RetrogeneDB ID: retro_cpor_399

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:24647631..24648049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLOD5
• Ensembl ID: ENSCPOG00000003997
• Aliases: None
• Description: None

Sequence

>retro_cpor_399
ACTCCAAGGATTCAGTCATGGAGTTACAGCAGTCCTTCCTCGTGTTTTATTCATAGACTCAACCACATGTAAAGACAGAA
AAGAACATCAAAGACTTCTGCATGTTTTACTCCAAAATCATGCATACCGAGACCCTAGCTTTCAAGAGAAACTGTAAAGT
GCTGTGTCTTAGAGACCAGATTTTTGACCTCCGTTAGAGGGGGAAGAAATTGAACCTAAAGCCATTCACCCACTCTGCAG
CTACACAGATATATGTTTGATCACAGAGATGCCTTTGGAGATCATTTAGCACCTTCAAGCTTTTGGTGACCTCAATGAAA
ATTGCTCATTCCTCAGAACAGGAGCAAAAGGGCCTATTATGTCCATCTGCTTCTGAGTCACATACAGAAATCTGATTGTG
TTGTCCAATTACCTCTCC

Alignment

ORF - retro_cpor_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.06 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TAGTQSWRNSSQTLSPSPCLIQRLDHI-VMTVKSIKDTTMFYSNVLGMKVTTFKGDRKALCFGDQKFNLH
          T...QSW..S....SPS.C.I.RL.H..V.T.K.IKD..MFYS.........FK...K.LC..DQ.F.L.
Retrocopy TPRIQSWSYS----SPSSCFIHRLNHM<VKTEKNIKDFCMFYSKIMHTETLAFKRNCKVLCLRDQIFDLR

Parental  EMGK-EFEPKAIHPLPGSLDICLITEAPLEEMIQRLKAFDVPIEEGPVPRTGAKGPIMSIYFRDPDRNLI
          ..GK.E.EPKAIHPL....DICLITE.PL.E.I..L.AF....E.....RTGAKGPIMSI.F....RNLI
Retrocopy *RGK<EIEPKAIHPLCSYTDICLITEMPL-EII*HLQAFGDLNENCSFLRTGAKGPIMSICF*VTYRNLI

Parental  EVSNYIS
          ..SNY.S
Retrocopy VLSNYLS

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	2.47 RPM
SRP017611_kidney	0.00 RPM	48.68 RPM
SRP017611_liver	0.00 RPM	8.01 RPM
SRP040447_lung	0.00 RPM	1.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_399 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_399 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003997	1 retrocopy	retro_cpor_399 ,