RetrogeneDB ID: retro_mmul_1145

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:44200910..44201333(+)
• Located in intron of: ENSMMUG00000007724

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAGE3
• Ensembl ID: ENSMMUG00000007739
• Aliases: None
• Description: L antigen family, member 3 [Source:HGNC Symbol;Acc:26058]

Sequence

>retro_mmul_1145
GACGCGGATGCAGACGCAGGCGGAAGCACCAACTGCGGGGATAGCCAGGGTGACCACAGCTGCCCCGGTGGCGCGGACAC
AGCGGCAGCTCCAGCTGGCGGAGCTCCCCCACCTCACGCCTCAGGTCCTGGCAGAGACGCCAAGTCTGTGGCCAGGGGGC
CAGGAATGCGGCCACACGTATTCACCCTCAGCGTGCCTTTTCCGACCCCCTTAGAGGCGGAAATTGCCCGTGGGTCCCTG
GCTCCAGATGCTGAGCCCCACCAAAGGGTGGTTGGGAAGAATCTCGCAGTGAGCGGCAGGATCTTGGCCGTCCGCTGGGA
AGCTGAAGACTGTCGCCTGCTCCGAATTTCCGTTATCAACTTTCTCGACCATCTTTCTCTGGTGGTGCAGACCATGCAGC
ACTTTGGGCCCCCCGTTTCCCGC

Alignment

ORF - retro_mmul_1145 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.4 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAEADAGGGADGGDGQGGHSFPGGADTAAAPASGAPPPHAPGPGRDAASAARGPGMRPHIFTLSVPFPTP
          .A.ADAGG....GD.QG.HS.PGGADTAAAPA.GAPPPHA.GPGRDA.S.ARGPGMRPH.FTLSVPFPTP
Retrocopy DADADAGGSTNCGDSQGDHSCPGGADTAAAPAGGAPPPHASGPGRDAKSVARGPGMRPHVFTLSVPFPTP

Parental  LEAEIAHGSLAPDAEPHQRVVGKELTVSGRILAIRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGPPVS
          LEAEIA.GSLAPDAEPHQRVVGK.L.VSGRILA.RW.AEDCRLLRISVINFLD.LSLVV.TMQ.FGPPVS
Retrocopy LEAEIARGSLAPDAEPHQRVVGKNLAVSGRILAVRWEAEDCRLLRISVINFLDHLSLVVQTMQHFGPPVS

Parental  R
          R
Retrocopy R

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	5.27 RPM
SRP007412_brain_prefrontal_cortex	1.59 RPM	14.04 RPM
SRP007412_cerebellum	0.19 RPM	2.78 RPM
SRP007412_heart	0.65 RPM	3.71 RPM
SRP007412_kidney	0.23 RPM	6.46 RPM
SRP007412_liver	4.28 RPM	10.05 RPM
SRP007412_testis	11.91 RPM	1.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1145 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1145 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145 ,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,