RetrogeneDB ID: retro_mmus_2566

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:50921538..50921901(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufb10
• Ensembl ID: ENSMUSG00000040048
• Aliases: Ndufb10, 0610011B04Rik, 22kDa, PDSW
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 [Source:MGI Symbol;Acc:MGI:1915592]

Sequence

>retro_mmus_2566
CAGCATGCCAATAACTGAACCTGCTATTATCAGCAATAGTAGGGACATGTGCTGGACCCTGCTGAATACAAGAAGGGTGA
TGTTCTCTGTTCAGTTGAGCCTGAGATGCAATTGCGAAGGGACTACAGAGTTGACCAGAATATCATCAGCATCATTCAGG
AAAGGCTTAAGGCGTGTCAGCAGAAGAAAGGAGCAAGCACAAGCAGAATTGTGCCAAGGCACCGGAGCAGTTTACCAAGG
TGGCTAAACTCTTATCACGACCAATTTTATGACCTGGGAGCATATTATTTCTGCCAGAAAGTGCCTGACAAAGCAGAAGC
AGGAGAGGCTAGAAAGAGAATGGCTGCTGAGGAGACTCTTGCT

Alignment

ORF - retro_mmus_2566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 68.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QHAKNRTYYYHRQYRRVPDITECKEGDVLCIYEAEMQWRRDFKVDQEIMNIIQERLKACQQREG-ENYQQ
          QHA.N.T.YY......V.D..E.K.GDVLC..E.EMQ.RRD..VDQ.I..IIQERLKACQQ..G.....Q
Retrocopy QHANN*TCYYQQ**GHVLDPAEYKKGDVLCSVEPEMQLRRDYRVDQNIISIIQERLKACQQKKG<SKHKQ

Parental  NCAKELEQFTKVTK-AYQDRYLDLGAYY-SARKCLAKQKQRMLE-ERKAARQEAA
          NCAK..EQFTKV.K..Y.D...DLGAYY.SARKCL.KQKQ..LE..R.AA....A
Retrocopy NCAKAPEQFTKVAK>SYHDQFYDLGAYY>SARKCLTKQKQERLE<KRMAAEETLA

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	0.00 RPM	86.00 RPM
SRP007412_cerebellum	0.00 RPM	119.50 RPM
SRP007412_heart	0.00 RPM	504.00 RPM
SRP007412_kidney	0.00 RPM	265.22 RPM
SRP007412_liver	0.00 RPM	124.01 RPM
SRP007412_testis	0.00 RPM	72.63 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2566 was not detected

EST

No EST(s) were mapped for retro_mmus_2566 retrocopy.

TSS

No TSS is located nearby retro_mmus_2566 retrocopy 5' end.

Lab

retro_mmus_2566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2566 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1056

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019476	1 retrocopy	retro_cfam_1861,
Echinops telfairi	ENSETEG00000017154	1 retrocopy	retro_etel_1955,
Felis catus	ENSFCAG00000011738	1 retrocopy	retro_fcat_307,
Homo sapiens	ENSG00000140990	2 retrocopies	retro_hsap_1573, retro_hsap_3801,
Gorilla gorilla	ENSGGOG00000009367	2 retrocopies	retro_ggor_1198, retro_ggor_2555,
Latimeria chalumnae	ENSLACG00000013152	1 retrocopy	retro_lcha_100,
Macaca mulatta	ENSMMUG00000029268	1 retrocopy	retro_mmul_2218,
Mus musculus	ENSMUSG00000040048	1 retrocopy	retro_mmus_2566 ,
Nomascus leucogenys	ENSNLEG00000008867	1 retrocopy	retro_nleu_1740,
Pongo abelii	ENSPPYG00000006974	2 retrocopies	retro_pabe_1297, retro_pabe_3106,
Pan troglodytes	ENSPTRG00000007618	2 retrocopies	retro_ptro_1060, retro_ptro_2578,
Rattus norvegicus	ENSRNOG00000014568	1 retrocopy	retro_rnor_1056,
Sus scrofa	ENSSSCG00000030328	1 retrocopy	retro_sscr_689,