RetrogeneDB ID: retro_cpor_575

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:20493348..20493720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBPL1
• Ensembl ID: ENSCPOG00000011899
• Aliases: None
• Description: None

Sequence

>retro_cpor_575
ATGGATGCAGACAGCCACGCTGCATTGGACATTTTAATTACAAATACACCCTGTGTTACATTCAGAACAACACGCCATTT
GAACCTGCGGAAGACTGCTTTGAAGGGAGCAAATGTCATTTCTAAGTGTTACGTTGGAAAAGCATTAGTGAAGCTTAGAA
AACCTAGATATACAGGTACAATCTGGTCCTTAGGAAAAATTATTTGCACTGGAGCAACGAGTGAAGAAGAAGCTAAATTT
GGTGCCAGACCTTTAACCCATAGTCTGCAGAAACTAGGTTTCCAGATAATATTTACAGATTTTAAGGTTGTTAACGTTTT
GGTAGTTTGCATTATGCCCTTTGAAATTTGTTTGCCAGAATTCACAAAGAAC

Alignment

ORF - retro_cpor_575 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 75.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDADSDVALDILITNVVCV-FRTRCHLNLRKIALEGANVIYKRDVGKVLMKLRKPRITATIWSSGKIICT
          MDADS..ALDILITN..CV.FRT..HLNLRK.AL.GANVI.K..VGK.L.KLRKPR.T.TIWS.GKIICT
Retrocopy MDADSHAALDILITNTPCVTFRTTRHLNLRKTALKGANVISKCYVGKALVKLRKPRYTGTIWSLGKIICT

Parental  GATSEEEAKFGARRLARSLQKLGFQVIFTDFKVVNVLAVCNMPFEIRLPEFTKN
          GATSEEEAKFGAR.L..SLQKLGFQ.IFTDFKVVNVL.VC.MPFEI.LPEFTKN
Retrocopy GATSEEEAKFGARPLTHSLQKLGFQIIFTDFKVVNVLVVCIMPFEICLPEFTKN

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	9.03 RPM
SRP017611_kidney	0.00 RPM	3.98 RPM
SRP017611_liver	0.00 RPM	4.05 RPM
SRP040447_lung	0.00 RPM	4.69 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_575 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_575 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007544	1 retrocopy	retro_chof_469,
Cavia porcellus	ENSCPOG00000011899	1 retrocopy	retro_cpor_575 ,
Echinops telfairi	ENSETEG00000015892	1 retrocopy	retro_etel_1883,
Monodelphis domestica	ENSMODG00000017515	1 retrocopy	retro_mdom_1220,
Otolemur garnettii	ENSOGAG00000006622	2 retrocopies	retro_ogar_1508, retro_ogar_1509,