RetrogeneDB ID: retro_mmul_1797

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:136543823..136544303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS24
• Ensembl ID: ENSMMUG00000013134
• Aliases: None
• Description: None

Sequence

>retro_mmul_1797
GTCAATGAGTGGTCATTGAAGATAAGAAAGGAAATGAGAGTTGTGGACAGGCAAATAAGCGATATCCAAAGAGAAAAAGA
AAAAGTGAAATGGTCTGTGAAAGATGCTGCCAAGAAGGGCCAGAAGGATATCTGTGTAGTTCTGGCCAAGGAGGTGATCA
GGTCAAGGAAGGCTGTGAGCAAGCTGTATGCATTCAAAGCACACATGAACTCAGTGCTGATGGGGATGAAGAACCAGCTC
GCCGTCTTGTGAGTGGCTGGTTCCCTGCAGAAGAGCACAGAAGTGATGAAGGCCATGCAACGTCTTGTGAAGATTCCAGA
AATTCAGGCCACCATGAGGGAGTTGTCCAAAGAAATGATGAAGGCTGGGATCATAGAGGAGATGTTAGAGGACACTTTTG
AAAGCATGGACGATCAGGAAGAAATGGAGGAAGAAGCAGAAATGGAAATTGACAGAATTCTGTTTGAAATTACAGAAGGG

Alignment

ORF - retro_mmul_1797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVVLAKEMIRSRKAVSKLYASKAHMN
          VNEWSLKIRKEMRVVDRQI.DIQRE.EKVK.SVKDAAKKGQKD.CVVLAKE.IRSRKAVSKLYA.KAHMN
Retrocopy VNEWSLKIRKEMRVVDRQISDIQREKEKVKWSVKDAAKKGQKDICVVLAKEVIRSRKAVSKLYAFKAHMN

Parental  SVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQE
          SVLMGMKNQLAVL.VAGSLQKSTEVMKAMQ.LVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQE
Retrocopy SVLMGMKNQLAVL*VAGSLQKSTEVMKAMQRLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQE

Parental  EMEEAAEMEIDRILFEITAG
          EMEE.AEMEIDRILFEIT.G
Retrocopy EMEEEAEMEIDRILFEITEG

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	1.68 RPM	28.24 RPM
SRP007412_brain_prefrontal_cortex	1.35 RPM	18.48 RPM
SRP007412_cerebellum	2.26 RPM	33.90 RPM
SRP007412_heart	4.06 RPM	33.21 RPM
SRP007412_kidney	2.82 RPM	42.72 RPM
SRP007412_liver	0.48 RPM	3.05 RPM
SRP007412_testis	3.32 RPM	35.17 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1797 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1797 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1797 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Macaca mulatta	ENSMMUG00000013134	1 retrocopy	retro_mmul_1797 ,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,