RetrogeneDB ID: retro_cpor_86

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_21:2007716..2008658(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000008047
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RRAGB
• Ensembl ID: ENSCPOG00000011266
• Aliases: None
• Description: None

Sequence

>retro_cpor_86
ATGCCAAATACAGCCATGAAGAAAAAGGTGCTGTTGATGGGAAAGAGCGGGTCGGGGAAGACCAGCATGAGATCCATTAT
CTTTGCAAATTATATTGCTCGCGACACCAGGCGTCTGGGTGCCACCATTGATGTGGAGCACTCCCACGTCCGATTCTTAG
GGAACCTGGTGCTGAACCTGTGGGATTGTGGCGGTCAGGACACCTTTATGGAAAATTACTTCACCAGCCAGCGAGACAAC
ATCTTCCGAAATGTCGAGGTTTTGATTTACGTGTTCGATGTAGAGAGCCGCGAACTGGAAAAGGACATGCATTATTACCA
GTCATGTCTGGAGGCCATCCTCCAGAACTCACCAGATGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTAGTTCAAG
AGGATCAGCGTGACCTGATTTTTAAGGAGCGAGAGGAAGACCTGAGGCGTTTGTCTCGCCCACTGGAGTGCGCCTGTTTT
CGAACATCTATCTGGGATGAAACGCTCTACAAGGCCTGGTCTAGTATTGTCTATCAGCTGATTCCCAACGTTCAGCAGCT
GGAGATGAACCTAAGGAATTTTGCTCAAATTATTGAGGCTGATGAAGTTCTGCTGTTTGAGAGAGCGACCTTCTTGGTGA
TTTCTCATTACCAGTGCAAAGAGCAGCGTGACGTCCACCGGTTTGAAAAGATCAGCAACATTATTAAGCAATTCAAGTTG
AGCTGCAGTAAGCTGGCCGCCTCCTTTCAGAGCATGGAAGTTAGGAATTCTAACTTCGCTGCTTTCATCGACATCTTCAC
ATCAAACACGTATGTGATGGTTGTTATGTCGGATCCCTCCATCCCTTCTGCCGCTACTCTGATCAACATTCGCAATGCCA
GGAAACACTTTGAGAAGCTAGAGAGAGTGGATGGCCCCAAGCACAGTCTCCTGATGCGTTAA

Alignment

ORF - retro_cpor_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.57 %
• Parental protein coverage: 72.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFDVEHSHVQFLGNLVLNLWDCGGQDSFMENYFTSQRDNIFQNVEVLIYVFDVESRELEKDMHYYQSCLE
          T.DVEHSHV.FLGNLVLNLWDCGGQD.FMENYFTSQRDNIF.NVEVLIYVFDVESRELEKDMHYYQSCLE
Retrocopy TIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLE

Parental  AILQNSPDARIFCLVHKMDLVQEDQRDLIFREREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYHLI
          AILQNSPDA.IFCLVHKMDLVQEDQRDLIF.EREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVY.LI
Retrocopy AILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLI

Parental  PNVQQLEMNLRNFAEIIEADEVLLFERATFLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQS
          PNVQQLEMNLRNFA.IIEADEVLLFERATFLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQS
Retrocopy PNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQS

Parental  MEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKQCLLM
          MEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPK..LLM
Retrocopy MEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKHSLLM

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	38.13 RPM	7.59 RPM
SRP017611_kidney	37.48 RPM	0.31 RPM
SRP017611_liver	24.38 RPM	0.30 RPM
SRP040447_lung	40.38 RPM	1.08 RPM
SRP040447_skeletal_muscle	35.40 RPM	0.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_86 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_86 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 21 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012920	1 retrocopy	retro_amel_1842,
Canis familiaris	ENSCAFG00000016503	1 retrocopy	retro_cfam_421,
Callithrix jacchus	ENSCJAG00000007317	1 retrocopy	retro_cjac_117,
Cavia porcellus	ENSCPOG00000011266	1 retrocopy	retro_cpor_86 ,
Equus caballus	ENSECAG00000006020	1 retrocopy	retro_ecab_608,
Felis catus	ENSFCAG00000013932	1 retrocopy	retro_fcat_21,
Homo sapiens	ENSG00000083750	1 retrocopy	retro_hsap_4,
Gorilla gorilla	ENSGGOG00000011501	1 retrocopy	retro_ggor_65,
Loxodonta africana	ENSLAFG00000016144	1 retrocopy	retro_lafr_102,
Myotis lucifugus	ENSMLUG00000015720	1 retrocopy	retro_mluc_40,
Macaca mulatta	ENSMMUG00000017635	1 retrocopy	retro_mmul_249,
Mustela putorius furo	ENSMPUG00000003730	1 retrocopy	retro_mputfur_87,
Mus musculus	ENSMUSG00000041658	1 retrocopy	retro_mmus_159,
Nomascus leucogenys	ENSNLEG00000016350	1 retrocopy	retro_nleu_13,
Oryctolagus cuniculus	ENSOCUG00000008666	1 retrocopy	retro_ocun_166,
Otolemur garnettii	ENSOGAG00000000345	1 retrocopy	retro_ogar_675,
Procavia capensis	ENSPCAG00000003417	1 retrocopy	retro_pcap_6,
Pongo abelii	ENSPPYG00000020398	1 retrocopy	retro_pabe_191,
Pan troglodytes	ENSPTRG00000021955	1 retrocopy	retro_ptro_48,
Rattus norvegicus	ENSRNOG00000003160	1 retrocopy	retro_rnor_2,
Sus scrofa	ENSSSCG00000029800	1 retrocopy	retro_sscr_15,