RetrogeneDB ID: retro_cjac_326

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:27933071..27933731(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031515
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009866
• Aliases: None
• Description: None

Sequence

>retro_cjac_326
ATGCCTGCCAGCATGTTCAGCATCGACAACATCCTGGCCGCCCAGCCGCGCTGCAAGGACTCGGTGCTGCCGGTGGCTCC
CAGCGCGACGGCTCTGGTCGTCTTCCCGGCCCTGCACGGGGATTCGCTCTACGGCGCCAGCGGCGGCGCCTCCTCGGACT
ATGGCACCTTCTACGGGCAGCTGCACGTGCAGGCAGCTCCCATGGGTCCGGCCTGCTGTGGGGCCGTGTCGCCCCTGGGT
GCCCAGCAGTGCTCCTGCGTCCCGACGCCCCCAGGCTATGAGAGCCCTGGCTCGGTGCTGGTGTCCCCGGTACCGCATCA
GATGCTGACCTACATGAACATGGGCATGCTGTCGCGCACCGAGTTGCAGCTTCTCAACCAGCTGCACTGCCGGCAGAAGC
GGTGGCACCGCACCATCTTCACTGACGAGCAGCTCGAAGCGCTTGAGAACCTCTTCCAGGAGACCAAGTACCCGGACGTG
GGCACGCGCGAGCAGCTGGCCGGGAAAGTACACCTCCCGGAGGAGAAAGTGGAGGTCTGGTTTAAGAACCCCCGCGCCAA
ATGGAGGCGGCAGAAGCGGTCTTCATCGGAGGAGTCCGAGAACGTGGAGAAGTGGAACAAGACGTCGTCCTCGAAGGCAT
CGCCGGAGAAAAGGAAATAG

Alignment

ORF - retro_cjac_326 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.74 %
• Parental protein coverage: 70.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAGLQAAVGGSRLGYNNYFYGQLHVQAAPVGPACCGAVPPLGAQQCSCVPTPPGYEGPGSVLVSPVPHQM
          G..L..A.GG....Y...FYGQLHVQAAP.GPACCGAV.PLGAQQCSCVPTPPGYE.PGSVLVSPVPHQM
Retrocopy GDSLYGASGGASSDYGT-FYGQLHVQAAPMGPACCGAVSPLGAQQCSCVPTPPGYESPGSVLVSPVPHQM

Parental  LPYMNVGTLSRTELQLLNQLHCRRKRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE
          L.YMN.G.LSRTELQLLNQLHCR.KR.HRTIFTDEQLEALENLFQETKYPDVGTREQLA.KVHL.EEKVE
Retrocopy LTYMNMGMLSRTELQLLNQLHCRQKRWHRTIFTDEQLEALENLFQETKYPDVGTREQLAGKVHLPEEKVE

Parental  VWFKNRRAKWRRQKRSSSEESENVEKWNKTSSSKASPEKRE
          VWFKN.RAKWRRQKRSSSEESENVEKWNKTSSSKASPEKR.
Retrocopy VWFKNPRAKWRRQKRSSSEESENVEKWNKTSSSKASPEKRK

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	0.09 RPM
SRP051959_heart	0.00 RPM	0.04 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_326 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_326 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009866	1 retrocopy	retro_cjac_326 ,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380,