RetrogeneDB ID: retro_cjac_1204

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:45402378..45402801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD10
• Ensembl ID: ENSCJAG00000010824
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 10 [Source:HGNC Symbol;Acc:15559]

Sequence

>retro_cjac_1204
ATGCCTCGGGGCAGCCGCAGTGCGGCGGCCCGGCCAGTCAGCAGTCCCGCCGCGCCCTCTGCCCACCCGCCCGCTCACCC
ACCGCCCTCGGCAGCAGCCCCGGCTCCTGCCCCTTCGGGCCAGCCGGACCTCATGGCTCAGATGGCATCCACGGCCGCAA
GGGTAGCCATGGGCTCGGCTGTGGGACATGTCATGGGCAATGCCCTGACCAGAGCCTTCAGCGGGGGGAGCTCGGAGCCG
GCCCAGCCTACCACCCTGCAGGCTCCCACCCATGCTGCCTCCCAGCCCCTGCAGATGGGGCCCTGCGCCTATGAGATCAG
GCAGTTCCTGGACTGTTCCACCACTCAGAGTGACCTGTCCCTGTGAGAGGGCTTCAGCGAGGTCCTGAAGCAGTGTAAGT
ACAACCACTGTCTGAGCTCCCTG

Alignment

ORF - retro_cjac_1204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRGSRSAAARPVSRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMASTAAGVAVGSAVGHVMGSALT
          MPRGSRSAAARPVS.PAAPSAHPPAHPPPSAAAPAPAPSGQP.LMAQMASTAA.VA.GSAVGHVMG.ALT
Retrocopy MPRGSRSAAARPVSSPAAPSAHPPAHPPPSAAAPAPAPSGQPDLMAQMASTAARVAMGSAVGHVMGNALT

Parental  GAFSGGSSEPAQPAAQQAPTHAASQPLQMGPCAYEIRQFLDCSTTQSDLSLCEGFSEVLKQCKYNHGLSS
          .AFSGGSSEPA.................MGPCAYEIRQFLDCSTTQSDLSL.EGFSEVLKQCKYNH.LSS
Retrocopy RAFSGGSSEPAXXXXXXXXXXXXXXXXXMGPCAYEIRQFLDCSTTQSDLSL*EGFSEVLKQCKYNHCLSS

Parental  L
          L
Retrocopy L

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	4.04 RPM
SRP051959_heart	0.04 RPM	22.40 RPM
SRP051959_kidney	0.02 RPM	15.49 RPM
SRP051959_liver	0.00 RPM	27.40 RPM
SRP051959_lung	0.00 RPM	3.07 RPM
SRP051959_lymph_node	0.00 RPM	1.51 RPM
SRP051959_skeletal_muscle	0.00 RPM	34.94 RPM
SRP051959_spleen	0.00 RPM	2.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1204 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010824	2 retrocopies	retro_cjac_1018, retro_cjac_1204 ,
Callithrix jacchus	ENSCJAG00000021267	1 retrocopy	retro_cjac_271,
Ictidomys tridecemlineatus	ENSSTOG00000008241	1 retrocopy	retro_itri_132,