RetrogeneDB ID: retro_cjac_3266

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:14501966..14502293(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018793
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARL2
• Ensembl ID: ENSCJAG00000002545
• Aliases: None
• Description: None

Sequence

>retro_cjac_3266
TTCAAGCTGAACATCTGGGATGTGGGTGGCCAGAAGTCCCTGCAGTCCTACTGGCAGAACTACTTTGAGAGCACCGACGG
CCTCATCTGGGTGGTGGACAGCGCGGACCACCAGCGCATGCAGGACTGCCGGCGGGAGCTCCACAGCCTGCTGCTGGAGG
AGTGCCTGGCCAGAGCAACCCTACTCATCTCTGCCAACAAGCAGGACCTGCCTAGAGCACTGTCCTCTAATGCCATCCAT
GAGGCCCTGGAGCTGAACTCCATCCACAGCCACCACTGGTGCATCCAGGGCTGCAGTGCTGTCACCAGGGAGAACCTGCT
GCAGGGC

Alignment

ORF - retro_cjac_3266 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.16 %
• Parental protein coverage: 66.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FKLNIWDVGGQK-LRSYWRNYFESTDGLIWVVDSADRQRMQDCHRELQSLLLEERLAGATLLIFANKQDL
          FKLNIWDVGGQK.L.SYW.NYFESTDGLIWVVDSAD.QRMQDC.REL.SLLLEE.LA.ATLLI.ANKQDL
Retrocopy FKLNIWDVGGQKSLQSYWQNYFESTDGLIWVVDSADHQRMQDCRRELHSLLLEECLARATLLISANKQDL

Parental  PGALSSNAIREALELDSIRSHHWCIQGCSAVTGENLLQG
          P.ALSSNAI.EALEL.SI.SHHWCIQGCSAVT.ENLLQG
Retrocopy PRALSSNAIHEALELNSIHSHHWCIQGCSAVTRENLLQG

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	1.31 RPM	2.15 RPM
SRP051959_heart	2.07 RPM	4.79 RPM
SRP051959_kidney	2.86 RPM	6.37 RPM
SRP051959_liver	1.60 RPM	3.14 RPM
SRP051959_lung	2.33 RPM	4.34 RPM
SRP051959_lymph_node	2.31 RPM	3.74 RPM
SRP051959_skeletal_muscle	5.33 RPM	12.19 RPM
SRP051959_spleen	1.93 RPM	3.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3266 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3266 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
Canis familiaris	ENSCAFG00000028760	1 retrocopy	retro_cfam_1116,
Callithrix jacchus	ENSCJAG00000002545	1 retrocopy	retro_cjac_3266 ,