RetrogeneDB ID: retro_cjac_2739

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:78944344..78944884(+)
• Located in intron of: ENSCJAG00000012158

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPRS
• Ensembl ID: ENSCJAG00000014110
• Aliases: None
• Description: coordinator of PRMT5, differentiation stimulator [Source:HGNC Symbol;Acc:28848]

Sequence

>retro_cjac_2739
ATGGACCTTCAGGCTGCCCAGGCTGAGGAGCAGGGGGCTACGGAGCCGTCTGGGGGCCCGCTGCTGCTGAGCTCACAGAA
AGCACCTCGCAGCTTTGCTGCCGCTGACTACTGTCAGGAGAGAGACTGAGAAGCCTATGTATTGACTAGCAGTTGGAGCA
CAGAGCGTCCTAATGACAGTCCAGCCCGGGGTGAGGGGAACCATTCTGAAAAGGAAGGGTTTGCTGTGCTGTGGATGAAG
AGGACTCTGATGGAGAACTGAATCCCTGGGAGCTGTCAGAGGGAACAAACTGTCCACCCAAGGAACAGCCTGGCAATTTT
TTTTAATGAGGACTGGGACTTGGAGTTGAAAGGAGGTCAAGGGAATCTATATGATGCTAATGACATCCAGGAGAGAATTT
CTCAAGATCTCAAACCTTGAATCAGCTGTGCCCCACAAGAAGACATGATCTATGACCCCAGCTGGTACCATCCACCTCCA
CTGACAACCCATTATTCCAAGATGGCCTATGAAACAGGACAGTTTGATGATGCCAAAGAC

Alignment

ORF - retro_cjac_2739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDPQAAGAQAQGAAEPSQGSPLQSAREATPSPEADFATVDYS-SRERETEKAMDRLACRAQSVPNDSPAQ
          MD.QAA.A..QGA.EPS.G..L.S...A..S....FA..DY..S.ER......D.......S....SP..
Retrocopy MDLQAAQAEEQGATEPSGGPLLLSSQKAPRS----FAAADYC<SGERLRSLCID*QLEHRAS**QSSPG*

Parental  GEGTHSEEEGFAVDEEDSDGELNTWELSGGTNCPPKEQPGGLF-HEDWDLELKADQGNPYDADDIQESIS
          GE.........AVDEEDSDGELN.WELS.GTNCPPKEQPG..F..EDWDLELK..QGN.YDA.DIQE.IS
Retrocopy GEPF*KGRVCCAVDEEDSDGELNPWELSEGTNCPPKEQPGNFF>NEDWDLELKGGQGNLYDANDIQERIS

Parental  QELKPWVCCAPRGDMIYDPSWHHPPPLIPHYSKMVFETGQFDDAED
          Q.LKP...CAP..DMIYDPSW.HPPPL..HYSKM..ETGQFDDA.D
Retrocopy QDLKP*ISCAPQEDMIYDPSWYHPPPLTTHYSKMAYETGQFDDAKD

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	1.75 RPM
SRP051959_heart	0.04 RPM	4.00 RPM
SRP051959_kidney	0.04 RPM	5.64 RPM
SRP051959_liver	0.00 RPM	1.73 RPM
SRP051959_lung	0.02 RPM	1.59 RPM
SRP051959_lymph_node	0.00 RPM	1.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.24 RPM
SRP051959_spleen	0.00 RPM	1.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2739 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2739 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001885	1 retrocopy	retro_btau_946,
Callithrix jacchus	ENSCJAG00000014110	1 retrocopy	retro_cjac_2739 ,
Myotis lucifugus	ENSMLUG00000016418	1 retrocopy	retro_mluc_1801,
Pongo abelii	ENSPPYG00000008153	1 retrocopy	retro_pabe_2109,
Rattus norvegicus	ENSRNOG00000000111	1 retrocopy	retro_rnor_2923,
Tupaia belangeri	ENSTBEG00000008542	1 retrocopy	retro_tbel_1528,
Tursiops truncatus	ENSTTRG00000009909	1 retrocopy	retro_ttru_225,