RetrogeneDB ID: retro_cpor_1457

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_87:5986817..5987379(-)
• Located in intron of: None

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_1457
GTGGCGAGGAGCAGAGTTTGTCCTACAACCTGTGTAACTCCACAGAGACCTTTTGAAAACCCTGCCTTGACCAAGAATTA
AAGCTGATTGACGAATATGGCCTCTGGAATAAGCACGAGGTCTGAAGGGTCAAATTTACTCTGTGTGAGGCTGCCCGGGA
GCTGCTAACATAGGGCAAAAAGGTTCGCGGAGTCTCTTTGAAGGTGACACTCTCCTGTGGCAACTTCTCCACATCAGGAT
GCTGGATGATGGCAAGATGAGGCTGGATTACATCCTGGGCGTAAAAATGGAAGACTTCCTAGAGAGGCACCTACTTACCC
AGGTCTTCCAGCTAGGCCTGGCCCTGACCATCTACCACGTCCATGTCCTCATCTGCCAGCACCACATCCAGGGCCTGCAA
CAGGTGAACATCCCGTCCTTCACTGATGCGCCTGGACCCCGAGATGCACATCGAGTTCTCCCTGCGCTCCCATACGAGGA
AGGCTGCCCAGGGCCACAAGAAGAAGAAGAATGCCAAGAAAGGCCAGGGTGGGGCTGGAGCCGGGGTGACCAGGAGAAGG
AT

Alignment

ORF - retro_cpor_1457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VARSWVCRKTYVTPRRPFE-KSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLT-LDEKDPRR
          VARS.VC..T.VTP.RPFE.K..LDQELKLI.EYGL.NK.EV.RVKFTL.....AARELLT....K..R.
Retrocopy VARSRVCPTTCVTPQRPFE<KPCLDQELKLIDEYGLWNKHEV*RVKFTLCE---AARELLT<IGQKGSRS

Parental  LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
          LFEG..LL..L..I..LD.GKM.LDYILG.K.EDFLER.L.TQVF.LGLA..I.H..VLI.Q.HI....Q
Retrocopy LFEGDTLLWQLLHIRMLDDGKMRLDYILGVKMEDFLERHLLTQVFQLGLALTIYHVHVLICQHHIQGLQQ

Parental  VVNIPSF-IVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAG-DDEEED
          .VNIPSF...RLD...HI.FSLRS.......G..K.KNAKKGQGGAGAG..D.E.D
Retrocopy -VNIPSF>LMRLDPEMHIEFSLRSHTRKAAQGHKKKKNAKKGQGGAGAG<GDQEKD

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	0.10 RPM	108.67 RPM
SRP017611_liver	0.04 RPM	88.40 RPM
SRP040447_lung	0.10 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_1457 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1457 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,