RetrogeneDB ID: retro_cjac_2878

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:52977035..52977593(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSCR3
• Ensembl ID: ENSCJAG00000002626
• Aliases: None
• Description: Down syndrome critical region gene 3 [Source:HGNC Symbol;Acc:3044]

Sequence

>retro_cjac_2878
ATGGGGACAGTCCTGGACATCAAGATTAAAAGAGCAAATAAAGTTTATGACACTGGGGAGGTGCTCTCCTGTGTGGTGGT
AACATCGAGTAAAGATTCAGTCCAACACAACGGACTGACTTGGCCCATGGAAGGAACTGTAAACCTCCACCTCAATGCCA
AAAGTCTGGGTGTGTTTGAAGCTTCTTATAATTCTGTTAAGCCTATCCAGATTATCATCAGCACCATAGAAATGGTGAAG
CTGGGGAAATCTCTCAGTGGCAAAACAGAAAGCCCTTTGAGTTTCCTCTGCACATGAAGGGTAACAAAGTTCTGTGTGAG
ACTTATCATGGCACGTTTGTCAACATTCAGAACATACTATGCTATGACTCGAGGCAATCTCTGTTGGCCAAGGACTTGAC
AAAGACCTGTGAATTTATCATTCACTGTTCCTCAGAAGGGGAAGTTGACTCCCAGTCCTGTGACCTTCATGAGTACACCT
GAAACCTTATAGAACGTCAAAGAGAGAGCTCTGCTTCCCAAATTTCTCATTCGAGGACATCTCAACAATAAACTGTGT

Alignment

ORF - retro_cjac_2878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFEAFYNSVKPIQ
          MGT.LDIKIKRANKVY..GEVLS.VVV.SSKDSVQH.G....MEGTVNL.L.AKS.GVFEA.YNSVKPIQ
Retrocopy MGTVLDIKIKRANKVYDTGEVLSCVVVTSSKDSVQHNGLTWPMEGTVNLHLNAKSLGVFEASYNSVKPIQ

Parental  ILNSTIEMVKPGKFPSGKTEI-PFEFPLHVKGNKVLYETYHGVFVNIQYTLRCDMRRSLLAKDLTKTCEF
          I..STIEMVK.GK..SGKTE..PFEFPLH.KGNKVL.ETYHG.FVNIQ..L..D.R.SLLAKDLTKTCEF
Retrocopy IIISTIEMVKLGKSLSGKTES<PFEFPLHMKGNKVLCETYHGTFVNIQNILCYDSRQSLLAKDLTKTCEF

Parental  IVHSAPQKGKL-TPSPVDFTITPETLQNVKERALLPKFLIRGHLNSTNC
          I.H.....G...TPSPV.F..TPETL.NVKERALLPKFLIRGHLN...C
Retrocopy IIHCS-SEGEV>TPSPVTFMSTPETL*NVKERALLPKFLIRGHLNNKLC

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	6.77 RPM
SRP051959_heart	0.00 RPM	10.23 RPM
SRP051959_kidney	0.00 RPM	10.56 RPM
SRP051959_liver	0.00 RPM	5.65 RPM
SRP051959_lung	0.00 RPM	10.20 RPM
SRP051959_lymph_node	0.00 RPM	11.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.63 RPM
SRP051959_spleen	0.00 RPM	10.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2878 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2878 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	ENSCJAG00000002626	1 retrocopy	retro_cjac_2878 ,
Macropus eugenii	ENSMEUG00000007920	1 retrocopy	retro_meug_1828,
Nomascus leucogenys	ENSNLEG00000004717	1 retrocopy	retro_nleu_696,
Pan troglodytes	ENSPTRG00000013900	1 retrocopy	retro_ptro_2418,
Rattus norvegicus	ENSRNOG00000001681	1 retrocopy	retro_rnor_1897,