RetrogeneDB ID: retro_cpor_1318

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:27465467..27466066(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000013269
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRPDL
• Ensembl ID: ENSCPOG00000015619
• Aliases: None
• Description: None

Sequence

>retro_cpor_1318
GCAGAGGGGTCTGAGATCAACGCGAGCAAAAATAACAATAAAATATTTATTGGAGGCTTGAGCTGGGATACAAGCAAGAA
AGATCTGACTGCGTATTTGTCTCAATTTGGGAGAGTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGAAAGAGCAA
GAGGATTTGTGCTTTTCCAAGATGCTGCTAGAGTTGATAAGGTTTTGGAACTTAAAGAACACAAACTGGATGGCAAATTA
ATAAATCCCTAAAGGGTCAAAGCTTTAAAGAGGAAAGAACCCCTAAAAAGGTGTTTGTGGCTGAATTGAGCCCCGATACT
TTTGAAGAACAAATTAAAGAATATTTTGGAGCCTTTGGAGATATTGAAAACACTGAACTTCCCATGGATACAAAAACAAA
TGAAAGGAGAGGAGGATTTTGTTTCATCACATACACAGATGAAGATCCAGTCAAGAAACTTGTTAGAAAGCAGATTCCAC
AAATTGGTTCTGGGAAGTGTGAAATCAAAGTTTCACAACCCAAAGAAGTAAATCAGCAGCAACAGCAACCACAGGAAGGA
GAAGGGCGCTGCAGCTGGGGTTCGAGGTGGACCCAAGGA

Alignment

ORF - retro_cpor_1318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 71.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEGSKINASKNQQDDGYKMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAAS
          AEGS.INASKN......K.FIGGLSWDTSKKDLT.YLS.FG.VVDCTIKTDPVT.R.RGF..VLF.DAA.
Retrocopy AEGSEINASKNNN----KIFIGGLSWDTSKKDLTAYLSQFGRVVDCTIKTDPVTERARGF--VLFQDAAR

Parental  VDKVLELKEHKLDGKLIDPKRAKALKGKEP-PKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKT
          VDKVLELKEHKLDGKLI.P.R.KALK.KEP.PKKVFV..LSPDT.EEQIKEYFGAFG.IEN.ELPMDTKT
Retrocopy VDKVLELKEHKLDGKLINP*RVKALKRKEP<PKKVFVAELSPDTFEEQIKEYFGAFGDIENTELPMDTKT

Parental  NERRG-FCFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRG
          NERRG.FCFITYTDE.PVKKL......QIGSGKCEIKV.QPKEV..QQQQ.Q..G.G....G...T.G
Retrocopy NERRGGFCFITYTDEDPVKKLVRKQIPQIGSGKCEIKVSQPKEVNQQQQQPQE-GEGRCSWGSRWTQG

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	105.77 RPM
SRP017611_kidney	0.00 RPM	87.00 RPM
SRP017611_liver	0.00 RPM	55.10 RPM
SRP040447_lung	0.00 RPM	89.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	57.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1318 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1318 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 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318 , retro_cpor_264, retro_cpor_274, retro_cpor_567,
Cavia porcellus	ENSCPOG00000020972	1 retrocopy	retro_cpor_1078,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,