RetrogeneDB ID: retro_cjac_2150

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:75345334..75345714(+)
• Located in intron of: None

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_2150
ATGACAACTATGTCCTCAACAGCCAGGCCTCAGGAATCGGTGGCTTTTGAGGACGTGGCTGTATACTTCACTAAGAAGGA
ACGGGCCATCTTGGTGCCTGACCAGAGGCCTTGTACTGTGTGATGCTGGAAAACTATGAGGCCGTGGCCTTTGTAGCAGT
GCTACCCACTTCCAAACTAGCTTCTGTCTCTCATCTGGAGCAAGGGAAAGAGCCCTGTTTCACCCAACTACAGGGAGTCC
TAAGCAGGAGGGGCTGGAGAGCAGGCTTTATAGGATATTTGGAACTGAGAAGATACACTTACTTAGCTAAAGCAATGTTA
TGTATAATAAAATCAAAAATTCTTCAAAATCATCAGTGCTGTGAAGACAGGAGAAAGAGT

Alignment

ORF - retro_cjac_2150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTVSSTARPQESVAFDDVAVYFTKKEWAIMVPDQR-ALYRDVMLENYEAVAFV-VPPTSKPALISHLEQ
          MTT.SSTARPQESVAF.DVAVYFTKKE.AI.VPDQR.ALY..VMLENYEAVAFV.V.PTSK.A..SHLEQ
Retrocopy MTTMSSTARPQESVAFEDVAVYFTKKERAILVPDQR<ALYC-VMLENYEAVAFVAVLPTSKLASVSHLEQ

Parental  GKEPCFTQPQGVLSRRDWRAGFIGHSELRRYTYLAKAMLYVIKSKILQNRRCWEDRRKA
          GKEPCFTQ.QGVLSRR.WRAGFIG..ELRRYTYLAKAML..IKSKILQN..C.EDRRK.
Retrocopy GKEPCFTQLQGVLSRRGWRAGFIGYLELRRYTYLAKAMLCIIKSKILQNHQCCEDRRKS

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	3.11 RPM
SRP051959_heart	0.04 RPM	3.53 RPM
SRP051959_kidney	0.00 RPM	6.88 RPM
SRP051959_liver	0.09 RPM	7.67 RPM
SRP051959_lung	0.00 RPM	2.38 RPM
SRP051959_lymph_node	0.00 RPM	0.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.19 RPM
SRP051959_spleen	0.02 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2150 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2150 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,