RetrogeneDB ID: retro_cjac_4116

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:110617861..110618428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN15
• Ensembl ID: ENSCJAG00000016486
• Aliases: None
• Description: tetraspanin 15 [Source:HGNC Symbol;Acc:23298]

Sequence

>retro_cjac_4116
ATGCCGCGCGGGGACTCGGAGCAGGTGCGCTACTGTGCGCACTTCTCTTACCTCTGGCTCAAGTTCTCACTTATCATTTA
CTCCACCGTGTTCTGGCTGATCGGGGTCCTGGTCCTGTCCGTGGGGATCTATGCAGAGGTCGAACGGCAGAAATATAAAA
CCCTTGAAAGTGCCTTCCTGGCTCCGGTCATCATCCTCATCCTCCTGGGTGTCGTCATGTGCATGGTCTCCTTCATTGGT
GTGCTGGCATCCCTCCGTGACAACCTGTTCCTTCTCCAAGCATTCATGTACATCCTTGGGATCTGCCTCATCATGGAGCT
CATTGGTGGCGTGATGGCCTTGATCTTCCGGAACCAGACCATTGACTTCCTGAATGACAACATTCGAAGAGGAATTGAGA
ACTACTATGACGATCTGGACTTCAAAAACATCATGGACTTTGTTCAGAAAAAGTTCAAGTGCAGTGGCGGGGAGGACTAC
CGAGACTGGAGCAAGAACCAGTACCATGACTGCAGCGCTCCTGGACCCCTGGCCTGCGGGGTGCCCTACACCTGCTGCAT
CCAGAAC

Alignment

ORF - retro_cjac_4116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.83 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRGDSEQVRYCAHFSYLWLKFSLIIYSTVFWLIGALVLSVGIYAEVERQKYKTLESAFLAPAIILILLG
          MPRGDSEQVRYCAHFSYLWLKFSLIIYSTVFWLIG.LVLSVGIYAEVERQKYKTLESAFLAP.IILILLG
Retrocopy MPRGDSEQVRYCAHFSYLWLKFSLIIYSTVFWLIGVLVLSVGIYAEVERQKYKTLESAFLAPVIILILLG

Parental  VVMFMVSFIGVLASLRDNLFLLQAFMYILGICLIMELIGGVVALIFRNQTIDFLNDNIRRGIENYYDDLD
          VVM.MVSFIGVLASLRDNLFLLQAFMYILGICLIMELIGGV.ALIFRNQTIDFLNDNIRRGIENYYDDLD
Retrocopy VVMCMVSFIGVLASLRDNLFLLQAFMYILGICLIMELIGGVMALIFRNQTIDFLNDNIRRGIENYYDDLD

Parental  FKNIMDFVQKKFKCCGGEDYRDWSKNQYHDCSAPGPLACGVPYTCCIRN
          FKNIMDFVQKKFKC.GGEDYRDWSKNQYHDCSAPGPLACGVPYTCCI.N
Retrocopy FKNIMDFVQKKFKCSGGEDYRDWSKNQYHDCSAPGPLACGVPYTCCIQN

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	0.02 RPM	44.46 RPM
SRP051959_heart	0.00 RPM	3.12 RPM
SRP051959_kidney	0.02 RPM	1.06 RPM
SRP051959_liver	0.00 RPM	0.80 RPM
SRP051959_lung	0.00 RPM	7.58 RPM
SRP051959_lymph_node	0.00 RPM	2.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.75 RPM
SRP051959_spleen	0.00 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4116 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4116 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	ENSCJAG00000007278	1 retrocopy	retro_cjac_2289,
Callithrix jacchus	ENSCJAG00000016486	1 retrocopy	retro_cjac_4116 ,