RetrogeneDB ID: retro_cpor_821

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:10531156..10531481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRELID2
• Ensembl ID: ENSCPOG00000001222
• Aliases: None
• Description: None

Sequence

>retro_cpor_821
AAGATGAGTGTTTTAAAGGTACCGAGTATCCAGTTAGAAGAAGAATCATGGCTCAGTCTTCAGAAAGAAACCTGGCTATG
CAGAGTAGCTGCCTTACATGGACACAGTATGCATCCATGAAGGAAGAGTCTTGTCTTCATGGAAAGTATGGAAAATCCAA
ATTGGACAGAGTTCATTCAAAGAGGCAGGATTTCAACCACAGGGGCTGGATTTCACAACTGTGTTTTAGAAACTTTTACC
AGCACTTTGTTAAGACAGGGAGCCCAGAAAGAATCAGAATAATGGAGATGCTGCTGAAGGAACAGTGTGGGCCCCTTTAG
CCGAA

Alignment

ORF - retro_cpor_821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QVSILKVPTVQLEEESWLNLQ-ERNMAIRSHCLTWTQYASLKEES-VFRESMENPNWTEFIQRGRISITG
          ..S.LKVP..QLEEESWL.LQ.ERN.A..S.CLTWTQYAS.KEES.VF.ESMENPNWTEFIQRGRIS.TG
Retrocopy KMSVLKVPSIQLEEESWLSLQ<ERNLAMQSSCLTWTQYASMKEES>VFMESMENPNWTEFIQRGRISTTG

Parental  AGFLNYILETFASTFLRQGAQK-GIRIMEMLLKEQCG-APLAE
          AGF.N..LETF.ST.LRQGAQK..IRIMEMLLKEQCG.APLAE
Retrocopy AGFHNCVLETFTSTLLRQGAQK<RIRIMEMLLKEQCG<APLAE

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	0.98 RPM
SRP017611_kidney	0.00 RPM	0.31 RPM
SRP017611_liver	0.00 RPM	0.17 RPM
SRP040447_lung	0.00 RPM	1.44 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_821 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_821 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001222	1 retrocopy	retro_cpor_821 ,
Echinops telfairi	ENSETEG00000005000	2 retrocopies	retro_etel_1464, retro_etel_1676,
Homo sapiens	ENSG00000186314	1 retrocopy	retro_hsap_1134,
Macaca mulatta	ENSMMUG00000013588	1 retrocopy	retro_mmul_877,
Mus musculus	ENSMUSG00000056671	1 retrocopy	retro_mmus_1260,
Nomascus leucogenys	ENSNLEG00000009800	1 retrocopy	retro_nleu_928,
Otolemur garnettii	ENSOGAG00000010025	2 retrocopies	retro_ogar_2400, retro_ogar_2477,
Pan troglodytes	ENSPTRG00000017368	1 retrocopy	retro_ptro_770,
Tursiops truncatus	ENSTTRG00000016708	1 retrocopy	retro_ttru_1875,