RetrogeneDB ID: retro_cpor_47

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_82:7083656..7084826(-)
• Located in intron of: ENSCPOG00000012792

Retrocopy information

• Ensembl ID: ENSCPOG00000015494
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009477
• Aliases: None
• Description: None

Sequence

>retro_cpor_47
ATGGCGGACCCTAGAGATAAGGCGCTTCAGGACTACCGCAAGAAGCTGCTGGAGCACAAGGAGATCGACGGCCGTCTGAA
GGAGTTAAGGGAACAATTAAAAGAACTTACCAAGCAGTATGAAAAGTCTGAAAATGATCTGAAGGCCCTGCAAAGTGTTG
GGCAGATTGTGGGTGAAGTGCTTAAACAATTAACTGAAGAAAAATTCATTGTTAAAGCTACGAATGGACCAAGATATGTT
GTGGGTTGTCGTCGACAGCTTGACAAAAGCAAGCTGAAGCCAGGAACAAGAGTTGCTTTGGATATGACTACACTAACTAT
CATGAGATACTTGCCGAGAGAGGTGGATCCATTGGTTTACAACATGTCTCATGAGGACCCTGGGAATGTTTCTTACTCAG
AGATTGGAGGGCTGTCAGAACAGATTCGAGAACTGAGAGAGGTAATAGAATTACCACTCACAAACCCAGAATTATTCCAG
CGTGTGGGAATAATACCTCCAAAAGGCTGTTTGTTATATGGACCACCAGGCACAGGAAAAACACTCTTGGCACGAGCTGT
TGCTAGCCAGCTGGACTGCAATTTCTTAAAGGTTGTATCTAGTTCTATTGTAGATAAGTACATTGGTGAAAGTGCCCGTT
TGATTAGAGAAATGTTTAATTATGCAAGGGACCATCAGCCATGCATCATTTTTATGGATGAAATCGATGCTATTGGTGGT
CGCCGGTTTTCTGAGGGTACTTCAGCTGACAGAGAGATCCAGAGAACTTTAATGGAGTTACTGAATCAGATGGATGGATT
TGATACTCTGCATAGAGTTAAAATGATCATGGCTACAAACAGACCAGATACACTGGATCCTGCGTTGCTGCGTCCAGGAA
GATTAGATAGAAAAATACATATTGATTTACCAAATGAACAAGCAAGATTAGATATATTGAAAATCCATGCAGGCCCCATT
ACAAAGCATGGCGAAATAGATTATGAAGCAATTGTGAAACTTTCAGATGGCTTTAATGGAGCAGACCTGAGAAATGTTTG
TACTGAAGCAGGTATGTTTGCAATTCGTGCTGATCATGATTTTGTAGTTCAGGAAGACTTCATGAAAGCAGTTAGAAAAG
TGGCTGATTCTAAGAAGCTAGAGTCGAAATTGGACTATAAACCTGTGTAA

Alignment

ORF - retro_cpor_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEEKFI
          MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEEKFI
Retrocopy MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEEKFI

Parental  VKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSE
          VKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSE
Retrocopy VKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSE

Parental  QIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGE
          QIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGE
Retrocopy QIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGE

Parental  SARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATN
          SARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATN
Retrocopy SARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATN

Parental  RPDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIETDYEAIVKLSDGFNGADLRNVCT
          RPDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEI..DYEAIVKLSDGFNGADLRNVCT
Retrocopy RPDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEI--DYEAIVKLSDGFNGADLRNVCT

Parental  EAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV
          EAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV
Retrocopy EAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV

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	2.70 RPM	13.34 RPM
SRP017611_kidney	3.04 RPM	15.91 RPM
SRP017611_liver	5.22 RPM	19.94 RPM
SRP040447_lung	2.82 RPM	27.21 RPM
SRP040447_skeletal_muscle	3.97 RPM	35.91 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_47 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_47 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47 ,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,