RetrogeneDB ID: retro_cpor_459

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:40809842..40810222(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000002576
• Aliases: None
• Description: selenoprotein T precursor [Source:RefSeq peptide;Acc:NP_001244921]

Sequence

>retro_cpor_459
ATGAGACTTCTGCTGCTGTTTCTGCTGCTGGCATCAGCAGTGGTCCAGAGCAAGGCCTCGGCCAATCTGGGCGGTGTGCC
CAGCAAGAGATTGAAGATGCATTACTCCACAGGGTTGGTGCTTATGTTCCAGATTTGTGTTTCCTGAGGATATAGGCAGG
TGCTTGAGGAGTACATGAGGGTTATTAGCCACCAGTACCAAGACATCCAAATTGAAGGAGAGAATTACCTTCCTCAACCA
ATTTATAGACACTTAGCATCTTTCCTGTCAATCTTCAAACTAGTATTAATAGTCTTAATAATTGTTGGAAAGGATCCTCT
TGCTTTCTTTAGCATGAAAGCTCCTAGCATCTGGCTGTGGGGCAAGAAAATAAGGTCTAC

Alignment

ORF - retro_cpor_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 65.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLLLLFLLAASAVVRSEASANLGGVPSKRLKMQYATGPLLKFQICCILCRYRRVFEEYMRVISQRYPDI
          MRLLLLFLL.ASAVV.S.ASANLGGVPSKRLKM.Y.TG..L.FQIC.....YR.V.EEYMRVIS..Y.DI
Retrocopy MRLLLLFLLLASAVVQSKASANLGGVPSKRLKMHYSTGLVLMFQIC-VS*GYRQVLEEYMRVISHQYQDI

Parental  RIEGENYLPQPIYRHIASFLSIFKLVLIVLIIVGKDPFAFFGMQAPSIWQW-GQENKVY
          .IEGENYLPQPIYRH.ASFLSIFKLVLIVLIIVGKDP.AFF.M.APSIW.W.GQENKVY
Retrocopy QIEGENYLPQPIYRHLASFLSIFKLVLIVLIIVGKDPLAFFSMKAPSIWLW<GQENKVY

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	29.33 RPM
SRP017611_kidney	0.10 RPM	41.14 RPM
SRP017611_liver	0.00 RPM	18.63 RPM
SRP040447_lung	0.03 RPM	39.98 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_459 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_459 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 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002576	1 retrocopy	retro_cpor_459 ,
Erinaceus europaeus	ENSEEUG00000013363	2 retrocopies	retro_eeur_63, retro_eeur_697,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Oryctolagus cuniculus	ENSOCUG00000013866	9 retrocopies	retro_ocun_1080, retro_ocun_1229, retro_ocun_1783, retro_ocun_1803, retro_ocun_1831, retro_ocun_327, retro_ocun_328, retro_ocun_557, retro_ocun_779,
Pongo abelii	ENSPPYG00000029483	1 retrocopy	retro_pabe_3478,
Tursiops truncatus	ENSTTRG00000007522	2 retrocopies	retro_ttru_1556, retro_ttru_694,