RetrogeneDB ID: retro_cjac_868

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:90761605..90761848(+)
• Located in intron of: ENSCJAG00000006191

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRB3
• Ensembl ID: ENSCJAG00000016567
• Aliases: None
• Description: crumbs homolog 3 (Drosophila) [Source:HGNC Symbol;Acc:20237]

Sequence

>retro_cjac_868
ATGGCGAACCCCGGCCTGGGGCTACTTTTGGTTCTGGGACTGCCGCTCCTGCTGGCCCGCTGGGGCTGAGCATGGAGCCA
AACATCGACCCCTTCTGCAAATGAGAGTAGCACTATTTTGCTTATACACACCAGCCCCAGCTCCAGCTCCCATGGCGCCC
TGTCTCAGGGGGCCATCACTGCTATCATCGTGGTCTTCTCCTTGCTCCTGGCAGTGGGGCTGGCACTGTTGGTGTGGAAG
CTT

Alignment

ORF - retro_cjac_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 70.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANPGLGLLLALGLPFLLARWGRAWGQVPTSSANESSTVLPTSTSPSSSSSSNGTLSQGAITAIIVVFSI
          MANPGLGLLL.LGLP.LLARWG.AW.Q..T.SANESST.L...TSP..SSSS.G.LSQGAITAIIVVFS.
Retrocopy MANPGLGLLLVLGLPLLLARWG*AWSQTSTPSANESSTILLIHTSP--SSSSHGALSQGAITAIIVVFSL

Parental  LAALLLAVGLALLVRKL
          L....LAVGLALLV.KL
Retrocopy L----LAVGLALLVWKL

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	5.52 RPM
SRP051959_heart	0.04 RPM	0.07 RPM
SRP051959_kidney	0.04 RPM	5.28 RPM
SRP051959_liver	0.09 RPM	1.39 RPM
SRP051959_lung	0.07 RPM	2.41 RPM
SRP051959_lymph_node	0.02 RPM	1.14 RPM
SRP051959_skeletal_muscle	0.59 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_868 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_868 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016567	1 retrocopy	retro_cjac_868 ,
Homo sapiens	ENSG00000130545	2 retrocopies	retro_hsap_2747, retro_hsap_3478,
Gorilla gorilla	ENSGGOG00000007070	2 retrocopies	retro_ggor_1910, retro_ggor_2345,
Macaca mulatta	ENSMMUG00000005599	1 retrocopy	retro_mmul_1434,
Nomascus leucogenys	ENSNLEG00000015936	1 retrocopy	retro_nleu_1543,
Pongo abelii	ENSPPYG00000009457	2 retrocopies	retro_pabe_2222, retro_pabe_2873,
Pan troglodytes	ENSPTRG00000010367	1 retrocopy	retro_ptro_2984,
Rattus norvegicus	ENSRNOG00000047322	1 retrocopy	retro_rnor_1506,
Ictidomys tridecemlineatus	ENSSTOG00000002396	1 retrocopy	retro_itri_781,