RetrogeneDB ID: retro_cpor_476

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_161:753895..754239(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP14
• Ensembl ID: ENSCPOG00000004281
• Aliases: None
• Description: None

Sequence

>retro_cpor_476
CATAGGAAAGAAGTTTACAAAAATTTCTCAGAATATCACTACATAAAAGTTCTCCTGGAATTTCAAGATCACAGATTTGA
ACTAAATGCTTCATAGTACAAGCAGGTTGTTTCTGCTGTAACGGATTTGTTTGGGCAGGTTGGCACTGCCTTACTTCTGG
ATGGCCTGACCTACGACAAGAAGACCTCATCAGCTGTTCTGAGAATACACAGAAGTGGGATGGTCAAATTGTGGAGCTGT
TTCACCCTGCTAGGGTCCTAGAAAGGCAAACGATGTGCTTTCAGAGTATTTGTGTTTCTCCCTTTTTCTTTGCATTATTT
GATAATAGTAGGGAACTAATATTG

Alignment

ORF - retro_cpor_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.81 %
• Parental protein coverage: 93.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YERIVYKNFSEYHYMKVCLEFQDHGVGLNVAQFKQLLVSALKDLFGEVGAALPLDVLTYEEKTLSAILRV
          ....VYKNFSEYHY.KV.LEFQDH...LN....KQ..VSA..DLFG.VG.AL.LD.LTY..KT.SA.LR.
Retrocopy HRKEVYKNFSEYHYIKVLLEFQDHRFELNAS*YKQV-VSAVTDLFGQVGTALLLDGLTYDKKTSSAVLRI

Parental  CSSGVVKLWSSLTLLGSYKGKKCAFRV-IQVSPFLLALSGNSRELVL
          ..SG.VKLWS..TLLGS.KGK.CAFRV.I.VSPF..AL..NSREL.L
Retrocopy HRSGMVKLWSCFTLLGS*KGKRCAFRV<ICVSPFFFALFDNSRELIL

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	5.64 RPM
SRP017611_kidney	0.00 RPM	10.68 RPM
SRP017611_liver	0.00 RPM	8.62 RPM
SRP040447_lung	0.00 RPM	6.20 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_476 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_476 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019987	1 retrocopy	retro_btau_1621,
Cavia porcellus	ENSCPOG00000004281	2 retrocopies	retro_cpor_476 , retro_cpor_566,
Dasypus novemcinctus	ENSDNOG00000013439	1 retrocopy	retro_dnov_762,
Macropus eugenii	ENSMEUG00000010883	1 retrocopy	retro_meug_838,
Microcebus murinus	ENSMICG00000014541	1 retrocopy	retro_mmur_142,
Myotis lucifugus	ENSMLUG00000007998	1 retrocopy	retro_mluc_2291,
Ornithorhynchus anatinus	ENSOANG00000022513	1 retrocopy	retro_oana_119,
Oryctolagus cuniculus	ENSOCUG00000027202	3 retrocopies	retro_ocun_1160, retro_ocun_1359, retro_ocun_1425,
Rattus norvegicus	ENSRNOG00000039829	1 retrocopy	retro_rnor_1530,
Ictidomys tridecemlineatus	ENSSTOG00000015394	1 retrocopy	retro_itri_1072,
Tarsius syrichta	ENSTSYG00000013343	1 retrocopy	retro_tsyr_218,
Vicugna pacos	ENSVPAG00000000935	1 retrocopy	retro_vpac_202,