RetrogeneDB ID: retro_cjac_4028

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL289951.1:215747..216291(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032770
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016528
• Aliases: None
• Description: None

Sequence

>retro_cjac_4028
CCGCACGTCGTTCCCGACCAGAGAAGCAAGTTGGAGAACTAGGAGTTCTTCAAGAAGCTGAGCCGCGAGTGTTAGATTAA
GTACACGGGATTCAGGGACCGGCCCCATGAGGAGCGCCAGGCGTACTTCCAGAACGCCTGCCGCGACGGCCGCTCGGAAA
TCGCTTTTGTGGCCACAGGAACCAACCTCTCTCTGCAGTTTTTTCCGGCCGGCTGCCAGGGGAGAACAGCGACAAACACC
TAGCCGAGAGTATGTCGACCTAGAAAGAGAAGCAGGCAAGGTATATTTGAAGGCTCCCATGATTCTGAATGGAGTCTGTG
TTACCAGCAAAGGCTGGATTGATCTCCAGAGACGGGATGGGATGGGCTGTCTGGAGTTTGATGAGGAGCGAGCCCTGCAG
GAGGACGCATTAGCCCAACAGGCCTTTGAAGAGACTCAGAGAAGGACACGAGAATTTGAAGAGAGAGACACGTCTCATCG
GGAGGAAATGGAGGTGAGAGTTTCACAGCTGCTGGCAGTAACTGACAAGAAGACAACAAGACCC

Alignment

ORF - retro_cjac_4028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.66 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPA
          P.VVPDQRSK.EN.EFF.KLSREC.IKYTGFRDRPHEERQA.FQNACRDGRSEIAFVATGTNLSLQFFPA
Retrocopy PHVVPDQRSKLEN*EFFKKLSREC*IKYTGFRDRPHEERQAYFQNACRDGRSEIAFVATGTNLSLQFFPA

Parental  SWQ-GEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQ
          ..Q.GEQRQTPSREYVDLEREAGKVYLKAPMILNGVCV..KGWIDLQR.DGMGCLEFDEERA.QEDALAQ
Retrocopy GCQ>GEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVTSKGWIDLQRRDGMGCLEFDEERALQEDALAQ

Parental  QAFEETRRRTREFEDRDRSHREEMEVRVSQLLAVTGKKTTRP
          QAFEET.RRTREFE.RD.SHREEMEVRVSQLLAVT.KKTTRP
Retrocopy QAFEETQRRTREFEERDTSHREEMEVRVSQLLAVTDKKTTRP

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	29.18 RPM
SRP051959_heart	0.02 RPM	20.68 RPM
SRP051959_kidney	0.00 RPM	19.50 RPM
SRP051959_liver	0.00 RPM	14.62 RPM
SRP051959_lung	0.00 RPM	41.94 RPM
SRP051959_lymph_node	0.00 RPM	73.51 RPM
SRP051959_skeletal_muscle	0.04 RPM	13.93 RPM
SRP051959_spleen	0.02 RPM	48.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4028 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4028 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016528	2 retrocopies	retro_cjac_1228, retro_cjac_4028 ,