RetrogeneDB ID: retro_cjac_323

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:6447990..6448404(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012684
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM183A
• Ensembl ID: ENSCJAG00000003315
• Aliases: None
• Description: family with sequence similarity 183, member A [Source:HGNC Symbol;Acc:34347]

Sequence

>retro_cjac_323
AAGGCCATGGCGGGGCGCCCGAAGGAGAGGGTGGTCACAGATGAGGTCCTTCAGAACCAGATCTTGCGGGAGCTGTACCT
CAAAGAGTTGCGAACCCAGAAACTCTTCACGCAGTACCATGTGAATCCGCTGCGCAAGTTTCACGGGTTTACGAGGAAGC
CCATGTCTTGGCATGATAACCTGGAAGAACCTGCAGATGCCAGGTTTCTGAATCTCATTCACCACGCTGCCCAGGGGCCA
AGGAAGAAGTACCCAGAGGCGCAGACTGAAAACCAGGAAATTGGGTGGGACTCAGAGCCCTTGATCGACCCAGAACGCAG
TGACCACAGGCTGAACCACTTCAGGGTCTACAATGACATCACTCTGTACAAAGCTAAAATGTGGAGCTTGGGAGAAGATG
ATCGCCATAAGTAG

Alignment

ORF - retro_cjac_323 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.0 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGQPSEKVIPDEVHQNQILRERYLKELRTQKLYTQYHVNPFCKIHTVTRKPMSWHDNLEEPADARFLNL
          MAG.P.E.V..DEV.QNQILRE.YLKELRTQKL.TQYHVNP..K.H..TRKPMSWHDNLEEPADARFLNL
Retrocopy MAGRPKERVVTDEVLQNQILRELYLKELRTQKLFTQYHVNPLRKFHGFTRKPMSWHDNLEEPADARFLNL

Parental  IHHAAQGPRKKYPETQTENQEVGWYLEPLV
          IHHAAQGPRKKYPE.QTENQE.GW..EPL.
Retrocopy IHHAAQGPRKKYPEAQTENQEIGWDSEPLI

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.02 RPM	0.00 RPM
SRP051959_lung	0.02 RPM	0.80 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_323 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005339	1 retrocopy	retro_cfam_671,
Callithrix jacchus	ENSCJAG00000003315	1 retrocopy	retro_cjac_323 ,
Homo sapiens	ENSG00000186973	1 retrocopy	retro_hsap_1,
Gorilla gorilla	ENSGGOG00000010892	2 retrocopies	retro_ggor_1704, retro_ggor_69,
Nomascus leucogenys	ENSNLEG00000013230	3 retrocopies	retro_nleu_147, retro_nleu_2537, retro_nleu_2865,
Pongo abelii	ENSPPYG00000001457	1 retrocopy	retro_pabe_48,
Pan troglodytes	ENSPTRG00000000624	1 retrocopy	retro_ptro_22,