RetrogeneDB ID: retro_cpor_939

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:15013911..15014456(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UNC119
• Ensembl ID: ENSCPOG00000002937
• Aliases: None
• Description: None

Sequence

>retro_cpor_939
GAATCTACTTCTGGGGCTTGGGGGTTGAGTGTACCACCCAAGCCCGGTCTGCATGTGGAAACTGAATCAAGAGTCCAAGT
TGGGACAGGAGTCAGGCCTGGGGACCAGGCCCGTGTTGCAGAGAAAGCAGCCCATTGGGCCAGAGCATGTGCTGGGGCTG
CAGCGGATCATGAGACTACTTGTGCTGTCCTGAGACGAATATCTACAAGATCAAGTTCGTCAGGTTCAAGACTTAGGACA
TGTACTCAGGCAGAGTCCTCTTTGAAATCAGGAAGCCCCCTGCTTCAGAACAGTTGCCCATCAACCAGCGGGACCTGGAC
CCCAATGCAGGGCTCTTTGTCCACCACCAGTTCACACTTGCCTTCCACGGCCTGAGGCAGGTGGGAGCCATAGTAGAGTT
CACAGTGGGAGCCAAGCCTATGAACAGCTTCTGCAAGATGGAGAGGAACTGTTTTGGAAACCAGCAGCTCAAAAGCATTG
ATTTCCATTTTGAATTCTGCATTCCCAGCAGCAAGAGCACCTGTGAGCACATCTATGTCTCCCCC

Alignment

ORF - retro_cpor_939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 81.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPAPGASGLSAQPTPGLQAESES-ESESEPESGLGPRPGPLQGKQ-PIGPEDVLGLQRITGDYLCSPEEN
          E...GA.GLS..P.PGL..E.ES.ES....ESGLG.RP..LQ.KQ.P.G.....G......DYLC.PE.N
Retrocopy ESTSGAWGLSVPPKPGLHVETES>ESKLGQESGLGTRP-VLQRKQ>PLGQSMCWGCSG-S*DYLCCPETN

Parental  IYKIDFVRFKIRDMDSGTVLFEIKKPPASERLPINRRDLDPNAGRFVRYQFTPAFLRLRQVGATVEFTVG
          IYKI.FVRFK..DM.SG.VLFEI.KPPASE.LPIN.RDLDPNAG.FV..QFT.AF..LRQVGA.VEFTVG
Retrocopy IYKIKFVRFKT*DMYSGRVLFEIRKPPASEQLPINQRDLDPNAGLFVHHQFTLAFHGLRQVGAIVEFTVG

Parental  DKPVNNFRMIERHYFRNQLLKSFDFHFGFCIPSSKNTCEHIYDFP
          .KP.N.F...ER..F.NQ.LKS.DFHF.FCIPSSK.TCEHIY..P
Retrocopy AKPMNSFCKMERNCFGNQQLKSIDFHFEFCIPSSKSTCEHIYVSP

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	8.28 RPM
SRP017611_kidney	0.00 RPM	11.31 RPM
SRP017611_liver	0.00 RPM	4.40 RPM
SRP040447_lung	0.00 RPM	10.97 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.19 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_939 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_939 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004930	1 retrocopy	retro_amel_1529,
Callithrix jacchus	ENSCJAG00000012712	1 retrocopy	retro_cjac_2311,
Cavia porcellus	ENSCPOG00000002937	1 retrocopy	retro_cpor_939 ,
Felis catus	ENSFCAG00000024212	1 retrocopy	retro_fcat_923,
Myotis lucifugus	ENSMLUG00000012359	1 retrocopy	retro_mluc_2325,
Vicugna pacos	ENSVPAG00000004356	1 retrocopy	retro_vpac_402,