RetrogeneDB ID: retro_cpor_1006

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:11541403..11542114(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSCPOG00000003854
• Aliases: None
• Description: None

Sequence

>retro_cpor_1006
CGGGAGCAGAGCAAAGGTGCGGGCTGTGTGTTTCGCTTGCACTTGAAGCTTTGCTAGGGCGCTGCTCCTCAACACGCGTG
GGCTTCGCGGAGCGACACTGCTCCATCAAGGGCATCATGAAGGACATCATCCGCGGCCCACGCCGGGCACACCCCTGGCT
GAGGTGTTCTTCCCGGATTCATTCCCATTTGAGAAGCCTACAAAGCTGTTCCTCACCTCCAAGGGCGTCCACAGAGCCCT
TGCGTGCATGTACTGCGGAAGGAGGGCCCAGCTCAGCATTGGCATTGTTCTCCCTGGGGGCACCATGCCTCAGGGGACCA
TCGTGCACTGCCTGGAGGAGAAGCCTCGGCTGGCTGGGGCAAGCTGGCGCGAGCCTCTGGGAATTATGCCACAGTCATTT
CCCCCAACCCCAAAACCAAGAGGAGCAGAATGAAGCTGCCTTCGGGTTCCAAGAAGGTCATGTCCTCTGCTTACCGAGCT
GTTGTGGGTGTAGTTGCTGGTGGTGGCAGAATTGATAAACCCATCTTGAAGGCTTGGCCGAGCCTACCACAAATGTAAGG
CAAAGAGGAACTGCTTGGCCACGTGTGTATGGTGTGGCCATGAATTGTGTGGAGCATCCCTTTGGAGATGGTAACCACTG
GCAGGCACATCAGCAAAGCCTCAACTCCCCGCAGAGATGCCCCTGCACAACACAAAGTGGGTCTCATTGCT

Alignment

ORF - retro_cpor_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.9 %
• Parental protein coverage: 91.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RGQRKGAGSVFRAHVKHRKGAARLRA-VDFAERHGYIKGIVKDIIHDPGR-GAPLAKVVFRDPYRFKKRT
          R.Q.KGAG.VFR.H.K...GAA...A.V.FAERH..IKGI.KDII..P.R.G.PLA.V.F.D...F.K.T
Retrocopy REQSKGAGCVFRLHLKLC*GAAPQHA<VGFAERHCSIKGIMKDIIRGPRR<GTPLAEVFFPDSFPFEKPT

Parental  ELFIAAEGIHTG-QFVYCGKKAQLNIGNVLPVGTMPEGTIV-CCLE-EKPGDRGKLARASGNYATVISHN
          .LF....G.H......YCG..AQL.IG.VLP.GTMP.GTIV.C..E.E.....GKLARASGNYATVIS.N
Retrocopy KLFLTSKGVHRALACMYCGRRAQLSIGIVLPGGTMPQGTIVHCLEE<EASAGWGKLARASGNYATVISPN

Parental  PETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKA-GRAYHKYKAKRNC-WPRVRGVAMNPVE
          P.TK..R.KLPSGSKKV.SSA.RAVVGVVAGGGRIDKPILKA.GRAYHK.KAKRNC.WPRV.GVAMN.VE
Retrocopy PKTKRSRMKLPSGSKKVMSSAYRAVVGVVAGGGRIDKPILKA>GRAYHKCKAKRNC>WPRVYGVAMNCVE

Parental  HPFG-GGNHQ-HIGKPSTIRRDAPAGRKVGLIA
          HPFG.G...Q.HI.K.ST.RRDAPA..KVGLIA
Retrocopy HPFGDGNHWQ>HISKASTPRRDAPAQHKVGLIA

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	0.12 RPM	160.13 RPM
SRP017611_kidney	0.00 RPM	262.87 RPM
SRP017611_liver	0.00 RPM	159.18 RPM
SRP040447_lung	0.20 RPM	425.96 RPM
SRP040447_skeletal_muscle	0.03 RPM	388.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1006 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1006 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus	ENSCPOG00000003854	2 retrocopies	retro_cpor_1006 , retro_cpor_1415,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Nomascus leucogenys	ENSNLEG00000010952	2 retrocopies	retro_nleu_1603, retro_nleu_594,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,