RetrogeneDB ID: retro_mmus_1490

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:14010942..14011503(-)
• Located in intron of: ENSMUSG00000044117

Retrocopy information

• Ensembl ID: ENSMUSG00000082554
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Akr1b10
• Ensembl ID: ENSMUSG00000061758
• Aliases: Akr1b10, 2310005E10Rik, Akr1b16
• Description: aldo-keto reductase family 1, member B10 (aldose reductase) [Source:MGI Symbol;Acc:MGI:1915111]

Sequence

>retro_mmus_1490
AGGAGGACCTACCTCTTCACCGTCAGCAAGCTGTGGCCCACCTTCTTTGAGAAAAGCCTGGTAAAGGAAGCCTTCCAGAA
AACCCTCTCAGATCTGAAGCTCGACTATCTGGACCTGTATCTAATCCACTGGCCACAGGGATTTCAATCTGGAAATGTCT
TTTTACCCACAGATGATAAAGGCAATGCTCTCAGCAGTAAATATACAAACTTGGATGCTTGGGAGGGCATGGAGGAACTG
GTGGACCAGGGGCTGGTGAGAACTCTGGGCATCTCCAACTTCAACCACTTCCAGATTGAAAGGCTCCTGAACAAGCCTGG
ACTAAAACATAGGCCAGTGACCAACCAAGTCGAGTATCACCCTTACCTCACCCAGGAAAAACTGATTCAGTACTGTCACT
CCAAGGGCATCACCATCACGGCCTATAGTCCCCTGGGCTCCCCAGACAGGCCTAGTGCCAAACCAGAGGAGCCCGAATTA
CTGGAGCGTCCCAAGATCAAAGAGATGGCTGCAAAGCATGAGAAAACTGCATCCCAGGTTCTGATTCAGCTCCATAGAGA
G

Alignment

ORF - retro_mmus_1490 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.1 %
• Parental protein coverage: 64.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KREDLFIVSKLWSTFFEKSLVKKAFQNTLSDLKLDYLDLYLIHWPQGFQSGNVFLPTDDKGSILSSKYTF
          .R..LF.VSKLW.TFFEKSLVK.AFQ.TLSDLKLDYLDLYLIHWPQGFQSGNVFLPTDDKG..LSSKYT.
Retrocopy RRTYLFTVSKLWPTFFEKSLVKEAFQKTLSDLKLDYLDLYLIHWPQGFQSGNVFLPTDDKGNALSSKYTN

Parental  LDAWEAMEELVDQGLVKALGVSNFNHFQIERLLNKPGLKHKPVTNQVECHPYLTQEKLIQYCHSKGITIT
          LDAWE.MEELVDQGLV..LG.SNFNHFQIERLLNKPGLKH.PVTNQVE.HPYLTQEKLIQYCHSKGITIT
Retrocopy LDAWEGMEELVDQGLVRTLGISNFNHFQIERLLNKPGLKHRPVTNQVEYHPYLTQEKLIQYCHSKGITIT

Parental  AYSPLGSPDRPSAKPEDPLLLEIPKIKEIAAKHKRTAAQVLIRFHIE
          AYSPLGSPDRPSAKPE.P.LLE.PKIKE.AAKH..TA.QVLI..H.E
Retrocopy AYSPLGSPDRPSAKPEEPELLERPKIKEMAAKHEKTASQVLIQLHRE

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	10.96 RPM
SRP007412_cerebellum	0.04 RPM	13.11 RPM
SRP007412_heart	0.00 RPM	33.37 RPM
SRP007412_kidney	0.06 RPM	20.77 RPM
SRP007412_liver	0.05 RPM	2.43 RPM
SRP007412_testis	0.00 RPM	1.69 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1490 was not detected

EST

No EST(s) were mapped for retro_mmus_1490 retrocopy.

TSS

No TSS is located nearby retro_mmus_1490 retrocopy 5' end.

Lab

retro_mmus_1490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1490 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000001642	10 retrocopies	retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490 ,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,