RetrogeneDB ID: retro_cjac_1494

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:3347995..3348400(-)
• Located in intron of: ENSCJAG00000015678

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB8A
• Ensembl ID: ENSCJAG00000014120
• Aliases: None
• Description: RAB8A, member RAS oncogene family [Source:HGNC Symbol;Acc:7007]

Sequence

>retro_cjac_1494
CTGCCGAAGACCTGCGATTACGTGTTCAAGCTGCTGCTGATCGGGGACTCGGGGGTGGGGAAGACCTGCGTCCTGTTCCG
CTTCTCCGAGGACGCCTTCAACTCCACGTTTATCTCCACCATAGGAATGGACTTTAAAATTAGGACCATAGAGCTCGACG
GCAAGAGAATGAAGCGGCAGATACGGGACACAGCCGGTCAGGGGCGGTTTCGGACGATCCGGACAGCCTACCGCAGGGGT
GCGATGGGCATCATGCTGGTTTATGACGTCACCGACGAGAAGTCCTTCCACAACACCCGGAACTGGATTCGGAACATTGA
GGAGCATGGCTCTGCATATGTTGAAACGATGATGCTCGGGAACACGTGTGATGAGAACCACAAGAGACAGGTTTCCAAGG
AACGG

Alignment

ORF - retro_cjac_1494 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 65.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERF
          ..KT.DY.FKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIG.DFKIRTIELDGKR.K.QI.DTAGQ.RF
Retrocopy LPKTCDYVFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGMDFKIRTIELDGKRMKRQIRDTAGQGRF

Parental  RTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKER
          RTI.TAY.RGAMGIMLVYD.T.EKSF.N.RNWIRNIEEH.SA.VE.M.LGN.CD.N.KRQVSKER
Retrocopy RTIRTAYRRGAMGIMLVYDVTDEKSFHNTRNWIRNIEEHGSAYVETMMLGNTCDENHKRQVSKER

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	14.27 RPM
SRP051959_heart	0.00 RPM	5.79 RPM
SRP051959_kidney	0.02 RPM	11.85 RPM
SRP051959_liver	0.00 RPM	9.44 RPM
SRP051959_lung	0.00 RPM	11.66 RPM
SRP051959_lymph_node	0.00 RPM	14.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.16 RPM
SRP051959_spleen	0.00 RPM	17.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1494 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1494 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001599	1 retrocopy	retro_cjac_931,
Callithrix jacchus	ENSCJAG00000014120	1 retrocopy	retro_cjac_1494 ,
Otolemur garnettii	ENSOGAG00000013894	1 retrocopy	retro_ogar_2356,
Pteropus vampyrus	ENSPVAG00000009756	1 retrocopy	retro_pvam_1354,