RetrogeneDB ID: retro_cpor_736

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:2658987..2660623(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NARS
• Ensembl ID: ENSCPOG00000013227
• Aliases: None
• Description: None

Sequence

>retro_cpor_736
GCAGAGCTATATGTGTCGGATCGAGAGGGAGATGATGCCACAGGAGATGGAACCAAGGAGAAACCATTTAAAACAGCTCT
AAAGGCTTTGATGACAGTAGGAAAAGAACCATTTCCTACCATTTACGTAGATTCACAAAAAGAAAATGAGAGGTGGGACG
TTATTTCTAAATCACAAATGAAGAACATTAAAAAACTGTGGCATAGGGAACAAATGAAGACTGAATCCCAGGAGAAGAGA
GAGGCAGAAGATAGTTTGCGAAGAGAAAAGAACCTGGAAGAAGCCAAGAAGATATCCATCAAAAAGGATCCAAGTCTGCC
ATAGCCAAAGTGTGTGAAAATTGGTGCATTAGAAGGCTATAGAGGCCAAAGAGTAAAGGTGTTTTGGCTGGGTCCATAGG
CTTCGTAGACAAGGAAAGAATTTAATGTTCCTGGTGTTGCGAGATGGTACGGGTAATCTTCATTGTGTCTTGTCAGATGA
TTTGTGTCTGTGTTACAATGGAGTAGTCTTGTCCACCGAGAGTAGTGTTGCAGTTTATGGAACACTGAATCTTACCCCAA
AGGGCAAGCAGGCTCCAGGGGGCCATGAGCTGAGCTGTGACTTCTGGGAGCTCATAGGCTTGGCCCCTGCTGGAGGAGCT
GATAACCTGATCAACGAGGAGTCTGACGTTGACGTCCAGCTCAACAACAGGCACATGATGATCCGGGGAGAAAACATGTC
CAAAATCCTGAGAGCACGTTCTGTGATCACCGCCTGCTTCCGAGAGCACTTCTTTGACAGGGGCTACTACGAAATGACCC
CTCCAACACTGGTGCAGACGCAGGTGGAAGGTGGCTCCACACTCTTCAAGCTGGACTACTTTGGGGAAGAGGCATTTCTG
ACTCAGTCCTCTCAGTTGTACCTGGAGACCTGCCTTCCCTCGCTAGGAGACGTGTTTTGTATTGCACAGTCATACAGGGC
AGAACAGTCCAGAACACGAAGGCACCTGGCTGAGTACACTCACGTGGAAGCAGAGTGCCCTTTCCTGACCTTTGAGGACC
TCCTGAACCGATTGGAAGACTTGGTTTGTGACGTCGTAGATAGAGTCTTAAAGTCGCCAGCAGGAAGCATAGTGTCTGAC
CTCAATCCGAACTTCAAGCCCCCCAAACGGCCTTTCAAAAGGGTGAACTACACAGATGCTATCGCGTGGCTGAAAGAACA
CGATGTAAAGAAAGAAGATGGGACTTTTTATGAGTTTGGAGAGGATATCCCGGAAGCTCCTGAGAGACTGATGACCGAAA
CCATTAATGAACCAATCTTGCTGTGTCGATTTCCTGTGGAGATCAAGTCCTTCTATATGCAGCGATGTCCTGAGGACCCC
CGTCTTACTGAATCAGTGGACGTGTTGATGCCCAATGTTGGTGAGATCGTGGGAGGCTCCATGCGTATCTGGGACAGTGA
AGAAATCCTGGCAGGTTATAAAAGGGAAGGCATTGATCCCACTCCCTACTACTGGTACACAGATCAGAGAAAATACGGTA
CATGCCCTCACGGAGGATATGGCCTGGGCTTGGAACGATTCCTGACGTGGCTCCTGAACAGATATCACATCTGAGATGTG
TGCTTGTACCCTCGGTTTGTCCAGCGCTGCAAGCCA

