RetrogeneDB ID: retro_mmus_843

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:4782169..4783117(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091269
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tuba1c
• Ensembl ID: ENSMUSG00000043091
• Aliases: Tuba1c, M[a]6, Tuba6
• Description: tubulin, alpha 1C [Source:MGI Symbol;Acc:MGI:1095409]

Sequence

>retro_mmus_843
ATGCGTGAGTGCATCTCCATCCACTTTGGCCAGGCTGGTGTCCAGATCAGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGCCTGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCA
GTGAGACAGGAGCTGGCAAGCATGTGCCCCGGGCAGTGTTCGTAGACCTGGAACCCACAGTCATCGATGAAGTTCGCACT
GGCACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAGGATGCTGCCAATAACTATGCCCGTGGCCA
CTACACCATTGGCAAGGAGATCATTGACCTTGTCCTGGACAGGATTCGCAAGCTGGCTGACCAGTGCACAGGTCTCCAGG
GCTTCTTGGTTTTCCACAGCTTTGGCGGGGGAACTGGCTCTGGCTTCACCTCCCTGCTGATGGAGCAGCTCTCTGTGGAT
TACGGAAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTTTCCACTGCTGTGGTTGAGCCCTACAATTC
CATCCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTC
GTAGAAACCTCGACATTGAGTGCCCAACCTACACCAACCTTAACGGCCTTATTAGCCAGATTGTGTCTTCCATCACTGCT
TCCCTCAGATTTGATGGGGCCCTGAATGTTGATCTGACAGAATTCCAGACCAACCTGGTACCCTACCCTCGCATCCACTT
CCCTCTGGCCACTTATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCACGAGCAGCTTATAGTAGCAGAGATCACCAATG
CCTGCTTTGAGCCAGCCAACCAGTTGGTAAAATGTGACCCTCCCCATTGTACATGGCTTGCTGCCTGC

Alignment

ORF - retro_mmus_843 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.89 %
• Parental protein coverage: 70.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIH.GQAGVQI.NACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
Retrocopy MRECISIHFGQAGVQISNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSGFTSLLME.LSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FGGGTGSGFTSLLMEQLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DICRRNLDIE.PTYTNLN.LISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
Retrocopy DICRRNLDIECPTYTNLNGLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  AYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACC
          AYHEQL.VAEITNACFEPANQ.VKCDP.H....A.C
Retrocopy AYHEQLIVAEITNACFEPANQLVKCDPPHCTWLAAC

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	0.23 RPM	1.31 RPM
SRP007412_cerebellum	0.04 RPM	1.65 RPM
SRP007412_heart	0.06 RPM	10.99 RPM
SRP007412_kidney	0.15 RPM	13.59 RPM
SRP007412_liver	0.30 RPM	28.37 RPM
SRP007412_testis	0.91 RPM	29.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_843 was not detected

EST

No EST(s) were mapped for retro_mmus_843 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_23393	233 libraries	374 libraries	388 libraries	67 libraries	10 libraries
TSS #2	TSS_23394	539 libraries	337 libraries	187 libraries	9 libraries	0 libraries

The graphical summary, for retro_mmus_843 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
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,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,