RetrogeneDB ID: retro_mmul_326

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:63204324..63204747(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000028707
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAPPC2
• Ensembl ID: ENSMMUG00000022619
• Aliases: None
• Description: None

Sequence

>retro_mmul_326
ATGTCTGGAAGCTTCTACTTTGTAATTGTTGGTCACCATGATAATCCAGTTTTTGAAATGGAGTTTTTGCCAGCTGGGAA
GGCAGAATCCAAAGACGACCATCGTCATCTGAACCAGTTCATAGCTCATGCTGCTCTCGACCTCGTAGATGAGAACATGT
GGCTGTCGAACAACATGTACTTGAAAACTGTGGACAAGTTCAACGAGTGGTTTGTGTCAGCATTTGTCACCGCGGGGCAT
ATGAGGTTTATTATGCTTCATGACATAAGACAAGAAGATGGAATAAAGAACTTCTTTACTGATGTTTATGATTTATATAT
AAAGTTTTCAATGAATCCATTTTATGAACCCAATTCTCCTATTCGATCAAGTGCATTTGACAGAAAAGTTCAGTTTCTTG
GGAAGAAACACCTTTTAAGCTGA

Alignment

ORF - retro_mmul_326 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
          MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
Retrocopy MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW

Parental  FVSAFKDCALIISHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKK
          FVSAF........HMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKK
Retrocopy FVSAF----VTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKK

Parental  HLLS
          HLLS
Retrocopy HLLS

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	2.91 RPM	3.59 RPM
SRP007412_brain_prefrontal_cortex	1.51 RPM	3.65 RPM
SRP007412_cerebellum	2.45 RPM	5.49 RPM
SRP007412_heart	0.88 RPM	1.59 RPM
SRP007412_kidney	1.29 RPM	2.11 RPM
SRP007412_liver	0.99 RPM	1.50 RPM
SRP007412_testis	13.83 RPM	0.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_326 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_326 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_73
Pan troglodytes	retro_ptro_72

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326 ,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,