RetrogeneDB ID: retro_cpor_1441

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_84:3325117..3326676(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000012523
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cpor_1441
GCAGAGCTGAATGTGTCAGATCGAGAGGGAGATGATGCCACAGGAGATGGAACCAAGGAGAAACCGTTTAAAACAGGTCT
AAAGGCTTTGATGACAGTAGGAAAAGAACCATTTCCTACCATTTACGTAGATTCACAAAAAGAAAATGAGAGGTGGGACA
TTATTTCTAAATCACAAATGAAGAACATTAAAAAACTGTGGCATAGGGAACAAATGAAGACTGAATCCCAGGAGAAGAGA
GAGGCAGAAGATAGTTTGCGAAGAGAAAAGAACCTGGAAGAAGCCAAGAAGATATCCATCAAAAAGGATCCAAGTCTGCC
AGAGCCAAAGTGTGTGAAGATTGGTGCATTAGAAGGCTATAGAGGCTGAAGAGTAAAGGTGTTTGGCTGGGTCCATAGGC
TTCGTAGACAAGGAAAGAATTTAATGTTCCTGGTGTTGCGAGATGGTACAGGTTATCTTCAGTGTGTCTTATCAGATGAT
TTGTGTCTGTGTTACAATGGAGTAGTCTTGTCCACTGAGAGTAGTGTTGCAGTTTATGGAACATTGAATCTTATCCCAAA
GGGCAAGCAGTCTCCTGGGGGCCATGAGCTGAGCTGTGACTTCTGGGAGCTCATAGGCTTGGCCCCTGCTGGAGGAGCTG
ATAACCTGATCAACGAGGAGTCTGACGTTGACGTCCAGCTCAACAACAGGCACATGATGATCCGGGGAGAAAACATGTCC
AAAATACTGAGAGCACGTTCTGTGATTACCGCCTGCTTCCGCGAGCACTTCTTTGACAGGGCTACTATGAAGTGACTTCT
CCAACACTGGTGCAGACGCAGGTGGAAGGTGGCTCCACACTCTTCAAGCTGGACTACTTTGGGGAAAAGGCATTTCTGAC
TCAGTCCTCTCAGTTGTACCTGGAGACCGGCCTTCCCTCGCTGGGAGACGTGTTTTGTATTGCGCAGTCATACAGGGCAG
AACAGGCCAGAACACGAAGGCACCTGGCTGAGTACACTCACATGGAAGCAGAGTGCCCTTTCCTGACCTTTGAGGACCTC
CTGAACCGATTGGAAGACTTGGTTTGTGACATGGAAGATAGAGTCTTGAAGTCGCCAGCAGGAAGCATGTCTGACCTCAA
TCCGAACTTCAAGCCGCCCAAACGACCTTTCAAAAGGATGAACTACACAGATGCTATGGCGTGGCTGAAAGAACACGATG
TAAAAAAAGATGGGACTTTCTATGAGTTTGGAGAGGATATCCCGGAAGCTCCTGAGAGACTGATGACAGACACCATTAAT
GAACTAATCTTGCTGTGTCGACTTCCTGTGGAGATCAAGTCCTTCTATATGCAGCGATGTCTTGAGGACCCCCGTCTTAC
TGAATCAGTGGACGTGTTGATGCCCAATGTTGGTGAGATCGTGGGAGGCTCCATGCGTATCTGGGACAGTGAAGAAATCC
TGGCAGGTTATAAAAGGGAAGGCATTGATCCCACTCCCTACTACTGGTACACAGATCAGAGAAAATACGGTACATGCCCT
CATGGACGATATGGCCTGGGCTTGGAACGATTCCTGAGT

Alignment

ORF - retro_cpor_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 95.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AELYVSDREGDDATGDGTKEKPFKTGLKALMTVGKEPFPTIYVDSQKENERWDVISKSQMKNIKKLWHRE
          AEL.VSDREGDDATGDGTKEKPFKTGLKALMTVGKEPFPTIYVDSQKENERWD.ISKSQMKNIKKLWHRE
Retrocopy AELNVSDREGDDATGDGTKEKPFKTGLKALMTVGKEPFPTIYVDSQKENERWDIISKSQMKNIKKLWHRE

Parental  QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKCVKIGALEGYRGQRVKVFGWVHRLRRQGKN
          QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKCVKIGALEGYRG.RVKVFGWVHRLRRQGKN
Retrocopy QMKTESQEKREAEDSLRREKNLEEAKKISIKKDPSLPEPKCVKIGALEGYRG*RVKVFGWVHRLRRQGKN

Parental  LMFLVLRDGTGYLQCVLSDDLCLCYNGVVLSTESSVAVYGTLNLIPKGKQAPGGHELSCDFWELIGLAPA
          LMFLVLRDGTGYLQCVLSDDLCLCYNGVVLSTESSVAVYGTLNLIPKGKQ.PGGHELSCDFWELIGLAPA
Retrocopy LMFLVLRDGTGYLQCVLSDDLCLCYNGVVLSTESSVAVYGTLNLIPKGKQSPGGHELSCDFWELIGLAPA

Parental  GGADNLINEESDVDVQLNNRHMMIRGENMSKILRARSMITACFREHFFDR-GYYEVTPPTLVQTQVEGGS
          GGADNLINEESDVDVQLNNRHMMIRGENMSKILRARS.ITACFREHFFDR.GYYEVT.PTLVQTQVEGGS
Retrocopy GGADNLINEESDVDVQLNNRHMMIRGENMSKILRARSVITACFREHFFDR<GYYEVTSPTLVQTQVEGGS

Parental  TLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRAEQSRTRRHLAEYTHVEAECPFLSFEDLLN
          TLFKLDYFGE.AFLTQSSQLYLET.LPSLGDVFCIAQSYRAEQ.RTRRHLAEYTH.EAECPFL.FEDLLN
Retrocopy TLFKLDYFGEKAFLTQSSQLYLETGLPSLGDVFCIAQSYRAEQARTRRHLAEYTHMEAECPFLTFEDLLN

Parental  RLEDLVCDVVDRVLKSPAGSIVSDLNPNFKPPKRPFKRMNYTDAIAWLKEHNVKKEDGTFYEFGEDIPEA
          RLEDLVCD..DRVLKSPAGS..SDLNPNFKPPKRPFKRMNYTDA.AWLKEH.VKK.DGTFYEFGEDIPEA
Retrocopy RLEDLVCDMEDRVLKSPAGS-MSDLNPNFKPPKRPFKRMNYTDAMAWLKEHDVKK-DGTFYEFGEDIPEA

Parental  PERLMTDTINEPILLCRFPVEIKSFYMQRCPEDPRLTESVDVLMPNVGEIVGGSMRIWDSEEILAGYKRE
          PERLMTDTINE.ILLCR.PVEIKSFYMQRC.EDPRLTESVDVLMPNVGEIVGGSMRIWDSEEILAGYKRE
Retrocopy PERLMTDTINELILLCRLPVEIKSFYMQRCLEDPRLTESVDVLMPNVGEIVGGSMRIWDSEEILAGYKRE

Parental  GIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLT
          GIDPTPYYWYTDQRKYGTCPHG.YGLGLERFL.
Retrocopy GIDPTPYYWYTDQRKYGTCPHGRYGLGLERFLS

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	3.28 RPM	119.06 RPM
SRP017611_kidney	1.88 RPM	93.07 RPM
SRP017611_liver	1.65 RPM	58.06 RPM
SRP040447_lung	6.00 RPM	256.90 RPM
SRP040447_skeletal_muscle	1.09 RPM	43.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1441 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1441 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,