RetrogeneDB ID: retro_cpor_407

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_143:1310198..1310782(-)
• Located in intron of: ENSCPOG00000010588

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSCPOG00000020893
• Aliases: None
• Description: None

Sequence

>retro_cpor_407
ATGCCAGTGACAAGGAGCTGGGTTTGTTGTAAAACCTACATAACCCCGCAGAGGTCCTTCAAGAAATCCTGCCTTGACCA
GAACTGAAGCTGATCTGCGAGTATGGGCTCTGGAACAGGTACGAGGTCTGGAGGGTCAAGTTTACTCTGGCCAAGATCTG
CAAGGCTGCCTGGGGGCTGCTGACACTGGACGAAAAGGACCCGCAGTATCTCTTCCAAGGCAACACTCTCCAGCCGTGAC
TTGTCCTTATCAGTGTGCTGGATGATGGCAAGATGAGGCTGGATTACATCCTGGACCTAAAAACCGAGGACCTAAAAACT
CTGGAAAGGGGCCTGCAGACCCAAGTCTTCAAGCTGGGCCTGGCCAATCCATCCACCATAAGTGTGTGCTCATCCGCCAG
CGCCACATCAGGGTCCGCAAGCGGGTGGTAAACACCCCCTCCTTTATCCTGTACCGGACTCCCAGAAGCACATCAACTTC
TCCCTGCACTGCCCATACTGGGAAGGCTGCCTGGGCCACCTGAAGAGGAAGAATCCAAGAAGGGCCAGGGTAGGGCCAGA
GCCAAGGAGGACAAGGAGGAGGAT

Alignment

ORF - retro_cpor_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQ-ELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPR
          MPV.RSWVC.KTY.TP.R.F.KS.LDQ.ELKLI.EYGL.N..EVWRVKFTLAKI.KAA..LLTLDEKDP.
Retrocopy MPVTRSWVCCKTYITPQRSFKKSCLDQ<ELKLICEYGLWNRYEVWRVKFTLAKICKAAWGLLTLDEKDPQ

Parental  RLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDF--LERRLQTQVFKLGLA-KSIHHARVLIRQRHIR
          .LF.GN.L...LV.I.VLD.GKM.LDYIL.LK.ED...LER.LQTQVFKLGLA..SIHH..VLIRQRHIR
Retrocopy YLFQGNTLQP*LVLISVLDDGKMRLDYILDLKTEDLKTLERGLQTQVFKLGLA<QSIHHKCVLIRQRHIR

Parental  VRKQVVNIPSFIVRL-DSQKHIDFSLRSPYGGGRPGRVKRKN-AKKGQGGAGAGDDEEED
          VRK.VVN.PSFI....DSQKHI.FSL..PY..G..G..KRKN..KKGQG.A.A..D.EED
Retrocopy VRKRVVNTPSFILYR<DSQKHINFSLHCPYWEGCLGHLKRKN<SKKGQGRARAKEDKEED

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	56.37 RPM
SRP017611_kidney	0.00 RPM	108.67 RPM
SRP017611_liver	0.00 RPM	88.40 RPM
SRP040447_lung	0.05 RPM	165.52 RPM
SRP040447_skeletal_muscle	0.00 RPM	189.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_407 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_407 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001130	3 retrocopies	retro_cjac_2034, retro_cjac_2993, retro_cjac_719,
Cavia porcellus	ENSCPOG00000020893	2 retrocopies	retro_cpor_1457, retro_cpor_407 ,
Gorilla gorilla	ENSGGOG00000027839	4 retrocopies	retro_ggor_1491, retro_ggor_160, retro_ggor_2190, retro_ggor_32,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pan troglodytes	ENSPTRG00000011449	1 retrocopy	retro_ptro_57,
Rattus norvegicus	ENSRNOG00000011355	7 retrocopies	retro_rnor_1298, retro_rnor_2577, retro_rnor_2849, retro_rnor_2902, retro_rnor_635, retro_rnor_663, retro_rnor_892,
Rattus norvegicus	ENSRNOG00000049813	3 retrocopies	retro_rnor_2082, retro_rnor_30, retro_rnor_78,