RetrogeneDB ID: retro_cjac_1656

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:2370093..2370540(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELOVL6
• Ensembl ID: ENSCJAG00000003975
• Aliases: None
• Description: ELOVL fatty acid elongase 6 [Source:HGNC Symbol;Acc:15829]

Sequence

>retro_cjac_1656
TTCCCGTTTTCTGCTCTGTATGCTGCCTTTATGTTTGGTGGTCGGCACCTAATGAACAGACGAGCAAAGTTTGAACTGGG
GAAGCCATTAGTGCTCTGGTCTCTGACCCTGGCAGTCTTCATTATATTCGGTGCTCTTTGAACTGGTGCTTACATGGTGT
ACATTTTGATGACCAAAGGCCTGAAGCAGCAGAGTTTCTACAACGGACCTGTCAGCAAATTCTTGGCGTATGCATTTGTG
CTAAGCAAAGCACCTGAACTAGGAGACACAATATTCATTATTCTGAGGAAGCAGAAGCTGATCTTCCTGCACTGGTACCA
CCACATCACTGTGCTCCTGGACTCTTGGTACTCCTACAAAGTCATGGTTGCTGGGGGAGGCTGGTTCATGACTATGAACT
ATGGCGTGCACGCCGTGATGTACTCTTACTATGCCTTGTGGGTGGCA

Alignment

ORF - retro_cjac_1656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.2 %
• Parental protein coverage: 57.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLFSALYAAFIFGGRHLMNKRAKFELRKPLVLWSLTLAVFSIFGALRTGAYMVYILMTKGLKQSVCDQSF
          F.FSALYAAF.FGGRHLMN.RAKFEL.KPLVLWSLTLAVF.IFGAL.TGAYMVYILMTKGLKQ....QSF
Retrocopy FPFSALYAAFMFGGRHLMNRRAKFELGKPLVLWSLTLAVFIIFGAL*TGAYMVYILMTKGLKQ----QSF

Parental  YNGPVSKFWAYAFVLSKAPELGDTIFIILRKQKLIFLHWYHHITVLLYSWYSYKDMVAGGGWFMTMNYGV
          YNGPVSKF.AYAFVLSKAPELGDTIFIILRKQKLIFLHWYHHITVLL.SWYSYK.MVAGGGWFMTMNYGV
Retrocopy YNGPVSKFLAYAFVLSKAPELGDTIFIILRKQKLIFLHWYHHITVLLDSWYSYKVMVAGGGWFMTMNYGV

Parental  HAVMYSYYALRAA
          HAVMYSYYAL..A
Retrocopy HAVMYSYYALWVA

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	9.23 RPM
SRP051959_heart	0.00 RPM	10.86 RPM
SRP051959_kidney	0.00 RPM	3.39 RPM
SRP051959_liver	0.04 RPM	311.83 RPM
SRP051959_lung	0.00 RPM	1.84 RPM
SRP051959_lymph_node	0.00 RPM	1.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.28 RPM
SRP051959_spleen	0.00 RPM	2.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1656 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1656 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003975	1 retrocopy	retro_cjac_1656 ,
Mus musculus	ENSMUSG00000041220	1 retrocopy	retro_mmus_999,