RetrogeneDB ID: retro_cpor_1176

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:11000928..11001475(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D4
• Ensembl ID: ENSCPOG00000008945
• Aliases: None
• Description: None

Sequence

>retro_cpor_1176
GTCAAATTTGAGCTGAACTCTCATCTCTCAGCACTGCAAATGTTCATAAGATCTACCACACCCTTCATAAACTAAATGTA
ACCAAGAACATTGGCCAAGAGGATCACCAAACAAGAAGCCTACAGTTTTGCACGTCTTCAGGCTGCTTTAGTAAAGTGAT
ACCCAAAGGAAAAACAGACGACCTGCCTCTGGGGAGGACTCATCGGCCAACAAGAGTAGACATGATAGCATGTAGAAAAT
ATTGATTCAGCTAGAATGAAGACTGAAGAAGAGGCCTTCTTAAGGAAGCCTGTGCTTGTTCTATGAATACGCAGGTGCTG
AGGATGTTGTAGGTCCTGAAGTAATGGAGACATGCTGTGAAGATGCTGGTGTAGAACTTGAGGATGTAGATGTGCTTGTC
CTAGCTTGGAAACTGAATGCAGAAAACATGGGTCATTTAACCCTAGAATAGTTTTTAATGGGAATGACTTCTTTACAACA
CGATTCAAAAGAAAATCTCAGAAATTTTTTGGATTGTTTGAGATCACTATTAAATGATTCTACAGAC

Alignment

ORF - retro_cpor_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.78 %
• Parental protein coverage: 63.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VDFQLNSHLSTL-ANIHKIYHTLNKLNLTEDVGQDDHQTGSLRSCSSSDCFSKVMPP-RKKRRPASGDDL
          V.F.LNSHLS.L.AN.HKIYHTL.KLN.T...GQ.DHQT.SL..C.SS.CFSKV.P..RK.RRPASG.D.
Retrocopy VKFELNSHLSAL<ANVHKIYHTLHKLNVTKNIGQEDHQTRSLQFCTSSGCFSKVIPK<RKNRRPASGEDS

Parental  SAKKSRHDSM-YRKYDSTRIKTEEEAFSSKR-CLEWFYEYAGTEDVVGPEGMEKFCEDIGVEPENVVMLV
          SA.KSRHDSM.....DS.R.KTEEEAF..K..CL..FYEYAG.EDVVGPE.ME..CED.GVE.E.V..LV
Retrocopy SANKSRHDSM<VENIDSARMKTEEEAFLRKP>CL--FYEYAGAEDVVGPEVMETCCEDAGVELEDVDVLV

Parental  LAWKLDAQNMGYFTLQEWLTGMTSLQCDTTEKLRNSLDCLRSLLNDSTN
          LAWKL.A.NMG..TL...L.GMTSLQ.D..E.LRN.LDCLRSLLNDST.
Retrocopy LAWKLNAENMGHLTLE*FLMGMTSLQHDSKENLRNFLDCLRSLLNDSTD

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	20.36 RPM
SRP017611_kidney	0.00 RPM	16.23 RPM
SRP017611_liver	0.00 RPM	13.10 RPM
SRP040447_lung	0.00 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.19 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1176 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1176 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018601	1 retrocopy	retro_cjac_3959,
Cavia porcellus	ENSCPOG00000008945	2 retrocopies	retro_cpor_1176 , retro_cpor_1179,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Sarcophilus harrisii	ENSSHAG00000017879	1 retrocopy	retro_shar_437,