RetrogeneDB ID: retro_cjac_1256

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:14399531..14400002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB25
• Ensembl ID: ENSCJAG00000007715
• Aliases: None
• Description: RAB25, member RAS oncogene family [Source:HGNC Symbol;Acc:18238]

Sequence

>retro_cjac_1256
GCAGTGGTGGAGCACTGGTTGAAGGAGCTCTATGACCATGCTGAAGCCACGATCGTTGTCATGCTCATGGGTAACAAGAG
TGACCTCAGCCAGTCCCGGGAAGTGCCCACTGATGAGGCCCGCATGTTCGCTGAAAACAATGGGCTGCTCTTCCTGGAGA
CGTCAGCCCTGGACTCCACCAATGTTGAGCTAGCCTTTGAGACTGTCCTGAAAGAGAGCTTTGAGAAGATATCCAAGCAG
AGACAGAACAGCACCCGGACCAATGCCATCACTCTGGACAGTGCTCAGGGTGGGCAGGAGCCTGGCTCTGGGGAGAAGAA
GGTCTGTTGCATCAGCCTCTGACCTTGGTCAGCACCACCCTGACCCAACTGGCTTCTGGTACCCCTTGTCCCCACCTCAG
CCCCAGGACCTTTCCCTGCCCTTTGGTTCCAGATGTCAGACTGTTCCCTGTTCACAGCACCCCCAGGGCCT

Alignment

ORF - retro_cjac_1256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 60.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVL
          AVVE.WLKELYDHAEATIVVML.GNKSDLSQ.REVPT.EARMFAENNGLLFLETSALDSTNVELAFETVL
Retrocopy AVVEHWLKELYDHAEATIVVMLMGNKSDLSQSREVPTDEARMFAENNGLLFLETSALDSTNVELAFETVL

Parental  KEIFEKVSKQRQNSTRTNAITLGGA-RVGRSLA-WGEEGLLHQPLTLASTTC-PHWLLVPLVPTSTPGPF
          KE.FEK.SKQRQNSTRTNAITL..A.RVGRSLA.WGEEGLLHQPLTL.STT..P.WLLVPLVPTS.PGPF
Retrocopy KESFEKISKQRQNSTRTNAITLDSA>RVGRSLA>WGEEGLLHQPLTLVSTTL>PNWLLVPLVPTSAPGPF

Parental  PALWFRMLDCSLFTAPPGP
          PALWF.M.DCSLFTAPPGP
Retrocopy PALWFQMSDCSLFTAPPGP

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	10.98 RPM
SRP051959_heart	0.00 RPM	0.02 RPM
SRP051959_kidney	0.00 RPM	1.82 RPM
SRP051959_liver	0.02 RPM	0.06 RPM
SRP051959_lung	0.00 RPM	1.69 RPM
SRP051959_lymph_node	0.00 RPM	0.18 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1256 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1256 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Callithrix jacchus	ENSCJAG00000007715	1 retrocopy	retro_cjac_1256 ,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Macropus eugenii	ENSMEUG00000016598	2 retrocopies	retro_meug_1684, retro_meug_770,
Monodelphis domestica	ENSMODG00000016955	1 retrocopy	retro_mdom_1710,