RetrogeneDB ID: retro_cjac_3018

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:118091621..118092164(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL46
• Ensembl ID: ENSCJAG00000013019
• Aliases: None
• Description: mitochondrial ribosomal protein L46 [Source:HGNC Symbol;Acc:1192]

Sequence

>retro_cjac_3018
AAAGAAAAAAAGGCTGACTTCTATGATGAAGAAGATGAACAGGATATATTACTGGTTGCAAGATCTGGAAGATATGTGGG
AACAGAGATTCGTACAGTTCAAACTTGGAGCTCGTGTAACAGAAGCTGACGAAAGAATGACCGAACATCCCTGAACCGGA
AGCTAGACAGGAACCTTGTTCTGTTAGTCAGAGAGAAGCTTGGAGATGAGGATGTTTGGATGCTGCCCCAGGCGGAATGG
CAGCCTGGGGAGACCCTTCGAGGAACTGCTGAACGAACCCTAGTGACACTCTCAGAAAACAATATGGAAGCCAAGTTCCT
GGGAAATGCACCCTGTGGGCACTACAAATTCAAGTTCCCCCAGGCAATGCGGACAGAGAGTAACCTCGGGGCCAAGGTGT
TCTTCTTCAAAGCACTGCTGTTAACTGGAGACTTTTCAGAGGCCGGGAAGAAGGGCCAGCATGTGTGGGTCACTAAGGAT
GAGCTGAGTGATTATTTGAAACCAAAATACCTGGCCCAAGTTAGGAGGTTTCTTTTGGACCTC

Alignment

ORF - retro_cjac_3018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.72 %
• Parental protein coverage: 65.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKKKADLYDEEDEQDILLV-QDLEDMWEQRFVQFKLGARVTEADE-KNDRTSLNRKLDRNLVLLVREKLG
          ..KKAD.YDEEDEQDILLV.QDLEDMWEQRFVQFKLGARVTEADE.KNDRTSLNRKLDRNLVLLVREKLG
Retrocopy KEKKADFYDEEDEQDILLV>QDLEDMWEQRFVQFKLGARVTEADE<KNDRTSLNRKLDRNLVLLVREKLG

Parental  DEDVWMLPQAEWQPGETLRGTAERTLVTLSENNMEAKFLGNAPCGHYKFKFPQAMRTESNLGAKVFFFKA
          DEDVWMLPQAEWQPGETLRGTAERTLVTLSENNMEAKFLGNAPCGHYKFKFPQAMRTESNLGAKVFFFKA
Retrocopy DEDVWMLPQAEWQPGETLRGTAERTLVTLSENNMEAKFLGNAPCGHYKFKFPQAMRTESNLGAKVFFFKA

Parental  LLLTGDFSQAGKKGQHVWVTKDELSDYLKPKYLAQVRRFLLDL
          LLLTGDFS.AGKKGQHVWVTKDELSDYLKPKYLAQVRRFLLDL
Retrocopy LLLTGDFSEAGKKGQHVWVTKDELSDYLKPKYLAQVRRFLLDL

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
SRP051959_colon	0.00 RPM	3.90 RPM
SRP051959_heart	0.00 RPM	5.12 RPM
SRP051959_kidney	0.02 RPM	6.01 RPM
SRP051959_liver	0.02 RPM	5.72 RPM
SRP051959_lung	0.00 RPM	3.61 RPM
SRP051959_lymph_node	0.00 RPM	4.54 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.79 RPM
SRP051959_spleen	0.02 RPM	3.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3018 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3018 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013019	1 retrocopy	retro_cjac_3018 ,
Felis catus	ENSFCAG00000014966	1 retrocopy	retro_fcat_480,
Microcebus murinus	ENSMICG00000015826	1 retrocopy	retro_mmur_741,
Otolemur garnettii	ENSOGAG00000004736	1 retrocopy	retro_ogar_1280,
Rattus norvegicus	ENSRNOG00000018547	1 retrocopy	retro_rnor_433,