RetrogeneDB ID: retro_mmul_643

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:70479484..70479765(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA2
• Ensembl ID: ENSMMUG00000006566
• Aliases: None
• Description: iron-sulfur cluster assembly 2 homolog, mitochondrial [Source:RefSeq peptide;Acc:NP_001247936]

Sequence

>retro_mmul_643
ATGGCTGCCGCCCGGATATTCTCCCTAACAGCCGCGACACAAAGAGCGCTCACTCCCTGGCCGAGGGGCAGGCTCCTCGC
GGCCTCCCCGGGACTCCGGGAGGGCGCGTCCTCCAGCCCCGAGGCTGGGGAAGGGCAGATCAGCCTCAGGACAGCTGCGT
CCAGAGGCTTCTGGAAATCACCAAAGGGTCAGAATTCCTCAGGATGCAGGTGGAGGGAGGTGGATGCGCCAGATTCCAAT
GCAGATGTTCACTGGATACAGTTATCAACCCCGATGACAGG

Alignment

ORF - retro_mmul_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 60.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAARGLSLTAATQRAVTPWPRGRLLAASLGLQARREASSSSPEAGEGQIRLT-DSCVQRLLEITEGSEF
          MAAAR..SLTAATQRA.TPWPRGRLLAAS.GL...RE..SSSPEAGEGQI.L..DSCVQRLLEIT.GSEF
Retrocopy MAAARIFSLTAATQRALTPWPRGRLLAASPGL---REGASSSPEAGEGQISLR<DSCVQRLLEITKGSEF

Parental  LRLQVEGGGCSGFQYKFSLDTVINPDDR
          LR.QVEGGGC..FQ...SLDTVINPDDR
Retrocopy LRMQVEGGGCARFQCRCSLDTVINPDDR

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	0.45 RPM	8.07 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	11.03 RPM
SRP007412_cerebellum	0.26 RPM	10.91 RPM
SRP007412_heart	0.29 RPM	12.90 RPM
SRP007412_kidney	0.47 RPM	19.48 RPM
SRP007412_liver	0.04 RPM	5.34 RPM
SRP007412_testis	0.04 RPM	7.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_643 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_643 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1504
Gorilla gorilla	retro_ggor_1610

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020479	1 retrocopy	retro_cjac_1450,
Dipodomys ordii	ENSDORG00000014857	1 retrocopy	retro_dord_762,
Gorilla gorilla	ENSGGOG00000012894	1 retrocopy	retro_ggor_1610,
Macaca mulatta	ENSMMUG00000006566	1 retrocopy	retro_mmul_643 ,
Nomascus leucogenys	ENSNLEG00000016268	1 retrocopy	retro_nleu_2754,
Ochotona princeps	ENSOPRG00000011684	2 retrocopies	retro_opri_1068, retro_opri_124,
Pan troglodytes	ENSPTRG00000006536	1 retrocopy	retro_ptro_1504,
Rattus norvegicus	ENSRNOG00000012085	1 retrocopy	retro_rnor_1009,