RetrogeneDB ID: retro_cpor_333

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:11606551..11607049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSCPOG00000011190
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_cpor_333
GGAGCAATAATACCTAACTGCCTAAATATTGGAAATAAAATATGCTAGTTGAAGCCAGTACTTCTTGGAGAGCTTGCTGT
TGGCAAATCAAGCCTAGTGCTTTGCTTTGTGAAAGGCTAGTTTCATTAATTTTAAGAGCGTACCATTGGGGCTGCTTTTC
TAACATAAACTCTGTCTTGATGACGTAACAGTTCTGAAGTCTGAAATATGAAAGACAACTCACCCAGAACGATATCATAG
CTTGGCACCAATGGACTACAGAGGAGCACAGGTGCTCATAGTTTTATATAATATCATGAATGAATCTTTTGCAAGAGTGA
CAAACTGTTTTAAAGCACTTCAGAGGTAAGCAAGTTCTAATCTGTAATATCTTTATCAGGATACAGGACTGATCTAGAAA
ATAAAGGAGCTATAGACTCTGAGGAAGTGCAGTCCTATGCAGATGACAGCAGCTTATTATTCATGGAAACACCAGCTAAA
CTATCAGTGAATGTTAGC

Alignment

ORF - retro_cpor_333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.99 %
• Parental protein coverage: 77.31 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAARPNGPASGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTV-CLDDTTVKFEI
          GA..PN....GNKIC..K.VLLGE.AVGKSSLVL.FVKG.FH...E.TIGAAFLT.T....D.T..K.EI
Retrocopy GAIIPNCLNIGNKIC*LKPVLLGELAVGKSSLVLCFVKG*FH*F*ERTIGAAFLT*TL>LDDVTVLKSEI

Parental  WDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFLRAKNWVKELQRQASPNI-VIALAGNKADLASKRA
          ..T...ERYHSLAPM.YRGAQ..IV.Y.I.N...F.R..N..K.LQR.AS.N..VI.L.G...DL..K.A
Retrocopy *KTTHPERYHSLAPMDYRGAQVLIVLYNIMN-ESFARVTNCFKALQR*ASSNL<VISLSGYRTDLENKGA

Parental  VEFQDAQAYAEDNSLLFMETSAKTAMNVN
          ......Q.YA.D.SLLFMET.AK...NV.
Retrocopy IDSEEVQSYADDSSLLFMETPAKLSVNVS

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	44.17 RPM
SRP017611_kidney	0.00 RPM	87.62 RPM
SRP017611_liver	0.00 RPM	44.62 RPM
SRP040447_lung	0.00 RPM	139.67 RPM
SRP040447_skeletal_muscle	0.14 RPM	23.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_333 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_333 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333 , retro_cpor_473,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,