RetrogeneDB ID: retro_cjac_1242

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:5600861..5601281(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021224
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFS7
• Ensembl ID: ENSCJAG00000005587
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7714]

Sequence

>retro_cjac_1242
TCAGCTCCTGGCCTGAGCGGCTTCTGGATCCTTGGTCTGCGCTCCAGCGTGGGCGCAGCTGTGCAGGCACGAGGTGTCCA
TCAGACCGTGGCTACCAAGGGCCCGAGCAGCACCCAGCCTGCCCTGCCGAAGGCCAGAGCTGTGGTTCCCAAACCCAGCA
GCCGGAGGGAGTATGTGGTGGCCAAGCTGGATGACCTCATCAACTGGGTCCATAGGAGCTCCCTGTGGCCCATGACCTTC
GGCCTGGCCTGCTGCGCCGTAGAGATGATGCACATGGCCGCACCCCGCTATGACATGGACCGCTTCGGTGTGGTCTTCCG
TGCCAGCCCACGCCAGTCTGACATGATGATCGTGGCCGGCACACTCACCAACAAGATGGCCCCCGCGCTCCGCAACGTCT
ACGACCAGATAGATGCCCGA

Alignment

ORF - retro_cjac_1242 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAPGLRGFWTLGLRSSVGAAVQARGVHQTVATNGPSSTQPALPKARAVVPKPSSRGEYVVAKLDDLINWA
          .APGL.GFW.LGLRSSVGAAVQARGVHQTVAT.GPSSTQPALPKARAVVPKPSSR.EYVVAKLDDLINW.
Retrocopy SAPGLSGFWILGLRSSVGAAVQARGVHQTVATKGPSSTQPALPKARAVVPKPSSRREYVVAKLDDLINWV

Parental  RRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRSPWPPLPSR
          .RSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSD.MIVAGTLTNKMAPALR........R
Retrocopy HRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDMMIVAGTLTNKMAPALRNVYDQIDAR

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	0.16 RPM	3.90 RPM
SRP051959_heart	0.40 RPM	9.84 RPM
SRP051959_kidney	0.18 RPM	6.30 RPM
SRP051959_liver	0.24 RPM	5.94 RPM
SRP051959_lung	0.05 RPM	2.07 RPM
SRP051959_lymph_node	0.05 RPM	1.87 RPM
SRP051959_skeletal_muscle	0.39 RPM	14.22 RPM
SRP051959_spleen	0.11 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1242 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1242 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005587	1 retrocopy	retro_cjac_1242 ,
Macaca mulatta	ENSMMUG00000003045	1 retrocopy	retro_mmul_746,
Xenopus tropicalis	ENSXETG00000003702	1 retrocopy	retro_xtro_48,