVTDKVLTANSNPSSPSA
          ....VD..SGADDVF.SSGS.GKATE.KSSKDKEKNSSDL.CKEGADKR.RSRVT..VLTANS.P..P..
Retrocopy ----VDQRSGADDVFPSSGSSGKATE<KSSKDKEKNSSDLECKEGADKRERSRVTHTVLTANSSPPAPAP

Parental  AKRR
          ...R
Retrocopy PRHR

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	3.80 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.00 RPM	2.00 RPM
SRP040447_lung	0.00 RPM	4.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1438 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1438 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000020272	1 retrocopy	retro_cpor_1438 ,
Monodelphis domestica	ENSMODG00000016803	1 retrocopy	retro_mdom_246,
Mus musculus	ENSMUSG00000027569	1 retrocopy	retro_mmus_1383,
Sarcophilus harrisii	ENSSHAG00000010685	1 retrocopy	retro_shar_128,
Ictidomys tridecemlineatus	ENSSTOG00000012953	1 retrocopy	retro_itri_634,