RetrogeneDB ID: retro_cpor_1482

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:46237758..46238059(+)
• Located in intron of: ENSCPOG00000000973

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLO1
• Ensembl ID: ENSCPOG00000010050
• Aliases: None
• Description: None

Sequence

>retro_cpor_1482
AAAGATAAAAATGAAAAAATAGCGTTCTCCAGAAAAGCTACACCTTAGTTGACATGCAATTGGGGCACTAAAGATGATGA
CACCCTAGGTTACCACAATGGTAATTCAGACCCTCGGGGATTTGGTCACATTGGAATTGCTGTTCCTAGTGTATATGGTG
CTTGTAAAAGATTTGAAGAACTAGGAGTCAAATTTGTAAGGAAACCTAATGATGGTAAAAATGAAAGGCCTGGCACTTAC
TCAGGATCCTGATGGCTACTGGATTGAAATTTTGAATCCTAACAAAATGAGTGAAATGCTC

Alignment

ORF - retro_cpor_1482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.67 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDKNDILAWAFSRKATLELTHNWGTEDDDNQSYHNGNSDPRGFGHIGIAVPDVYGACKRFEELGVKFVKK
          .DKN...A..FSRKAT..LT.NWGT.DDD...YHNGNSDPRGFGHIGIAVP.VYGACKRFEELGVKFV.K
Retrocopy KDKNEKIA--FSRKATP*LTCNWGTKDDDTLGYHNGNSDPRGFGHIGIAVPSVYGACKRFEELGVKFVRK

Parental  PDEG-KMKGLAFIQDPDGYWIEILSPNTMTEML
          P..G.KMKGLA..QDPDGYWIEIL.PN.M.EML
Retrocopy PNDG>KMKGLALTQDPDGYWIEILNPNKMSEML

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	19.96 RPM
SRP017611_kidney	0.00 RPM	16.54 RPM
SRP017611_liver	0.00 RPM	46.70 RPM
SRP040447_lung	0.00 RPM	11.90 RPM
SRP040447_skeletal_muscle	0.00 RPM	35.70 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1482 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1482 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482 ,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,