Alignment

ORF - retro_cpor_736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.62 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AELYVSDREGDDATGDGTKEKPFKTGLKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKKLWHRE
          AELYVSDREGDDATGDGTKEKPFKT.LKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKKLWHRE
Retrocopy AELYVSDREGDDATGDGTKEKPFKTALKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKKLWHRE

Parental  QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKCVKIGALEGYRGQRVKVF-GWVHRLRRQGK
          QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLP.PKCVKIGALEGYRGQRVKVF.GWVHRLRRQGK
Retrocopy QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLP*PKCVKIGALEGYRGQRVKVF>GWVHRLRRQGK

Parental  NLMFLVLRDGTGYLQCVLSDDLCLCYNGVVLSTESSVAVYGTLNLIPKGKQAPGGHELSCDFWELIGLAP
          NLMFLVLRDGTG.L.CVLSDDLCLCYNGVVLSTESSVAVYGTLNL.PKGKQAPGGHELSCDFWELIGLAP
Retrocopy NLMFLVLRDGTGNLHCVLSDDLCLCYNGVVLSTESSVAVYGTLNLTPKGKQAPGGHELSCDFWELIGLAP

Parental  AGGADNLINEESDVDVQLNNRHMMIRGENMSKILRARSMITACFREHFFDRGYYEVTPPTLVQTQVEGGS
          AGGADNLINEESDVDVQLNNRHMMIRGENMSKILRARS.ITACFREHFFDRGYYE.TPPTLVQTQVEGGS
Retrocopy AGGADNLINEESDVDVQLNNRHMMIRGENMSKILRARSVITACFREHFFDRGYYEMTPPTLVQTQVEGGS

Parental  TLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRAEQSRTRRHLAEYTHVEAECPFLSFEDLLN
          TLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRAEQSRTRRHLAEYTHVEAECPFL.FEDLLN
Retrocopy TLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRAEQSRTRRHLAEYTHVEAECPFLTFEDLLN

Parental  RLEDLVCDVVDRVLKSPAGSIVSDLNPNFKPPKRPFKRMNYTDAIAWLKEHNVKKEDGTFYEFGEDIPEA
          RLEDLVCDVVDRVLKSPAGSIVSDLNPNFKPPKRPFKR.NYTDAIAWLKEH.VKKEDGTFYEFGEDIPEA
Retrocopy RLEDLVCDVVDRVLKSPAGSIVSDLNPNFKPPKRPFKRVNYTDAIAWLKEHDVKKEDGTFYEFGEDIPEA

Parental  PERLMTDTINEPILLCRFPVEIKSFYMQRCPEDPRLTESVDVLMPNVGEIVGGSMRIWDSEEILAGYKRE
          PERLMT.TINEPILLCRFPVEIKSFYMQRCPEDPRLTESVDVLMPNVGEIVGGSMRIWDSEEILAGYKRE
Retrocopy PERLMTETINEPILLCRFPVEIKSFYMQRCPEDPRLTESVDVLMPNVGEIVGGSMRIWDSEEILAGYKRE

Parental  GIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLTWLLNRYHIRDVCLYPRFVQRCKP
          GIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLTWLLNRYHI.DVCLYPRFVQRCKP
Retrocopy GIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLTWLLNRYHI*DVCLYPRFVQRCKP

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	15.53 RPM	119.06 RPM
SRP017611_kidney	6.91 RPM	93.07 RPM
SRP017611_liver	4.48 RPM	58.06 RPM
SRP040447_lung	22.14 RPM	256.90 RPM
SRP040447_skeletal_muscle	5.49 RPM	43.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_736 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_736 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003837	2 retrocopies	retro_cjac_2194, retro_cjac_3091,
Cavia porcellus	ENSCPOG00000013227	3 retrocopies	retro_cpor_1441, retro_cpor_429, retro_cpor_736 ,
Loxodonta africana	ENSLAFG00000000559	1 retrocopy	retro_lafr_955,
Macropus eugenii	ENSMEUG00000000774	1 retrocopy	retro_meug_2019,
Otolemur garnettii	ENSOGAG00000016302	1 retrocopy	retro_ogar_1061,
Ictidomys tridecemlineatus	ENSSTOG00000002118	1 retrocopy	retro_itri_591,