RetrogeneDB ID: retro_mmus_1881

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:3531284..3531599(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081278
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufb2
• Ensembl ID: ENSMUSG00000002416
• Aliases: Ndufb2, 1810011O01Rik, 8kDa, AGGG, AI325567, CI-AGGG
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2 [Source:MGI Symbol;Acc:MGI:1915448]

Sequence

>retro_mmus_1881
ATGTCTGCGCTGACCCGCTTGGTACCTTTTGGTCCCGTCGGAGGCCTCCTGCTCTGGGGCTGCCGCCTGTGGGGAGCTGG
AGACCATGGAGTCCGTCATGCTGGCGGTGGTGTACATATTCAGCCCTGGTACAGGGAGTTTCCCCAGCTTACCTGGTCCC
AGGTGATCCACGGTGAGTTCTTAAGCTCACTCATGTGGTTCTGGATTCTTTGGTGATTTTGGCATGAGTCAGATGCTGTG
CTGGGTCACCTTTCATATCCAGATCCTTCACAGTGGACAGATGAAGAACTGGGAATCCCTCCCGATGATGAGGAC

Alignment

ORF - retro_mmus_1881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSALTRLVPFGRVGGRLLRGCRARAAGDSGVRHAGGGVHIQPRYREFPQLTRSQVIQGEFLSSLMWFWIL
          MSALTRLVPFG.VGG.LL.GCR...AGD.GVRHAGGGVHIQP.YREFPQLT.SQVI.GEFLSSLMWFWIL
Retrocopy MSALTRLVPFGPVGGLLLWGCRLWGAGDHGVRHAGGGVHIQPWYREFPQLTWSQVIHGEFLSSLMWFWIL

Parental  WRFWHDSDAVLGHFSYPDPSQWTDEELGIPPDDED
          W.FWH.SDAVLGH.SYPDPSQWTDEELGIPPDDED
Retrocopy W*FWHESDAVLGHLSYPDPSQWTDEELGIPPDDED

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	0.02 RPM	23.95 RPM
SRP007412_cerebellum	0.00 RPM	30.83 RPM
SRP007412_heart	0.03 RPM	22.44 RPM
SRP007412_kidney	0.04 RPM	17.32 RPM
SRP007412_liver	0.00 RPM	10.65 RPM
SRP007412_testis	0.00 RPM	2.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1881 was not detected

EST

No EST(s) were mapped for retro_mmus_1881 retrocopy.

TSS

No TSS is located nearby retro_mmus_1881 retrocopy 5' end.

Lab

retro_mmus_1881 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1881 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881 ,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,