RetrogeneDB ID: retro_cpor_71

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_108:4142950..4144015(+)
• Located in intron of: ENSCPOG00000012254

Retrocopy information

• Ensembl ID: ENSCPOG00000023684
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000008919
• Aliases: None
• Description: None

Sequence

>retro_cpor_71
ATGGCGGCCCCGGCCCAGCAGCCTCCTCAGCCTGGGGGTGGGAAGCGCAAAGGCAAGGCTCAGTACGTGCAGGCCAAGCG
GGCTCGGCGCTGTGATGCGGGCGGGCCGCGGCAGCTGGAACCTGGACTGCAGGGAATCCTCATCACCTGTAATATGAACG
AACGCAAATGCGTGGAGGAGGCCTACAGCCTGCTCAACGAATACGGCGATAATCTGTACGGGCCCGAAAAGTTCACAGAC
AAGGATCAGCAGCTCTCTGGAAGTGAGGGAGAAGATGATATGGAGGCTGCCTTGAAGAAGGAGGTTGATGACATTAAGGC
TTCTACAGAGAAGAGGCTAAGAAGATTCCAGTCAATAGAGAGTGGAGCAAATAATGTAGTCTTCATCAGGACACTTGGGA
TAGAACCTGAGAAATTGGTGCATCACATTCTCCAGGATGTGTATAAAACTAAGAAGAAGAAGACTCGAGTTATTTTGCGA
ATGTTACCCATCTCAGGCACATGCAAAGCTTTCTTAGAGGATATGAAAAAATATGCAGAAACATTTTTGGAACCCTGGTT
TAAAGCACCAAACAAAGGGACATTTCAGATTGTGTACAAATCTCGTAATAACAGTCACATGAATAGAGAAGAAGTTATCA
AAGAATTGGCAGGAATTGTGGGCTGTCTGAATTCAGAAAACAAAGTGGATCTCACCAATCCACAATACACGGTGGTAGTT
GAAATCATCAAAGCTGTCTGTTGTCTGAGTGTTGTGAAAGATTACATGTTGTTCAGAAAATATAATCTTCAGGAGGTGGT
GAAGACTGCTAACGATCCATCACAGCCTTCCCCAAAGCTGAGAAATGGGAAAGAAGCAAGATTGGAAACTGATAACAAAT
TAAATCAAAATGACCCAAAAGAAGGGGAAGATAACCAACAGGTTGTGCCACAGAATAATGAGGAGAAACTAGAAGAAGCA
AAACCAGGATCTGAGACTCAGGTGGAGACTGAGGAAGGCACTAAAGCTGAACCATCCATTCAGATTCAAGAAGGATCCAA
GTCAAATGAAAATGATCTCTCATAG

Alignment

ORF - retro_cpor_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 91.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPAQQPPQPGGGKRKGKAQYVQAKRARRCDAGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYGD
          MAAPAQQPPQPGGGKRKGKAQYVQAKRARRCDAGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYGD
Retrocopy MAAPAQQPPQPGGGKRKGKAQYVQAKRARRCDAGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYGD

Parental  NLYGPEKFTDKDQQLSGSEGEDDMEAALKKEVDDIKASTEKRLRRFQSIESGANNVVFIRTLGIEPEKLV
          NLYGPEKFTDKDQQLSGSEGEDDMEAALKKEVDDIKASTEKRLRRFQSIESGANNVVFIRTLGIEPEKLV
Retrocopy NLYGPEKFTDKDQQLSGSEGEDDMEAALKKEVDDIKASTEKRLRRFQSIESGANNVVFIRTLGIEPEKLV

Parental  HHILQDVYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHMNRE
          HHILQDVYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHMNRE
Retrocopy HHILQDVYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHMNRE

Parental  EVIKELAGIVGCLNSENKVDLTNPQYTVVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKTANDPSQPSPKL
          EVIKELAGIVGCLNSENKVDLTNPQYTVVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKTANDPSQPSPKL
Retrocopy EVIKELAGIVGCLNSENKVDLTNPQYTVVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKTANDPSQPSPKL

Parental  RNGKEARLETDNKLNQNDPKEGEDNQQVVPQNNEEKLEEAKPGSETQVETEEGTKAEPSIQIQEGSKSNE
          RNGKEARLETDNKLNQNDPKEGEDNQQVVPQNNEEKLEEAKPGSETQVETEEGTKAEPSIQIQEGSKSNE
Retrocopy RNGKEARLETDNKLNQNDPKEGEDNQQVVPQNNEEKLEEAKPGSETQVETEEGTKAEPSIQIQEGSKSNE

Parental  NDLS
          NDLS
Retrocopy NDLS

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	0.92 RPM	1.21 RPM
SRP017611_kidney	0.94 RPM	1.67 RPM
SRP017611_liver	0.78 RPM	1.09 RPM
SRP040447_lung	0.83 RPM	1.21 RPM
SRP040447_skeletal_muscle	1.38 RPM	1.44 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_71 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_71 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71 ,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466,