RetrogeneDB ID: retro_cpor_1475

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:38399162..38399486(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO27
• Ensembl ID: ENSCPOG00000004611
• Aliases: None
• Description: None

Sequence

>retro_cpor_1475
CCAGAACTGGAGGACAGTGACAAGATTGAACTCCATGCCTCAGACTGGTGGGGAGCCCGACATGACAGTGGCTGTAGGTA
TCCACTGCTTATCCAACTTCTAGATGCCGGCCAGACTGTCCTAGATAAATTCTCTGCTGTGCCTGATCCCATTGAACAAT
GGAACAACAATGTCTGCTTTCAGGTCACCCACGTCTTCTCCAACATCAAGATGGGTGTCCGTTTTGTGTCTTTTGAACAC
TGAGGCCAGGACACACAGTTCTGGGTTGGCCACTACGAAGCCCAAGTGACCAATTCTAGTGTGATTGTGCAAGTCAGCCA
GCCC

Alignment

ORF - retro_cpor_1475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PELLDSGKIEIHVSDWWGARHDSGCRYRLLVQLLDAGQTVLDKFSAVPDPIEQWNNNVCFQVTHVFSNIK
          PEL.DS.KIE.H.SDWWGARHDSGCRY.LL.QLLDAGQTVLDKFSAVPDPIEQWNNNVCFQVTHVFSNIK
Retrocopy PELEDSDKIELHASDWWGARHDSGCRYPLLIQLLDAGQTVLDKFSAVPDPIEQWNNNVCFQVTHVFSNIK

Parental  MGVRFVSFEHWGQDTQFWAGHYGARVTNSSVIVQVSQP
          MGVRFVSFEH.GQDTQFW.GHY.A.VTNSSVIVQVSQP
Retrocopy MGVRFVSFEH*GQDTQFWVGHYEAQVTNSSVIVQVSQP

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	2.88 RPM
SRP017611_kidney	0.00 RPM	5.13 RPM
SRP017611_liver	0.00 RPM	0.96 RPM
SRP040447_lung	0.03 RPM	16.22 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.27 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1475 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1475 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000656	1 retrocopy	retro_cpor_1474,
Cavia porcellus	ENSCPOG00000004611	1 retrocopy	retro_cpor_1475 ,
Mustela putorius furo	ENSMPUG00000017748	3 retrocopies	retro_mputfur_1473, retro_mputfur_465, retro_mputfur_965,
Ictidomys tridecemlineatus	ENSSTOG00000027765	1 retrocopy	retro_itri_401,
Tupaia belangeri	ENSTBEG00000010522	1 retrocopy	retro_tbel_1067,
Tursiops truncatus	ENSTTRG00000009850	1 retrocopy	retro_ttru_1161,
Vicugna pacos	ENSVPAG00000004974	1 retrocopy	retro_vpac_470,