RetrogeneDB ID: retro_mmus_1411

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:78554407..78554848(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000068226
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lage3
• Ensembl ID: ENSMUSG00000015289
• Aliases: Lage3, 1110049G11Rik, Eso3, Itba2
• Description: L antigen family, member 3 [Source:MGI Symbol;Acc:MGI:1913442]

Sequence

>retro_mmus_1411
ATGCAGACAGCACACACAGGTTTAAGCCACACTGCAGATGGCGCCTACGGTCCGACTAGCCGCTGCTGTCCTGGTAATGC
AGGCACAAAGGCAGTTATTCCCAGTGGAGCGCACCCTGTTGGAAGAGCACTGGAAGCCTCCCGAAATCCCAGCAAAAGCA
TCGTGCCTTTAACCCAAAGGCCTGGAAGCCGATATCGTAGATTTGCCCTCTTCGTGCCTTTCCCGACCTCTTTGGAGGCA
GAAATCGCCTGTGGGTCCCTAGTTCCAGATGTCGAACCACACCGAGGACTGGTAGGGAAGGAGCTTAAAGTGAGCGGCTG
CCTGCTGGAGGTACGCTGGATCGCGGAAGATTCTCGACTCCTCCGAATTTCCATCATCAACTTTCTTGACCAGCTTTCCC
TAGTGGTAAACACCATACAGCTTTTTGGGCCCCCGGTTTCC

Alignment

ORF - retro_mmus_1411 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTAHTGLSHTADGADGQTSRCCPGNAGTKAVIPSGAHPVARALEASRNSSKSMVPLTQRPGTRHHRFSL
          MQTAHTGLSHTADGA.G.TSRCCPGNAGTKAVIPSGAHPV.RALEASRN.SKS.VPLTQRPG.R..RF.L
Retrocopy MQTAHTGLSHTADGAYGPTSRCCPGNAGTKAVIPSGAHPVGRALEASRNPSKSIVPLTQRPGSRYRRFAL

Parental  FVPFPTSLEAEIACGSLVPDVEPHRGLVGKELKVSGCMLEVRWIAEDSRLLRLSIINFLDQLSLVVNTIQ
          FVPFPTSLEAEIACGSLVPDVEPHRGLVGKELKVSGC.LEVRWIAEDSRLLR.SIINFLDQLSLVVNTIQ
Retrocopy FVPFPTSLEAEIACGSLVPDVEPHRGLVGKELKVSGCLLEVRWIAEDSRLLRISIINFLDQLSLVVNTIQ

Parental  LFGPPVS
          LFGPPVS
Retrocopy LFGPPVS

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	0.19 RPM	6.71 RPM
SRP007412_cerebellum	0.13 RPM	7.38 RPM
SRP007412_heart	0.12 RPM	9.81 RPM
SRP007412_kidney	0.19 RPM	14.75 RPM
SRP007412_liver	0.03 RPM	10.54 RPM
SRP007412_testis	0.59 RPM	1.23 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_1411 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	15:78554947..78555246
ENCFF001YKA	POLR2A	15:78554704..78555466

EST

No EST(s) were mapped for retro_mmus_1411 retrocopy.

TSS

No TSS is located nearby retro_mmus_1411 retrocopy 5' end.

Lab

retro_mmus_1411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1411 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,