RetrogeneDB ID: retro_cjac_8

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:94854017..94854425(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023181
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TSC22D1
• Ensembl ID: ENSCJAG00000019808
• Aliases: None
• Description: None

Sequence

>retro_cjac_8
ATGAAATCCCAATGGTGTAGACCAGTGGTGATGGATCTAGGAGTTTACCAACTGAGACATTTTTCAATTTCTTTCTTGTC
ATCCTTGCAGGGGACTGAAAACGCTTCTGTGAGGCTTGATAATAGCTCGTCTGGTGCAAGTGTGGTAGCTATTGACAACA
AAATCGAGCAAGCTATGGATCTGGTGAAAAGCCATTTGATGCATGCCGTCAGAGAGGAAGTGGAGGTCCTCAAAGAGCAA
ATCAAAGAACTAATAGAGAAAAATTCCCAGCTGGAGCAGGAGAACAATCTGCGGAAGACACTGGCCAGTCCTGAGCAGCT
TGCCCAGTTTCAGGCCCAGCTGCAGACTGGTTACCCCTTGCCACCACCCAGCCATAGGGCACCACACAGCCCCCTGCCGA
GCCAGCAT

Alignment

ORF - retro_cjac_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 82.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSQWCRPVAMDLGVYQLRHFSISFLSSLLGTENASVRLDNSSSGASVVAIDNKIEQAMDLVKSHLMYAV
          MKSQWCRPV.MDLGVYQLRHFSISFLSSL.GTENASVRLDNSSSGASVVAIDNKIEQAMDLVKSHLM.AV
Retrocopy MKSQWCRPVVMDLGVYQLRHFSISFLSSLQGTENASVRLDNSSSGASVVAIDNKIEQAMDLVKSHLMHAV

Parental  REEVEVLKEQIKELIEKNSQLEQENNLLKTLASPEQLAQFQAQLQTGSP
          REEVEVLKEQIKELIEKNSQLEQENNL.KTLASPEQLAQFQAQLQTG.P
Retrocopy REEVEVLKEQIKELIEKNSQLEQENNLRKTLASPEQLAQFQAQLQTGYP

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	90.08 RPM
SRP051959_heart	0.00 RPM	71.21 RPM
SRP051959_kidney	0.04 RPM	88.72 RPM
SRP051959_liver	0.00 RPM	23.61 RPM
SRP051959_lung	0.00 RPM	65.61 RPM
SRP051959_lymph_node	0.00 RPM	16.94 RPM
SRP051959_skeletal_muscle	0.02 RPM	71.39 RPM
SRP051959_spleen	0.00 RPM	27.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_8 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_8 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019808	1 retrocopy	retro_cjac_8 ,