RetrogeneDB ID: retro_cpor_482

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_166:1804546..1804970(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD1
• Ensembl ID: ENSCPOG00000002088
• Aliases: None
• Description: None

Sequence

>retro_cpor_482
GTGTTACCTGAGGAGTTCCATCTACTTCCAGCAGAAATGATAGGAATTCTTACCTCGACTGCATCTGCAGGCATGGATTT
CAACTAGCTGGAGGCATTCTTAACTGCTCAAACCAAAGAACAAGGTTGGATCCCACCTGACCAAGGTGCTGCTATTTCCA
AATTCTGAAAAAGCCACAGGGCAAAAATCCAAGAGAGCCCCATGAACCAGAGCCCTTGGGAAAATGGACTTAGGGGCCCG
AGCTGGAGAGCTGACAGCAAGTCTCAGGCAAGGCACCCAGCTCAGATGCACACACCTGTGGCCATAACAGAGCTAGGACT
TGGGAATCAGGGACAGGAATCAGAATTTCTGTCTGGAGTTTGATGGGATGAAGGTCATCCAAATCTTAAAGAAGCTCTCA
GAGGCAGAAGAAAATGTCAACACT

Alignment

ORF - retro_cpor_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.03 %
• Parental protein coverage: 77.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSPEEFRPFLAKMKGILKSIASADMDFNQLEAFLTAQTKKQGGITSDQAAVISKFWKSHKTKIRESLVNQ
          V.PEEF....A.M.GIL.S.ASA.MDFN.LEAFLTAQTK.QG.I..DQ.A.ISKF.KSH..KI.ES..NQ
Retrocopy VLPEEFHLLPAEMIGILTSTASAGMDFN*LEAFLTAQTKEQGWIPPDQGAAISKF*KSHRAKIQESPMNQ

Parental  SRWENELRGLSWRVDGRSQSRHSAQIQTPVAIIEL-EFGKHGQESEFLCLEFDEVKVNQILKKLSEVEEN
          S.WEN.LRG.SWR.D..SQ.RH.AQ..TPVAI.EL...G.......F.CLEFD..KV.QILKKLSE.EEN
Retrocopy SPWENGLRGPSWRADSKSQARHPAQMHTPVAITEL>DLGIRDRNQNF-CLEFDGMKVIQILKKLSEAEEN

Parental  INT
          .NT
Retrocopy VNT

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	12.31 RPM
SRP017611_kidney	0.00 RPM	18.84 RPM
SRP017611_liver	0.00 RPM	11.80 RPM
SRP040447_lung	0.03 RPM	8.20 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_482 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_482 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003090	1 retrocopy	retro_cfam_343,
Cavia porcellus	ENSCPOG00000002088	1 retrocopy	retro_cpor_482 ,
Mustela putorius furo	ENSMPUG00000005842	1 retrocopy	retro_mputfur_1120,
Ictidomys tridecemlineatus	ENSSTOG00000015062	1 retrocopy	retro_itri_562,
Tarsius syrichta	ENSTSYG00000000812	1 retrocopy	retro_tsyr_88,