RetrogeneDB ID: retro_mmus_1562

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:30177607..30178788(+)
• Located in intron of: ENSMUSG00000044477

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tuba1b
• Ensembl ID: ENSMUSG00000023004
• Aliases: Tuba1b, Tuba2
• Description: tubulin, alpha 1B [Source:MGI Symbol;Acc:MGI:107804]

Sequence

>retro_mmus_1562
GACAAGACCATTGGACGAAGAGAGGACTCCTTCATCACCTTCCTCAGTGAGACGGGCACTGGCAAGCATGTGCCTTGGGC
AGTTTTTGTTGCCCTGGAAGCCACAGTTATTGATGAAGTTCACACTAGTCTCTACCACCAGCTCTTCCACCCTAAGCAGC
TCATCACAGGCCAAGAGGATGCTGCCAGTAAATATGCCCGCGGCCACTACACCACTGCAAGGAGCTCATTGGCCTTGTCT
TGGACAGAATTTGCAAACTGGCTAATCATTGCATAGGTCTTTGGGGCTTCTTGGTTTCCTACAGCTTTGGCAAGGGAACT
GGCTCTGGAATGGAGAGGGTCTCTGTTGATTACCAAAAGAAATCCGAGCTGGAGCTCTCCATTAACCTGTCCCCTAGGTT
TCCACTGCTATGATTGAGCTCTACACCTCCATGCTCATCACCCACACCACCTTGGAGTTCTCTGATTGTGCCTTCATGAT
AGACAGTGAAGTCATCTATAACACGTCTAGAAACCTCAATACTGAGTGCCCGACTTAGACTAACCTTTATCGCATTATTA
GCCTGATTAGTGTCTTCCAACACTGCTTCCCTCAGCTTTGATGGAGCCCTGAATGTTGATCTGACAGAATTCCAGACCAG
CCTGGTGCTCTACCCTCACATCCACTTCCCTCTCGCCACTTATGCTCCTGTCATCTCTGCTGAGAAAGCCTACCAGGAGC
AGCTTTCTATAGAAAAGATTACTAGTGCCTGCTTTGAGCCAGCCAACCAGAAGGTGAAATGTGATTCTTGTCATGGTAAA
TACATGGCTTGCTGCCTATTGTACCACAGTGGTATGATTCCCAAAGATATCCATGCTGCTATTGCCACCACCAAGACCAG
GTGCAGCATCCAGCTTGTGGACTGGTACCCCACTGGCTTCAAGGTTGGCATTAATTACCAGCCTCACTGTGGTCCCTGGA
GCAACCTGGCCAAGGTCCAGAGAGCTGTGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCCTGTAGAC
CACAAGTTTGATCTGTTGCATGCCAAGCGTGCCTTTGTGCACTGGTGTGTGGGTGAGGACATGGCTGCCCTAGAGAAGGG
TTATGAGGAGGTTGGTATGGGTTCTGTTGAAGCTGAGGGTGAGGAGGAGGACAGGGATACT

Alignment

ORF - retro_mmus_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.56 %
• Parental protein coverage: 88.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHY
          DKTIG...DSF.TF.SETG.GKHVP.AVFV.LE.TVIDEV.T..Y.QLFHP.QLITG.EDAA..YARGHY
Retrocopy DKTIGRREDSFITFLSETGTGKHVPWAVFVALEATVIDEVHTSLYHQLFHPKQLITGQEDAASKYARGHY

Parental  TIG-KEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIY-PAPQ
          T...KE.I.LVLDRI.KLA..C.GL.GFLV..S...G.G...T...MER.SVDY.KKS.LE.SI..P.P.
Retrocopy TTA<KELIGLVLDRICKLANHCIGLWGFLV--SYSFGKG---TGSGMERVSVDYQKKSELELSIN<PVP*

Parental  VSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQI-VSSITASLRFD
          VSTA..E.Y.S.L.THTTLE.SDCAFM.D.E.IY...R.NL..E.PT.TNL.R.IS.I.VSS.TASL.FD
Retrocopy VSTAMIELYTSMLITHTTLEFSDCAFMIDSEVIYNTSR-NLNTECPT*TNLYRIISLI>VSSNTASLSFD

Parental  GALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMAC
          GALNVDLTEFQT.LV.YP.IHFPLATYAPVISAEKAY.EQLS...IT.ACFEPANQ.VKCD..HGKYMAC
Retrocopy GALNVDLTEFQTSLVLYPHIHFPLATYAPVISAEKAYQEQLSIEKITSACFEPANQKVKCDSCHGKYMAC

Parental  CLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIA
          CLLY.....PKD..AAIAT.KT..SIQ.VDW.PTGFKVGINYQ.P...P...LAKVQRAVCMLSNTTAIA
Retrocopy CLLYHSGMIPKDIHAAIATTKTRCSIQLVDWYPTGFKVGINYQ-PHCGPWSNLAKVQRAVCMLSNTTAIA

Parental  EAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS
          EAWA..DHKFDL..AKRAFVHW.VGE.M...E.......M...E...EE...D.
Retrocopy EAWAPVDHKFDLLHAKRAFVHWCVGEDMAALEKGYEEVGMGSVEAEGEEEDRDT

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	0.14 RPM	77.45 RPM
SRP007412_cerebellum	0.09 RPM	63.92 RPM
SRP007412_heart	0.03 RPM	36.14 RPM
SRP007412_kidney	0.10 RPM	16.90 RPM
SRP007412_liver	0.08 RPM	8.82 RPM
SRP007412_testis	0.46 RPM	8.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1562 was not detected

EST

No EST(s) were mapped for retro_mmus_1562 retrocopy.

TSS

No TSS is located nearby retro_mmus_1562 retrocopy 5' end.

Lab

retro_mmus_1562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562 , retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,