RetrogeneDB ID: retro_cpor_956

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_37:4942915..4943333(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD2
• Ensembl ID: ENSCPOG00000005273
• Aliases: None
• Description: None

Sequence

>retro_cpor_956
ATGCTGCTGGACTTGCCAGAGGACCATAAGGAGCACCTGCCTTTCCTGCAGCAAGCGGACAGCTCAGCGGTTGCCGAGTT
TGGGTGGATAGCAGTGGAGTTCCTGAGGCGAGGACTGAACCCTAAGATCTAAGAAGGCGCCATCGGAAGACTCCTCGTGA
GCAGTGACACCACCCAGCGTGGCGTAGGAGGAGTGACCTGTCCCCTCGCTCAGAGCTCCAAGCTCATGATCTCTGAATTT
CCAAGACTCTCTTTCTGTTTGGGGATTCTCTGAAGAATTAAACGAATTACTGCTTCTGCTTTATCTGGACAACAGAAAGG
AAATCAGAACTATTCTAAGCAAACAGGCACCTGGCCTTCCCACTTACCATAGCCTTGATGTCCAGTTGGCAAGGGGTCTC
CGGCAACAGCTTAAACCT

Alignment

ORF - retro_cpor_956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.71 %
• Parental protein coverage: 73.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLLDLSEEHKEHLAFLPQVDSAVVAEFGRIAVEFLRRGSNPKIYEGAARKLNVSSETVQHGVEGLTYLLT
          MLLDL.E.HKEHL.FL.Q.DS..VAEFG.IAVEFLRRG.NPKI.EGA...L.VSS.T.Q.GV.G.T..L.
Retrocopy MLLDLPEDHKEHLPFLQQADSSAVAEFGWIAVEFLRRGLNPKI*EGAIGRLLVSSDTTQRGVGGVTCPLA

Parental  ESSKLMISELDFQDSVFVLG-FSEELNKLLLQLYLDNRKEIRTILNELTPDLPTYHSLEWRLDVQLASRS
          .SSKLMISE..F....F.LG.FSEELN.LLL.LYLDNRKEIRTIL....P.LPTYHSL.....VQLA.R.
Retrocopy QSSKLMISE--FPRLSFCLG>FSEELNELLLLLYLDNRKEIRTILSKQAPGLPTYHSLD----VQLA-RG

Parental  LRQQIKP
          LRQQ.KP
Retrocopy LRQQLKP

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	6.15 RPM
SRP017611_kidney	0.00 RPM	12.56 RPM
SRP017611_liver	0.00 RPM	6.44 RPM
SRP040447_lung	0.00 RPM	14.17 RPM
SRP040447_skeletal_muscle	0.01 RPM	8.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_956 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_956 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013809	1 retrocopy	retro_chof_1601,
Cavia porcellus	ENSCPOG00000005273	2 retrocopies	retro_cpor_520, retro_cpor_956 ,
Rattus norvegicus	ENSRNOG00000043386	1 retrocopy	retro_rnor_2231,
Ictidomys tridecemlineatus	ENSSTOG00000010888	4 retrocopies	retro_itri_180, retro_itri_1803, retro_itri_1880, retro_itri_1899,
Tupaia belangeri	ENSTBEG00000003545	1 retrocopy	retro_tbel_2895,
Tursiops truncatus	ENSTTRG00000003450	1 retrocopy	retro_ttru_1759,