RetrogeneDB ID: retro_mmus_2376

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:91365378..91365785(+)
• Located in intron of: ENSMUSG00000008489

Retrocopy information

• Ensembl ID: ENSMUSG00000083377
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nme6
• Ensembl ID: ENSMUSG00000032478
• Aliases: Nme6, nm23-M6
• Description: NME/NM23 nucleoside diphosphate kinase 6 [Source:MGI Symbol;Acc:MGI:1861676]

Sequence

>retro_mmus_2376
ATGACCTCCATCGTATAAAGTCCCCAGGCTCTTCAGCTCACGCTAGCCCTGATCAAGCCTGACGCAGTTGCCCACCCACT
GATCCTGGAGGCTGTTCATCAGCAGATTCTGAGCGACAACTCCCTCACTGTATGAACAAGAGAACTGCAGTGGAAGCCAG
AGGACTGCCTGGGTTTTACCGAGAGCGTGAAGGGTTTTTTTTTTTCTATCAGCGGCTGGTGGAATTCACGACAAGAGGGC
CAATCCGAGCCTATATCCTTACCTACAAAGATACCATGCAACTTTGGAGGACACGGATGGGACCTACCAGAGAATTTCGA
GCACGCCATATAGCCCCAGACTCAATTCGTGGGAGTTTGTGCCTCACTGACACCTGAAATGCTACCCGTGGCTCAGACTC
CGTGGTT

Alignment

ORF - retro_mmus_2376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.83 %
• Parental protein coverage: 85.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSILRSPQALQLTLALIKPDAVAHPLILEAVHQQILSNKFLIVRTRELQWKLEDCRRF-YREHEGRFF-
          MTSI..SPQALQLTLALIKPDAVAHPLILEAVHQQILS...L.V.TRELQWK.EDC..F.YRE.EG....
Retrocopy MTSIV*SPQALQLTLALIKPDAVAHPLILEAVHQQILSDNSLTV*TRELQWKPEDCLGF<YREREGXXXX

Parental  YQRLVEFMTSGPIRAYILAHKDAIQLWRTLMGPTRVFRARYIAPDSIRGSLGLTDTRNTTHGSDSVV
          YQRLVEF.T.GPIRAYIL..KD..QLWRT.MGPTR.FRAR.IAPDSIRGSL.LTDT.N.T.GSDSVV
Retrocopy YQRLVEFTTRGPIRAYILTYKDTMQLWRTRMGPTREFRARHIAPDSIRGSLCLTDT*NATRGSDSVV

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	0.14 RPM	3.83 RPM
SRP007412_cerebellum	0.13 RPM	3.47 RPM
SRP007412_heart	0.00 RPM	9.87 RPM
SRP007412_kidney	0.04 RPM	5.99 RPM
SRP007412_liver	0.00 RPM	8.11 RPM
SRP007412_testis	0.00 RPM	31.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2376 was not detected

EST

No EST(s) were mapped for retro_mmus_2376 retrocopy.

TSS

No TSS is located nearby retro_mmus_2376 retrocopy 5' end.

Lab

retro_mmus_2376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2376 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376 ,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Sus scrofa	ENSSSCG00000011347	1 retrocopy	retro_sscr_1076,
Ictidomys tridecemlineatus	ENSSTOG00000002690	1 retrocopy	retro_itri_675,