RetrogeneDB ID: retro_mmus_3181

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:29286430..29286954(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nudc
• Ensembl ID: ENSMUSG00000028851
• Aliases: Nudc, SIG-92, Silg92
• Description: nuclear distribution gene C homolog (Aspergillus) [Source:MGI Symbol;Acc:MGI:106014]

Sequence

>retro_mmus_3181
AAAGGAAAACTGAAGCCCAACCTAGGCAATGGGGCTGACCTGCCCAACTACCGCTGGACCCAGACCCTGGCAGAACTGGA
TCTGGCAGTGCCCTTCCGGGTCAGCTTCCGGCTGAAGGGAAAGGATGTGGTGGTGGACATCCAGCGGCACTCCGGGTGGG
CCTTAAAGGACAGCCACCAGTGGTTGATGGAGAACTCTACAATGAAGTCAAGGTGGAGGAGAGCTCGTGGCTCATCGAGG
ATGGCAAGGTGGTGACAGTGCATCTGGAGAAGATCAATAAGATGGAATGGTGGAACCGCTTGGTTACCAGTGACCCCGAA
ATCAATACCAAGAAGATTAACCCTGAGAACTCCAAGCTATCAGACCTCGACAGTGAGACTCGCAGCATGGTGGAAAAGAT
GATGTATGACCAGAGGCAGAAGTCCATGGGCTTGCCCACCTCTGATGAGCAGAAGAAACAGGAAATCCTGAAGAAGTTCA
TGGACCAGCACCCAGAGATGGATTTCTCCAAGGCCAAATTCAAC

Alignment

ORF - retro_mmus_3181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.87 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGKLKPNLGNGADLPNYRWTQTLAELDLAVPFRVSFRLKGKDVVVDIQRRH-LRVGLKGQPPVVDGELYN
          KGKLKPNLGNGADLPNYRWTQTLAELDLAVPFRVSFRLKGKDVVVDIQR.H.LRVGLKGQPPVVDGELYN
Retrocopy KGKLKPNLGNGADLPNYRWTQTLAELDLAVPFRVSFRLKGKDVVVDIQR-H<LRVGLKGQPPVVDGELYN

Parental  EVKVEESSWLIEDGKVVTVHLEKINKMEWWNRLVTSDPEINTKKINPENSKLSDLDSETRSMVEKMMYDQ
          EVKVEESSWLIEDGKVVTVHLEKINKMEWWNRLVTSDPEINTKKINPENSKLSDLDSETRSMVEKMMYDQ
Retrocopy EVKVEESSWLIEDGKVVTVHLEKINKMEWWNRLVTSDPEINTKKINPENSKLSDLDSETRSMVEKMMYDQ

Parental  RQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
          RQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
Retrocopy RQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN

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	1.00 RPM	64.53 RPM
SRP007412_cerebellum	3.39 RPM	98.70 RPM
SRP007412_heart	0.19 RPM	60.64 RPM
SRP007412_kidney	2.04 RPM	75.90 RPM
SRP007412_liver	0.87 RPM	54.18 RPM
SRP007412_testis	2.33 RPM	90.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3181 was not detected

EST

No EST(s) were mapped for retro_mmus_3181 retrocopy.

TSS

No TSS is located nearby retro_mmus_3181 retrocopy 5' end.

Lab

retro_mmus_3181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168, retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181 ,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055, retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655, retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009, retro_rnor_2108,