RetrogeneDB ID: retro_cjac_2942

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:125748654..125748986(+)
• Located in intron of: ENSCJAG00000001934

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_2942
ATGGCGTCCGCCACCCGTATCGTCCAGCGGCTGCGGAACTGGGCGTCCGGGCATGACCTGCTGGCGAAGCTGCAGCTGCA
TTACCAGGAGATCTCCAAGTGAACTCAGCCTCTTCCCAAGCTCCCTGTGGGTCCCAACCGCAAGCTCTCCAACAATTACT
ATTGTACTCGCGATGGCTGCCAGGAATCTGTGCCCCCTTCCAACATCATGTCCTCGCAGAAGGTGCTGGTGTCAGGCAAG
CCAGCAGAGAGCTCTGCTGTAGCAGCCACTGAGAAGAAGGCGGTGACTCTAGCGCCTCCCATAAGAGGTGGGAGCTGTCC
TCGGACCAGCCC

Alignment

ORF - retro_cjac_2942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.07 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASATRIVQRLRNWASGHDLQAKLQLRYQEISKRTQPPPKLPVGPNHKLSNNYYCTRDGRRESVPPSIIM
          MASATRIVQRLRNWASGHDL.AKLQL.YQEISK.TQP.PKLPVGPN.KLSNNYYCTRDG..ESVPPS.IM
Retrocopy MASATRIVQRLRNWASGHDLLAKLQLHYQEISK*TQPLPKLPVGPNRKLSNNYYCTRDGCQESVPPSNIM

Parental  SSQKVLVSGKPAESSAVAATEKKAVTPAPPI-KRWELSSDQP
          SSQKVLVSGKPAESSAVAATEKKAVT.APPI.KRWELSSDQP
Retrocopy SSQKVLVSGKPAESSAVAATEKKAVTLAPPI<KRWELSSDQP

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	0.07 RPM	5.57 RPM
SRP051959_heart	0.40 RPM	10.37 RPM
SRP051959_kidney	0.09 RPM	8.76 RPM
SRP051959_liver	0.04 RPM	10.12 RPM
SRP051959_lung	0.34 RPM	5.60 RPM
SRP051959_lymph_node	0.84 RPM	4.45 RPM
SRP051959_skeletal_muscle	0.15 RPM	24.98 RPM
SRP051959_spleen	0.36 RPM	4.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2942 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2942 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,