RetrogeneDB ID: retro_cpor_371

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_135:1226534..1226725(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSCPOG00000010930
• Aliases: None
• Description: None

Sequence

>retro_cpor_371
ATGCTAATGAAGGTAAAGAGGCTGACCCGGAAAGCAGATTGAAACTGGCATTGAACCCACAGACAAGGTGGAGCGAGTCA
AGGAGCAGGAGGAGCAGACAGAGGGCACCGCCTCAACAGCAAAGGCTCAGCTACGGTGGCAAACAGATGCACGACGAGAA
GACGGCAGCTGATTACGAGATTCTGGGTGGT

Alignment

ORF - retro_cpor_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 79.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFLKVVTLT-GKEIEIDIEPTDKVERIKERVEE-KEGIPPQQQRLIYSGKQMNDEKTAADYKILGG
          ...KV..LT.GK.IE..IEPTDKVER.KE..EE.....PPQQQRL.Y.GKQM.DEKTAADY.ILGG
Retrocopy MLMKVKRLT>GKQIETGIEPTDKVERVKEQ-EE>RQRAPPQQQRLSYGGKQMHDEKTAADYEILGG

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	38.71 RPM
SRP017611_kidney	0.00 RPM	39.26 RPM
SRP017611_liver	0.22 RPM	25.90 RPM
SRP040447_lung	0.00 RPM	30.79 RPM
SRP040447_skeletal_muscle	0.00 RPM	40.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_371 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_371 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Canis familiaris	ENSCAFG00000012097	1 retrocopy	retro_cfam_1789,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Cavia porcellus	ENSCPOG00000010930	1 retrocopy	retro_cpor_371 ,
Gorilla gorilla	ENSGGOG00000016105	1 retrocopy	retro_ggor_261,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,