RetrogeneDB ID: retro_mmul_2256

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:121827491..121828102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000013311
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM98
• Ensembl ID: ENSMMUG00000022356
• Aliases: None
• Description: transmembrane protein 98 [Source:HGNC Symbol;Acc:24529]

Sequence

>retro_mmul_2256
TTGGTGCTGGATTGCAGGCAGCGCTACTACCAGCCCCGAGACCTCTGCAGCGCTATGATTCTAAGCCCATTATGGACCTC
ATCGGTGCCATGGTGACCCAGTCTGAGCCCTCTGAGTTAGAACTGGATGATGTTGTTATCACCAACCCCCACATTGAGAC
CATTCTGGAGAACAAAGACTGGATCAAAGATGCCTCAGGTCTCATGTCCCACTGCATTGCCATCTTGAAGATTTGTCACA
CTCTGACAGAGGAGCTTGTTGCCATCACAATGGGTTCTGGGGCCAAGATGAAGACTTCAGCCATTGTCAGCAACATCATT
GTGGCGGCCAAGTGGAACAGCCCCAGGGTGGATGATGTTGTGAAGTCGATGTACCCTCCATTGGACCCCAAGCTCCTGGA
TGCAGGGATGACTGCCCTGCTCCTGTCTTGTCAGTCATCTGGTGCTGGTGACAAGGAATGCCTGCCATCTGACAGGGTCC
TGGACTGGATTGACCAGTCACTGTCAGCTGCTGAGGAGCATTTGAAAGTCCTTCGAGAAGCAGCCCTAGCTTTTGAGCCA
GATAAAGGCCTCCCAGGCCCAGAAGGCTTCCTGCAGGAGCAGTCCGCAATT

Alignment

ORF - retro_mmul_2256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVLVCRQRYCRPRDL-LQRYDSKPIVDLIGAMETQSEPSELELDDVVITNPHIEAILENEDWIEDASGLM
          LVL.CRQRY..PRDL.LQRYDSKPI.DLIGAM.TQSEPSELELDDVVITNPHIE.ILEN.DWI.DASGLM
Retrocopy LVLDCRQRYYQPRDL<LQRYDSKPIMDLIGAMVTQSEPSELELDDVVITNPHIETILENKDWIKDASGLM

Parental  SHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVSDIIVVAKRISPRVDDVVKSMYPPLDPKLLDARTTA
          SHCIAILKICHTLTE.LVA.TMGSGAKMKTSA.VS.IIV.AK..SPRVDDVVKSMYPPLDPKLLDA..TA
Retrocopy SHCIAILKICHTLTEELVAITMGSGAKMKTSAIVSNIIVAAKWNSPRVDDVVKSMYPPLDPKLLDAGMTA

Parental  LLLS-VSHLVLVTRNACHLTGG-LDWIDQSLSAAEEHLEVLREAALASEPDKGLPGPEGFLQEQSAI
          LLLS.VSHLVLVTRNACHLTG..LDWIDQSLSAAEEHL.VLREAALA.EPDKGLPGPEGFLQEQSAI
Retrocopy LLLS>VSHLVLVTRNACHLTGS<LDWIDQSLSAAEEHLKVLREAALAFEPDKGLPGPEGFLQEQSAI

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	0.11 RPM	2.91 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	3.81 RPM
SRP007412_cerebellum	0.13 RPM	2.00 RPM
SRP007412_heart	0.47 RPM	5.95 RPM
SRP007412_kidney	0.82 RPM	8.69 RPM
SRP007412_liver	0.28 RPM	3.72 RPM
SRP007412_testis	1.58 RPM	5.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2256 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2256 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1421
Pan troglodytes	retro_ptro_971
Gorilla gorilla	retro_ggor_1098
Pongo abelii	retro_pabe_1175

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014550	1 retrocopy	retro_cjac_2447,
Homo sapiens	ENSG00000006042	2 retrocopies	retro_hsap_1421, retro_hsap_3605,
Gorilla gorilla	ENSGGOG00000013333	2 retrocopies	retro_ggor_1098, retro_ggor_2432,
Myotis lucifugus	ENSMLUG00000001191	1 retrocopy	retro_mluc_130,
Macaca mulatta	ENSMMUG00000022356	2 retrocopies	retro_mmul_1835, retro_mmul_2256 ,
Nomascus leucogenys	ENSNLEG00000006038	3 retrocopies	retro_nleu_1233, retro_nleu_1840, retro_nleu_2635,
Pongo abelii	ENSPPYG00000008166	2 retrocopies	retro_pabe_1175, retro_pabe_2961,
Pan troglodytes	ENSPTRG00000008993	3 retrocopies	retro_ptro_2436, retro_ptro_2990, retro_ptro_971,