RetrogeneDB ID: retro_mmus_2480

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:91805549..91806550(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000049494
• Aliases: Gm12669, OTTMUSG00000007920
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Glrx3
• Ensembl ID: ENSMUSG00000031068
• Aliases: Glrx3, PICOT, Txnl2
• Description: glutaredoxin 3 [Source:MGI Symbol;Acc:MGI:1353653]

Sequence

>retro_mmus_2480
GGCGGGGGCGGCCCAGGCGAGGCAGCCGTGGCAGTGGTGGAAGTCGGCTCTGCCCAGCAGTTTGAAGAGCTACTGCGCCT
CAAAACCAAGTCACTCCTTGTGGTTCATTTCTGGGCACCATGGGCTCCACAGTGTGTACAGATGAACGATGTCATGGCAG
AGTTAGCTAAAGAACACCCTCATGTTTCATTTGTGAAGCTGGAAGCCGAAGCTGTTCCTGAAGTATCTGAAAAATATGAA
ATTAGCTCTGTCCCCAGCTTCCTGTTCTTCAAGAATTCTCAGAAAGTCGACCGGTTAGATGGTGCACATGCCCCAGAGTT
GACCAAAAAAGTCCAGCGACACGTGTCTAGCGGAGCCTTTCGCCTAGTACTAATGAACATCTTAAAGAAGACCTCAGCCT
TCGCCTGAAAAAGCTGACTCACGCTGCCCCCTGCATGCTGTTCATGAAGGGAACACCTCAAGAACCGCGCTGTGGTTTCA
GCAAGCAGATGGTGGAAATCCTTCACAAACACAATATTCAGTTCAGCAGCTTTGATATCTTCTCAGATGAAGAAGTTCGA
CAGGGGCTCAAAACGTACTCTAATTGGCCCACCTATCCTCAGCTCTATGTTTCTGGAGAGCTAATAGGAGGACTTGACAT
AATTAAGGAGCTGGAAGCATCAGAAGAGCTGGACACGATCTGTCCCAAAGCACCCAAGTTAGAGGAAAGGCTCAAAGTGC
TGACCAATAAAGCTTCGGTGATGCTCTTTATGAAAGGAAACAAACAGGAAGCAAAATGTGGATTCAGCAAACAAATTCTG
GAAATACTGAATAGTACTGGGGTTGAATATGAAACTTTTGATATACTGGAAGATGAAGAAGTGCGTCAGGGATTAAAAAC
GTTCTCAAATTGGCCAACCTACCCTCAGCTGTATGTGAGAGGGGATCTTGTTGGAGGATTGGATATTGTCAAGGAACTGA
AAGACAACGGTGAATTGCTGCCTATACTGAAAGGAGAAAAT

Alignment

ORF - retro_mmus_2480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.91 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAAEAGEAAVAVVEVGSAQQFEELLRLKTKSLLVVHFWAPWAPQCVQMNDVMAELAKEHPHVSFVKLEAE
          G....GEAAVAVVEVGSAQQFEELLRLKTKSLLVVHFWAPWAPQCVQMNDVMAELAKEHPHVSFVKLEAE
Retrocopy GGGGPGEAAVAVVEVGSAQQFEELLRLKTKSLLVVHFWAPWAPQCVQMNDVMAELAKEHPHVSFVKLEAE

Parental  AVPEVSEKYEISSVPTFLFFKNSQKVDRLDGAHAPELTKKVQRHVSSGAF-PPSTNEHLKEDLSLRLKKL
          AVPEVSEKYEISSVP.FLFFKNSQKVDRLDGAHAPELTKKVQRHVSSGAF..PSTNEHLKEDLSLRLKKL
Retrocopy AVPEVSEKYEISSVPSFLFFKNSQKVDRLDGAHAPELTKKVQRHVSSGAF<SPSTNEHLKEDLSLRLKKL

Parental  THAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGELI
          THAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGELI
Retrocopy THAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGELI

Parental  GGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYET
          GGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYET
Retrocopy GGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYET

Parental  FDILEDEEVRQGLKTFSNWPTYPQLYVRGDLVGGLDIVKELKDNGELLPILKGEN
          FDILEDEEVRQGLKTFSNWPTYPQLYVRGDLVGGLDIVKELKDNGELLPILKGEN
Retrocopy FDILEDEEVRQGLKTFSNWPTYPQLYVRGDLVGGLDIVKELKDNGELLPILKGEN

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	0.47 RPM	29.11 RPM
SRP007412_cerebellum	0.48 RPM	20.63 RPM
SRP007412_heart	0.31 RPM	30.29 RPM
SRP007412_kidney	0.89 RPM	26.16 RPM
SRP007412_liver	0.25 RPM	21.82 RPM
SRP007412_testis	3.11 RPM	101.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2480 was not detected

EST

No EST(s) were mapped for retro_mmus_2480 retrocopy.

TSS

No TSS is located nearby retro_mmus_2480 retrocopy 5' end.

Lab

retro_mmus_2480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2480 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480 ,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,