RetrogeneDB ID: retro_cjac_2790

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:22746974..22747337(-)
• Located in intron of: ENSCJAG00000015841

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRBOX1
• Ensembl ID: ENSCJAG00000031316
• Aliases: ZNF662, KRBOX1
• Description: None

Sequence

>retro_cjac_2790
ATGACAACTGTGTCCTCAACAGCCAGGCCCCAGGAATCAGTGGCTTTTGATGACGTGGCTGTGTACTTCACTAAGAAGGA
ATGGGCCATCATGGTGCCTGACCAGAGAGCCTTATACAGGGATGTGATGCTGGAGAACTATGAGGCTGTGGCCTTTGTAG
CAGTACCACCGACTTCTAAACCAGCTTTGGTCTCTCATCTGGAGCAAGGGAAAGAGCCCTGTTTCACCCAACCACAGGGA
GTCCTAAGCAGGAGGGACTGGAGAGCAGGCTTTATAGGACACTCAGAACTGAGAAGATATACTTACTTAGCTAAAGCAAT
GTTATATGTAATAAAATCAAAAATTCTTCAAAATCGTCGATGC

Alignment

ORF - retro_cjac_2790 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.35 %
• Parental protein coverage: 94.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTVSSTARPQESVAFDDVAVYFTKKEWAIMVPDQRALYRDVMLENYEAVAFV-VPPTSKPALISHLEQG
          MTTVSSTARPQESVAFDDVAVYFTKKEWAIMVPDQRALYRDVMLENYEAVAFV.VPPTSKPAL.SHLEQG
Retrocopy MTTVSSTARPQESVAFDDVAVYFTKKEWAIMVPDQRALYRDVMLENYEAVAFVAVPPTSKPALVSHLEQG

Parental  KEPCFTQPQGVLSRRDWRAGFIGHSELRRYTYLAKAMLYVIKSKILQNRRC
          KEPCFTQPQGVLSRRDWRAGFIGHSELRRYTYLAKAMLYVIKSKILQNRRC
Retrocopy KEPCFTQPQGVLSRRDWRAGFIGHSELRRYTYLAKAMLYVIKSKILQNRRC

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	1.09 RPM	3.11 RPM
SRP051959_heart	1.18 RPM	3.53 RPM
SRP051959_kidney	0.95 RPM	6.88 RPM
SRP051959_liver	1.10 RPM	7.67 RPM
SRP051959_lung	1.30 RPM	2.38 RPM
SRP051959_lymph_node	1.16 RPM	0.80 RPM
SRP051959_skeletal_muscle	1.70 RPM	9.19 RPM
SRP051959_spleen	1.05 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2790 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2790 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000031316	3 retrocopies	retro_cjac_2150, retro_cjac_2724, retro_cjac_2790 ,