RetrogeneDB ID: retro_mmul_1372

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:21673890..21674208(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000028816
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHIC2
• Ensembl ID: ENSMMUG00000006382
• Aliases: None
• Description: cysteine-rich hydrophobic domain 2 protein [Source:RefSeq peptide;Acc:NP_001244474]

Sequence

>retro_mmul_1372
GTGGTGGATTTTGACGAAATCTATGAGGAAGAGGAGGACGAGGAGTGGGCCCTGGAGGAGCAGCTGCTCAAGTACTCGCC
GGACCCGGTGGTCGTCCGCGGCTCCGGTCACGTCACGGTATTTGGACTGAGCAACAAATTTGAATCAGAATTCCCTTCTT
CGTTAACTGGAAAAGTAGCTCCTGAAGAATTTAAAGCCAGCATCAACAGAGTTAACAGTTGTCTTAAGAAGAACCTTCCC
GTTAATGTACGTTGGCTACTTTGTGGCTGCCTTTGTTGCTGCTGCACGTTAGGTTGCAGTATGTGGCCAGTTATTTGC

Alignment

ORF - retro_mmul_1372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.17 %
• Parental protein coverage: 64.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADFDEIYEEEEDEERALEEQLLKYSPDPVVVRGSGHVTVFGLSNKFESEFPSSLTGKVAPEEFKASINR
          ..DFDEIYEEEEDEE.ALEEQLLKYSPDPVVVRGSGHVTVFGLSNKFESEFPSSLTGKVAPEEFKASINR
Retrocopy VVDFDEIYEEEEDEEWALEEQLLKYSPDPVVVRGSGHVTVFGLSNKFESEFPSSLTGKVAPEEFKASINR

Parental  VNSCLKKNLPVNVRWLLCGCLCCCCTLGCSMWPVIC
          VNSCLKKNLPVNVRWLLCGCLCCCCTLGCSMWPVIC
Retrocopy VNSCLKKNLPVNVRWLLCGCLCCCCTLGCSMWPVIC

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
SRP007412_brain	0.00 RPM	4.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.86 RPM
SRP007412_cerebellum	0.00 RPM	4.20 RPM
SRP007412_heart	0.00 RPM	2.36 RPM
SRP007412_kidney	0.00 RPM	3.52 RPM
SRP007412_liver	0.00 RPM	1.86 RPM
SRP007412_testis	0.30 RPM	14.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1372 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024493	1 retrocopy	retro_cpor_1448,
Echinops telfairi	ENSETEG00000004296	1 retrocopy	retro_etel_1804,
Latimeria chalumnae	ENSLACG00000006603	1 retrocopy	retro_lcha_22,
Loxodonta africana	ENSLAFG00000012248	1 retrocopy	retro_lafr_953,
Macaca mulatta	ENSMMUG00000006382	1 retrocopy	retro_mmul_1372 ,