RetrogeneDB ID: retro_mmus_990

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:8128180..8129061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bzw1
• Ensembl ID: ENSMUSG00000051223
• Aliases: Bzw1, 1200015E15Rik, mKIAA0005
• Description: basic leucine zipper and W2 domains 1 [Source:MGI Symbol;Acc:MGI:1914132]

Sequence

>retro_mmus_990
AAACCAGAAAAAGAGAGATTTGACCCTACTAAGTTTCATGACTGTATTATTCAAGTCTTAACTGAAACTGGTACTGATTT
GGAAGCAGTAGCTAAGTTTCTTGATGCTTCTGGAGCAAAAGTTGACTACTGCCGCTATGCAGAAACACTCTTTGACATTC
TGGTGGCTGGCGGAATGGTGGCCCCAGGTGGTACACTGGCAGATGACATGATGCGCACAGATGTCTATGTGTTTGCAGCA
CAAGAAGACCTAAAGACCATGCAAGCATTCGCTCAGGTTTTTAACAAGCTAACCAGGCGCTACAAATACCCGGAGAAAGG
TTTTGAAGATGAAGTTAAAAAGTTACTGCTCTTCCTAAAGGGATTTTCAGAGTCGGAGAGGAACAAGCTCGCCATGTTGA
CTGGGGTCCTTCTGGCTAATGGAACCCTTAATGCATCCGTTCTTAACAGCCTTTATAATGAGAATTTGGTTAAAGAAGGG
GTTTCGCAGCTTTTGCTGTAAAGCTCTTTAAATCATGGATAAATGAAAAGACATCAATGCAGTTGCTGCAAGTCTTCAGA
AAGTCAGCATGGACAATAGACTGATGGAGCTGTTCCCTGCCAGTAAACGGAGTGATGGGCATTTCACTAAGTATTTCACT
GAGGCGGGCTTGAAGGAGCTTTCGGAGTATGTCCGCAACCAGCAGACCACTGAGGCTTGGAAGGAGCTGCAGGAGCAGAT
GTCCCGCGGTGACCCATTCAAGGACATATTTTTATATGTCAAGGAGGAGATGAAAAAAACTAACATTCCAGAACCAGTGG
TCATTGGGATGGATAGTCTGGTCCAGTGTGATGAGCACCGTGGAGTGGAATAAAAAAGAGGAGCTTGTAGCAGAACAAGC
C

Alignment

ORF - retro_mmus_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.37 %
• Parental protein coverage: 70.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RDEKERFDPTQFQDCIIQGLTETGTDLEAVAKFLDASGAKLDYRRYAETLFDILVAGGMLAPGGTLADDM
          ..EKERFDPT.F.DCIIQ.LTETGTDLEAVAKFLDASGAK.DY.RYAETLFDILVAGGM.APGGTLADDM
Retrocopy KPEKERFDPTKFHDCIIQVLTETGTDLEAVAKFLDASGAKVDYCRYAETLFDILVAGGMVAPGGTLADDM

Parental  MRTDVCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFLKGFSESERNKLAMLTGVLLAN
          MRTDV.VFAAQEDL.TMQAFAQVFNKL.RRYKY.EKGFEDEVKKLLLFLKGFSESERNKLAMLTGVLLAN
Retrocopy MRTDVYVFAAQEDLKTMQAFAQVFNKLTRRYKYPEKGFEDEVKKLLLFLKGFSESERNKLAMLTGVLLAN

Parental  GTLNASILNSLYNENLVKEGVS-AAFAVKLFKSWINEK-DINAVAASLRKVSMDNRLMELFPANKQSVEH
          GTLNAS.LNSLYNENLVKEGVS.AAFAVKLFKSWINEK.DINAVAASL.KVSMDNRLMELFPA.K.S..H
Retrocopy GTLNASVLNSLYNENLVKEGVS<AAFAVKLFKSWINEK<DINAVAASLQKVSMDNRLMELFPASKRSDGH

Parental  FTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMKKNNIPEPVV-IG-IV
          FTKYFTEAGLKELSEYVRNQQT.....E..KELQEQMSRGDPFKDI.LYVKEEMKK.NIPEPVV..G.IV
Retrocopy FTKYFTEAGLKELSEYVRNQQTT----EAWKELQEQMSRGDPFKDIFLYVKEEMKKTNIPEPVV>LGWIV

Parental  WSSVMSTVEWNKKEELVAEQA
          WSSVMSTVEWNKKEELVAEQA
Retrocopy WSSVMSTVEWNKKEELVAEQA

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	117.94 RPM
SRP007412_cerebellum	0.00 RPM	79.63 RPM
SRP007412_heart	0.00 RPM	50.00 RPM
SRP007412_kidney	0.04 RPM	108.74 RPM
SRP007412_liver	0.00 RPM	108.11 RPM
SRP007412_testis	0.05 RPM	158.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_990 was not detected

EST

No EST(s) were mapped for retro_mmus_990 retrocopy.

TSS

No TSS is located nearby retro_mmus_990 retrocopy 5' end.

Lab

retro_mmus_990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_990 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011878	1 retrocopy	retro_cfam_2150,
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus	ENSCPOG00000010449	1 retrocopy	retro_cpor_331,
Homo sapiens	ENSG00000082153	2 retrocopies	retro_hsap_2832, retro_hsap_2881,
Gorilla gorilla	ENSGGOG00000016296	1 retrocopy	retro_ggor_1997,
Mustela putorius furo	ENSMPUG00000012344	1 retrocopy	retro_mputfur_1174,
Mus musculus	ENSMUSG00000051223	3 retrocopies	retro_mmus_2499, retro_mmus_751, retro_mmus_990 ,
Nomascus leucogenys	ENSNLEG00000006929	1 retrocopy	retro_nleu_621,
Pan troglodytes	ENSPTRG00000012791	1 retrocopy	retro_ptro_1949,