RetrogeneDB ID: retro_cpor_478

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_165:1062622..1063003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR2
• Ensembl ID: ENSCPOG00000023729
• Aliases: None
• Description: None

Sequence

>retro_cpor_478
CACAATGTTGGCTCAAGTCCTGCATTGGATGTGTAATTATCTGATGATTCCTTCTGCCCTAGAAGACTTTGACATTGGTT
GTGGTATGCTCAGGGTCAAATGGGACCGGATTGACCCCACTAGCAACAATTCCACACTGTGGTTCTACATCTTAAGACTA
GTTACTTCGGCTTCACCTTGGAAAACATCACAAATCTGGCCCAAGAGGACAGGCCTGTTATGATTGGCTCTGCCAGTGCC
CTTGGAGAGTATGGGTTCCTGGCTCTGCAAAACTTTGATAGGAGATTCTCCTCCTGCTTTCTGGACTGGGCAGCCTTTGC
AATTATGCTCTCCCCCTTCATTGGGATCCCTCTGCTTTTGTGACAGTTCAGCAAACCCAAG

Alignment

ORF - retro_cpor_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 69.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YNVGSSAALDVELSDDSFPP-EDFGIVSGMLNVKWDRIAPASNVS-HTVVLRPLKAGYFNFTSATITYLA
          .NVGSS.ALDV.LSDDSF.P.EDF.I..GML.VKWDRI.P.SN.S.HTVVL..LK..YF.FT...IT.LA
Retrocopy HNVGSSPALDV*LSDDSFCP>EDFDIGCGMLRVKWDRIDPTSNNS<HTVVLH-LKTSYFGFTLENITNLA

Parental  QEDGPVVIGSTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRK
          QED.PV.IGS.SA.G..G.LA...FDRRFS..FLDWAAF..M..P.IGIPLLL...SK.K
Retrocopy QEDRPVMIGSASALGEYGFLALQNFDRRFSSCFLDWAAFAIMLSPFIGIPLLL*QFSKPK

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	24.67 RPM
SRP017611_kidney	0.00 RPM	54.54 RPM
SRP017611_liver	0.00 RPM	50.06 RPM
SRP040447_lung	0.00 RPM	100.18 RPM
SRP040447_skeletal_muscle	0.00 RPM	35.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_478 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_478 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001212	2 retrocopies	retro_btau_1165, retro_btau_675,
Cavia porcellus	ENSCPOG00000023729	1 retrocopy	retro_cpor_478 ,
Nomascus leucogenys	ENSNLEG00000012304	1 retrocopy	retro_nleu_3102,
Ictidomys tridecemlineatus	ENSSTOG00000028971	1 retrocopy	retro_itri_1381,