RetrogeneDB ID: retro_mmus_2456

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:46243278..46243935(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082194
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Otud6b
• Ensembl ID: ENSMUSG00000040550
• Aliases: Otud6b, 2600013N14Rik, AU015433
• Description: OTU domain containing 6B [Source:MGI Symbol;Acc:MGI:1919451]

Sequence

>retro_mmus_2456
AGGTGCGGATCTCCTTCAGCTCGAGTGCCGGGCCGCCTGGTCGTCATGGACGAGGTCGTGGCTGAAGAGCTCGATGATGA
GGAGCAGCTGGTGAGAAGGCATCAGAAGGAGAAGAAGGAGCTGCAAGCTAAAATTCAGGGAATGAAGAACGCTGTTCCCA
AAAACGACAAAAAGAGGAGGAAGCAGCTCACAGAAGATGTTGCTAAATTGGAAAGAGAAATGGAGCAAAAACACAGGGAA
GAACTGGAGCAATTGAAGCAATTGACTTTCAAGGACAGTAAGACAGATTCTGTTGCTGTTAACATTTCAAATTTGGTACT
TGAGAATCAACCACCTCGGATTTCAAAAGCACAAAAGAGATGGGAAAAGAAGGCTGCATTGGAAAAGGAGCGGGAAGAAA
GGATAGCAGAGGCTGAAATTGAGAACTTATCTGGAGCCAGACATCTTGAGAGTGAAAAACTTGCTCAAATATTGGCAGCC
AGAGAATTGGAAATTAAACAGATTCCATCTGATGGTCATTGTATGTATGGAGCACTTGAGGATCAGCTGAGAGAACAAGA
CTGTGCACTGACTGTGGCTTCCCTGAGGAGGCAGACTGCTGAGTACATGCAAAGCCATTCAGATGACTTCCTGCCGTTTC
TAACAAACCCCAGCACA

Alignment

ORF - retro_mmus_2456 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.72 %
• Parental protein coverage: 67.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RCGSPSARVPGRLVVMEEVVAEELDDEEQLVRRHRKEKKELQAKIQGMKNAVPKNDKKRRKQLTEDVAKL
          RCGSPSARVPGRLVVM.EVVAEELDDEEQLVRRH.KEKKELQAKIQGMKNAVPKNDKKRRKQLTEDVAKL
Retrocopy RCGSPSARVPGRLVVMDEVVAEELDDEEQLVRRHQKEKKELQAKIQGMKNAVPKNDKKRRKQLTEDVAKL

Parental  EREMEQKHREELEQLKQLTFKDSKIDSVAVNISNLVLENQPPRISKAQKRREKKAALEKEREERIAEAEI
          EREMEQKHREELEQLKQLTFKDSK.DSVAVNISNLVLENQPPRISKAQKR.EKKAALEKEREERIAEAEI
Retrocopy EREMEQKHREELEQLKQLTFKDSKTDSVAVNISNLVLENQPPRISKAQKRWEKKAALEKEREERIAEAEI

Parental  ENLSGARHLESEKLAQILAARELEIKQIPSDGHCMYGALEDQLREQDCALTVASLRRQTAEYMQTHSDDF
          ENLSGARHLESEKLAQILAARELEIKQIPSDGHCMYGALEDQLREQDCALTVASLRRQTAEYMQ.HSDDF
Retrocopy ENLSGARHLESEKLAQILAARELEIKQIPSDGHCMYGALEDQLREQDCALTVASLRRQTAEYMQSHSDDF

Parental  LPFLTNPST
          LPFLTNPST
Retrocopy LPFLTNPST

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	42.85 RPM
SRP007412_cerebellum	0.00 RPM	39.08 RPM
SRP007412_heart	0.06 RPM	52.89 RPM
SRP007412_kidney	0.08 RPM	45.58 RPM
SRP007412_liver	0.03 RPM	30.42 RPM
SRP007412_testis	0.14 RPM	24.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2456 was not detected

EST

No EST(s) were mapped for retro_mmus_2456 retrocopy.

TSS

No TSS is located nearby retro_mmus_2456 retrocopy 5' end.

Lab

retro_mmus_2456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2456 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456 ,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,