RetrogeneDB ID: retro_cpor_78

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:8188443..8189400(+)
• Located in intron of: ENSCPOG00000003871

Retrocopy information

• Ensembl ID: ENSCPOG00000023888
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000001432
• Aliases: None
• Description: None

Sequence

>retro_cpor_78
ATGGAGACCCGCTACAACCTGAAGAGCCCGGCTGTTAAACGTTTAATGAAAGAAGCAGCAGAATTGAAAGATCCAACAGA
TCATTACCATGCGCAGCCTTTAGAGGATAATCTTTTTGAATGGCACTTCACAGTAAGAGGGCCCCCAGATTCTGATTTTG
ATGGAGGAGTTTATCATGGACGAATAGTACTGCCACCAGAGTATCCGATGAAACCACCAAGCATTATTCTCCTAACAGCT
AATGGACGATTTGAAGTCGGCAAGAAAATCTGTTTGAGCATCTCAGGACATCATCCTGAAACTTGGCAGCCTTCCTGGAG
TATAAGGACAGCGTTACTAGCCATCATTGGGTTTATGCCAACAAAAGGAGAGGGAGCCATAGGTTCTCTTGATTACACAC
CTGAAGAAAGAAGAGCACTTGCCAAAAAATCACAAGATTTCTGTTGTGAAGGCTGTGGCTCTGCCATGAAGGATGTCCTG
TTGCCTTTAAAATCAGGAAGCGACTCAAGCCAGGCTGACCAAGAAGCCAAGGAACTTGCAAGACAAATCAGTTTTAAGGC
AGAAGTCAATTCATCTGGAAAGAGTATTGCTGAGTCAGAGTTAAACCACTCTTTTTCACTAAATGACTTACAAGATAACA
TACCTACAACATTCCAGGATACCACGGCCAGCACCTCGTATGGAGTCCAGAATCCCTCAGCAGCACCCTTTGAACAACCT
ACCCAACCTGCAGCTAAGAATACCTCCATGAGCCCTCGACAGCGCCGGGCCCAACAGCAGAGTCAAAGAAGGTCATCCCT
GTCACCAGATGTAATACAGGGCCAGCAGCCAAGGGACAACCATACGGATCATGGTGGATCAGCTGTACTGATTGTCATCC
TGACTTTGGCATTGGCAGCTCTTATATTCCGACGAATATATATGGCCAATGAATACATATTTGACTTTGAGTTATAA

Alignment

ORF - retro_cpor_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LESQCYLQALAVKRLMKEAAELKDPTDHYHAQPLEDNLFEWHFTVRGPPDSDFDGGVYHGRIVLPPEYPM
          .E....L...AVKRLMKEAAELKDPTDHYHAQPLEDNLFEWHFTVRGPPDSDFDGGVYHGRIVLPPEYPM
Retrocopy METRYNLKSPAVKRLMKEAAELKDPTDHYHAQPLEDNLFEWHFTVRGPPDSDFDGGVYHGRIVLPPEYPM

Parental  KPPSIILLTANGRFEVGKKICLSISGHHPETWQPSWSIRTALLAIIGFMPTKGEGAIGSLDYTPEERRAL
          KPPSIILLTANGRFEVGKKICLSISGHHPETWQPSWSIRTALLAIIGFMPTKGEGAIGSLDYTPEERRAL
Retrocopy KPPSIILLTANGRFEVGKKICLSISGHHPETWQPSWSIRTALLAIIGFMPTKGEGAIGSLDYTPEERRAL

Parental  AKKSQDFCCEGCGSAMKDVLLPLKSGSDSSQADQEAKELARQISFKAEVNSSGKSIAESELNHSFSLNDL
          AKKSQDFCCEGCGSAMKDVLLPLKSGSDSSQADQEAKELARQISFKAEVNSSGKSIAESELNHSFSLNDL
Retrocopy AKKSQDFCCEGCGSAMKDVLLPLKSGSDSSQADQEAKELARQISFKAEVNSSGKSIAESELNHSFSLNDL

Parental  QDNIPTTFQDTTASTSYGVQNPSAAPFEQPTQPAAKNTSMSPRQRRAQQQSQRRSSLSPDVIQGQQPRDN
          QDNIPTTFQDTTASTSYGVQNPSAAPFEQPTQPAAKNTSMSPRQRRAQQQSQRRSSLSPDVIQGQQPRDN
Retrocopy QDNIPTTFQDTTASTSYGVQNPSAAPFEQPTQPAAKNTSMSPRQRRAQQQSQRRSSLSPDVIQGQQPRDN

Parental  HTDHGGSAVLIVILTLALAALIFRRIYMANEYIFDFEL
          HTDHGGSAVLIVILTLALAALIFRRIYMANEYIFDFEL
Retrocopy HTDHGGSAVLIVILTLALAALIFRRIYMANEYIFDFEL

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	1.50 RPM	3.45 RPM
SRP017611_kidney	2.41 RPM	4.19 RPM
SRP017611_liver	2.13 RPM	4.96 RPM
SRP040447_lung	2.17 RPM	13.24 RPM
SRP040447_skeletal_muscle	1.30 RPM	7.51 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_78 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_78 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001432	1 retrocopy	retro_cpor_78 ,
Dasypus novemcinctus	ENSDNOG00000006232	1 retrocopy	retro_dnov_2680,