RetrogeneDB ID: retro_cpor_429

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:177458..178399(-)
• Located in intron of: ENSCPOG00000004451

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_429
GCAGAGATGTATGTGTTGGATCGAGAGGGAGATGATGCCACAGGAGATGGAACCAAGGAGAAACAGTTTAAAATAGGTCT
AAAGGCTTTGATGACAGTAGGAAAAGAACCATTTCCTACCATTTACGTAGATTCACAAAAAGAAAATGAGAGGTGGGACG
TTATTTCTAAATCACAAATGAAGAACATTAAAAAAATGTGGCATAGGGAACAAATGAAGACTGAATCCCAGGAGAAGAGA
GAGGCAGAAGATAGTTTGCGAAGAGAAAAGAACCTAGAAGAAGCCAAGAAGATATCCATCAAAAAGGATCCAAGTCTGCC
AGAGCCAAAGTGTATGAAGATTGGTGCATTAGAAGGCTATAGAGGCCGAAGAGTAAAGGTGTTTGGCTGGGTCCATAGGC
TTTGTAGACAAGGAAAGAATTTAATGTTCCTGGTGTTGTGAGATGGTACAGGTTATCTTCAGTGTGTCTTGTCAGATGAT
TTGTGTCTGTGTTACAATGGAGTAGACTTGTCCACCGAGAGTACTGTTGCAGTTTATGAAACACTGAATCTTATCCCAAA
GGGCAAGTAGGCTCCGGGGGGGCCATGAGCTGAGCTGTGACTTCTGGGAACTCATAGGCTTGGCCCTGCTGGAGGAGCTG
ATAACCTGATCAACAAGGAGTCTGACATTGACGTCCAGCTCAACAACAGGCACATGATGATCCGGGAGAAAACATGTCCA
AAATCCTGAGAGCACGTTCTGTGATCACCACCTGCTTCCAAGAGCACTTCTTTGACAGGGGCTACTACGAAGTGACTTCT
CCAACGCTGGTGCAGACGCAGGTGGAAGATGGTTCCACACTCTTTAAGCTGGACTACTTTGGGGAACAGGCATTTCTGAC
TCAGTCCTCTCAGTTGTACCTGGAGACCTGCCTTCCCTCGCTGGGAGACATGTTTTGTATT

Alignment

ORF - retro_cpor_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 57.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AELYVSDREGDDATGDGTKEKPFKTGLKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKKLWHRE
          AE.YV.DREGDDATGDGTKEK.FK.GLKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKK.WHRE
Retrocopy AEMYVLDREGDDATGDGTKEKQFKIGLKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKKMWHRE

Parental  QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKCVKIGALEGYRGQRVKVFGWVHRLRRQGKN
          QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKC.KIGALEGYRG.RVKVFGWVHRL.RQGKN
Retrocopy QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKCMKIGALEGYRGRRVKVFGWVHRLCRQGKN

Parental  LMFLVLRDGTGYLQCVLSDDLCLCYNGVVLSTESSVAVYGTLNLIPKGKQAP-GGHELSCDFWELIGLA-
          LMFLVL.DGTGYLQCVLSDDLCLCYNGV.LSTES.VAVY.TLNLIPKGK.AP.GGHELSCDFWELIGLA.
Retrocopy LMFLVL*DGTGYLQCVLSDDLCLCYNGVDLSTESTVAVYETLNLIPKGK*AP>GGHELSCDFWELIGLA<

Parental  PAGGADNLINEESDVDVQLNNRHMMIR-GENMSKILRARSMITACFREHFFDRGYYEVTPPTLVQTQVEG
          PAGGADNLIN.ESD.DVQLNNRHMMIR.GENMSKILRARS.IT.CF.EHFFDRGYYEVT.PTLVQTQVE.
Retrocopy PAGGADNLINKESDIDVQLNNRHMMIR<GENMSKILRARSVITTCFQEHFFDRGYYEVTSPTLVQTQVED

Parental  GSTLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCI
          GSTLFKLDYFGE.AFLTQSSQLYLETCLPSLGD.FCI
Retrocopy GSTLFKLDYFGEQAFLTQSSQLYLETCLPSLGDMFCI

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	0.52 RPM	119.06 RPM
SRP017611_kidney	0.84 RPM	93.07 RPM
SRP017611_liver	0.22 RPM	58.06 RPM
SRP040447_lung	0.15 RPM	256.90 RPM
SRP040447_skeletal_muscle	0.01 RPM	43.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_429 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_429 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,