RetrogeneDB ID: retro_cjac_956

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:12210525..12210860(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032428
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010709
• Aliases: None
• Description: None

Sequence

>retro_cjac_956
ATGGCGTCCACCACCCGTATTGTCCAGCGGCTGCAGAACTGGGAGTCCGGGCATGACCTGCAGGCGAAGCTGCAGCTGCC
CTACCAGGAGATCTCCAAGAGAACTCAGCCTCCTCCCAAGCTCCCTGTGGATCCCAACCACAAGCTCTCCAACAATTACT
ATTGCACTCGCGATGGTCGCTGGGAATCTGTGCCCCCTTCCATTATCATGTCCTCGCAGAAGGCGCTGGTGTCAGGCAAG
CCAGCAGAGAGCTCTGCTGTAGCAGCCACTGAGAAGGCGATGATTCCAGGGCCTCCCATAAAGAGGTGGGAGCTGTCCTC
GACCAGCCTTACCTG

Alignment

ORF - retro_cjac_956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASATRIVQRLRNWASGHDLQAKLQLRYQEISKRTQPPPKLPVGPNHKLSNNYYCTRDGRRESVPPSIIM
          MAS.TRIVQRL.NW.SGHDLQAKLQL.YQEISKRTQPPPKLPV.PNHKLSNNYYCTRDGR.ESVPPSIIM
Retrocopy MASTTRIVQRLQNWESGHDLQAKLQLPYQEISKRTQPPPKLPVDPNHKLSNNYYCTRDGRWESVPPSIIM

Parental  SSQKVLVSGKPAESSAVAATEKKAVTPAPPIKRWELSS-DQPYL
          SSQK.LVSGKPAESSAVAATEK.A..P.PPIKRWELSS.DQPYL
Retrocopy SSQKALVSGKPAESSAVAATEK-AMIPGPPIKRWELSS<DQPYL

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	5.57 RPM
SRP051959_heart	0.02 RPM	10.37 RPM
SRP051959_kidney	0.02 RPM	8.76 RPM
SRP051959_liver	0.28 RPM	10.12 RPM
SRP051959_lung	0.00 RPM	5.60 RPM
SRP051959_lymph_node	0.00 RPM	4.45 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.98 RPM
SRP051959_spleen	0.00 RPM	4.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_956 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_956 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_956 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000685	1 retrocopy	retro_chof_2004,
Callithrix jacchus	ENSCJAG00000010709	2 retrocopies	retro_cjac_2942, retro_cjac_956 ,
Dipodomys ordii	ENSDORG00000012324	1 retrocopy	retro_dord_155,
Macropus eugenii	ENSMEUG00000015637	3 retrocopies	retro_meug_1487, retro_meug_149, retro_meug_587,
Rattus norvegicus	ENSRNOG00000006939	2 retrocopies	retro_rnor_1491, retro_rnor_1793,