RetrogeneDB ID: retro_cpor_185

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:1574441..1574932(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBEY
• Ensembl ID: ENSCPOG00000002415
• Aliases: None
• Description: None

Sequence

>retro_cpor_185
ATGAGTTCGGTGATTAGAAATCTGCAGGGCACGATTCCCATGAGGAGAGTGACACTTCTGAGGGTTGTGGAGATTGTAAG
GAATATTTTAGGAGTGGAGAAATTTGACTTGGGATAATCTTTCTTGACAACAAGAATATTCAACACACTAATAGGATCTA
CAGAAAGAAAAATATCCCAACCAATGTGTTTTCGTTTCCATTTTATGAGTATCTGAAAGCAGGTGATGTTCCCCAGCCCA
GTTTTCCAAACGACTGTAACTTGGGAGATATTTTTTTTAGGAGTGGAGTATATCTTTGAGCAGGGCAAAAAAAATGAAGA
TTACTATGACATTCTGACTGTGAAGGCCACTCATGGACTCTGTCACTTACTTGAGTTCACACACAATTTGGAAGCAGAGT
GGACAAAATGTACAACCAGGAGAAGCAGGTGCTAGAGGAGCTAAGCCAGCACACTGGGGCTCAGCTCCAGCCTCTTAGCA
GGGGCCTCTTC

Alignment

ORF - retro_cpor_185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLVIRNLQRTIPIRRVPLRRNVEIVRNILGVEKFDLG-IIFLDNKNIQHINRIYRKKNIPTDVLSFPFY
          MS.VIRNLQ.TIP.RRV.L.R.VEIVRNILGVEKFDLG.IIFLDNKNIQH.NRIYRKKNIPT.V.SFPFY
Retrocopy MSSVIRNLQGTIPMRRVTLLRVVEIVRNILGVEKFDLG<IIFLDNKNIQHTNRIYRKKNIPTNVFSFPFY

Parental  ENLKAGEVPQPSFPDDYNLGDI-FLGVEYIFQQCKENEDYYDILTVTATHGLCHLLGFTHNSEAEW-HKM
          E.LKAG.VPQPSFP.D.NLGDI.FLGVEYIF.Q....EDYYDILTV.ATHGLCHLL.FTHN.EAEW..KM
Retrocopy EYLKAGDVPQPSFPNDCNLGDI>FLGVEYIFEQGXXXEDYYDILTVKATHGLCHLLEFTHNLEAEW<DKM

Parental  YHQEKQVLEELSQRTGAQLQPLSRGLF
          Y.QEKQVLEELSQ.TGAQLQPLSRGLF
Retrocopy YNQEKQVLEELSQHTGAQLQPLSRGLF

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	4.14 RPM
SRP017611_kidney	0.00 RPM	4.40 RPM
SRP017611_liver	0.00 RPM	3.79 RPM
SRP040447_lung	0.00 RPM	3.23 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_185 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_185 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002415	1 retrocopy	retro_cpor_185 ,
Tursiops truncatus	ENSTTRG00000000360	1 retrocopy	retro_ttru_925,