RetrogeneDB ID: retro_cpor_1383

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_79:3671421..3671673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSCPOG00000011872
• Aliases: None
• Description: None

Sequence

>retro_cpor_1383
ATGTTGACTTCCTTAGTCTGGGTCACCCTCTAGGTTCCAAGCAAGAGGAAACCACAGTCCGTGGGAGCCACCCTCAGCCT
CACACTTCCTGCAATAAACAGGATAAAACAACTTCTTAAACATAAACTTGAACTGATAGGTTTCATAGTTGATGTCCAAA
CCAGAGGCTGTAAGGTCCTTTCCCACATTCTAGGATATAAGAAAAACAAAGGAGATTCTGATGAGGTTGTATGAGATGAA
ATCAGAATGTAC

Alignment

ORF - retro_cpor_1383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 65.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLQDKPEHVGLKVGVRTRGCNGLSYTLEYTKTK
          M..SLV..T....SKRK.Q...A.L.LT..A.N.IKQLL..K.E..G..V.V.TRGC..LS..L.Y.K.K
Retrocopy MLTSLVWVTL*VPSKRKPQSVGATLSLTLPAINRIKQLLKHKLELIGFIVDVQTRGCKVLSHILGYKKNK

Parental  GDSDEEVVQDGVRVF
          GDSDE.VV.D..R..
Retrocopy GDSDE-VV*DEIRMY

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	50.33 RPM
SRP017611_kidney	0.00 RPM	69.09 RPM
SRP017611_liver	0.00 RPM	49.40 RPM
SRP040447_lung	0.00 RPM	29.63 RPM
SRP040447_skeletal_muscle	0.00 RPM	64.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1383 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1383 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 13 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Cavia porcellus	ENSCPOG00000011872	2 retrocopies	retro_cpor_1383 , retro_cpor_768,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Microcebus murinus	ENSMICG00000003889	1 retrocopy	retro_mmur_1399,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Otolemur garnettii	ENSOGAG00000015628	5 retrocopies	retro_ogar_1267, retro_ogar_1545, retro_ogar_2186, retro_ogar_2813, retro_ogar_935,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,