RetrogeneDB ID: retro_cpor_882

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_31:2042925..2043512(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3ORF33
• Ensembl ID: ENSCPOG00000006620
• Aliases: None
• Description: None

Sequence

>retro_cpor_882
GACCAAGCGGCCCCTAATAGGGTAACGTGGGTCTCGCAGTGGGTGGGTGATCACTTGCACTCTTCCAGGACATCAGCACT
GGGATGGCCATAACTGGAATAATGTTATTTCTAAGCAGTGTTCAACTAACATCAGAATTCACTAGATCTTCAGATATTCT
AGTAGAATTCATTAAAAAAGAATGTTAATCTATATGGACAAATCACACCCTACAACTGAGAATGGTCTAGAAATTGAAGG
TGATTCCCATCACTTTACCTATTATATCTTCATGGATAAAAGAGCCATGCGGTGTTTTGCTGGTTAAACTGGCTGGGGTA
GAACTCGCAGGAAGGGGGAAGGTATAGTTACAAAAATAACTCAAAGATCCCCAACTACCAAGGTTCCAATTCTCAGAAAG
GAGAATTCAGTACTCTTGGCTATCTTTTAGTTAATAAGGGTGGCTATTTAGTGTGAATCTGAATGAAGAAATTTTGCAAA
GAGGCCAGGATAAAACTGTTGTTGTTAAAGGGCTGAACCACGATTCTAAAACTTACTGGACGGTTCACCGAAAATTACTA
AAAGCTGAATTAGCAGCCATAATCAAA

Alignment

ORF - retro_cpor_882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DRAAYNVVTRVSQWADDHLRSSN-NISTGMAIAGIMLFLRSVRLTSKFTRSADIPAEFIRK-NVKLRGRL
          D.AA.N.VT.VSQW..DHL.SS...ISTGMAI.GIMLFL.SV.LTS.FTRS.DI..EFI.K.NV.L.G..
Retrocopy DQAAPNRVTWVSQWVGDHLHSSR<DISTGMAITGIMLFLSSVQLTSEFTRSSDILVEFIKK>NVNLYGQI

Parental  -HRITENGFEIEH-IPITLPIISSWRKEPYGVLLVKLAGVELTESGKIWLQKELKVSQQVWFQ-LLGKEN
          .H..TENG.EIE..IPITLPIISSW.KEP.GVLLVKLAGVEL...GK..LQK.LK..Q...FQ..L.KEN
Retrocopy >HPTTENGLEIEG>IPITLPIISSWIKEPCGVLLVKLAGVELAGRGKV*LQK*LKDPQLPRFQ<ILRKEN

Parental  STLFC-YILVNKKFKGGY-FNMNLNEEILRRGLGKTVLVKGLDYDSKTYWTIHRKLLKAELTAVKK
          S.L...Y.LVN...KGGY.F..NLNEEIL.RG..KTV.VKGL..DSKTYWT.HRKLLKAEL.A..K
Retrocopy SVLLA<YLLVN---KGGY<FSVNLNEEILQRGQDKTVVVKGLNHDSKTYWTVHRKLLKAELAAIIK

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	0.46 RPM	6.67 RPM
SRP017611_kidney	1.15 RPM	3.14 RPM
SRP017611_liver	0.04 RPM	1.52 RPM
SRP040447_lung	0.03 RPM	2.40 RPM
SRP040447_skeletal_muscle	0.01 RPM	1.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_882 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_882 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013532	1 retrocopy	retro_chof_2019,
Cavia porcellus	ENSCPOG00000006620	1 retrocopy	retro_cpor_882 ,