RetrogeneDB ID: retro_mmus_329

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:65028079..65028550(+)
• Located in intron of: ENSMUSG00000025955

Retrocopy information

• Ensembl ID: ENSMUSG00000090042
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tma16
• Ensembl ID: ENSMUSG00000025591
• Aliases: Tma16, 1810029B16Rik
• Description: translation machinery associated 16 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913532]

Sequence

>retro_mmus_329
ATGCCTAAAGGACTGAAAGGAAAAATGGTAGGATGGGGAAAAAACGTCATCGATCCGTACAGTAGAAAAGCAGCTCAGAT
TACAAGAGAGTCTCACAAACAAGACAAGAAGCAAAGATTGGAGACTGAGAGGGCCTTGCGTCTCAACCTTATTGGTGACA
AACTTCAGTGGTTTCACAGTTATCTGGATACAAAAAGACCCGATATATTCAAAGAAAGATGCCTGTGAATTAATTGAAAG
GTACTTGGATCAGTTCAGCAGTGAGCTGGAGCAGATTGAATTACACAACAGCATCAAGGACAGGCAGGGAAGCGGCACCC
TTCCCGGGAGGCCGTCATCAAGCAGACCTCGAAGCGGGAGCAGCAGCAGTAAGAAGGCTATGGCTTTGAGATCCCAGACA
TTTTAGACTCTAATACTTGGCAGACTTTCCGGGAATGGGATTTTGATCTGAAGAAATTGCCAAACATCAAA

Alignment

ORF - retro_mmus_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 71.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKGLKGKMVGREKKVIHPYSRKAAQITRESHKQDKKERLKTEKALRLNLIGDKLQWFHSHLDMKKTR-Y
          MPKGLKGKMVG..K.VI.PYSRKAAQITRESHKQDKK.RL.TE.ALRLNLIGDKLQWFHS.LD.K....Y
Retrocopy MPKGLKGKMVGWGKNVIDPYSRKAAQITRESHKQDKKQRLETERALRLNLIGDKLQWFHSYLDTKRPD>Y

Parental  SKKDACELVERYLDRFSSELEQIELQNSIKDRQ-GRRHHSREAVIKQTLERERQQYEGYGFEIPDILDSN
          SKKDACEL.ERYLD.FSSELEQIEL.NSIKDRQ.G.RH.SREAVIKQT..RE.QQ.EGYGFEIPDILDSN
Retrocopy SKKDACELIERYLDQFSSELEQIELHNSIKDRQ<GKRHPSREAVIKQTSKREQQQ*EGYGFEIPDILDSN

Parental  TLQTFREWDFDLKKLPNIK
          T.QTFREWDFDLKKLPNIK
Retrocopy TWQTFREWDFDLKKLPNIK

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	0.00 RPM	7.55 RPM
SRP007412_cerebellum	0.00 RPM	5.12 RPM
SRP007412_heart	0.00 RPM	4.11 RPM
SRP007412_kidney	0.00 RPM	4.25 RPM
SRP007412_liver	0.00 RPM	3.00 RPM
SRP007412_testis	0.96 RPM	4.89 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_329 was not detected

EST

No EST(s) were mapped for retro_mmus_329 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_75612	838 libraries	112 libraries	96 libraries	18 libraries	8 libraries

The graphical summary, for retro_mmus_329 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_329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_329 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006702	2 retrocopies	retro_chof_1717, retro_chof_2104,
Cavia porcellus	ENSCPOG00000001119	1 retrocopy	retro_cpor_444,
Dasypus novemcinctus	ENSDNOG00000006820	1 retrocopy	retro_dnov_489,
Echinops telfairi	ENSETEG00000009734	1 retrocopy	retro_etel_1378,
Homo sapiens	ENSG00000198498	2 retrocopies	retro_hsap_378, retro_hsap_879,
Gorilla gorilla	ENSGGOG00000025324	1 retrocopy	retro_ggor_713,
Macropus eugenii	ENSMEUG00000001134	3 retrocopies	retro_meug_1830, retro_meug_1895, retro_meug_396,
Macaca mulatta	ENSMMUG00000004482	2 retrocopies	retro_mmul_184, retro_mmul_276,
Monodelphis domestica	ENSMODG00000002170	1 retrocopy	retro_mdom_881,
Mus musculus	ENSMUSG00000025591	2 retrocopies	retro_mmus_299, retro_mmus_329 ,
Nomascus leucogenys	ENSNLEG00000006466	2 retrocopies	retro_nleu_1631, retro_nleu_2590,
Otolemur garnettii	ENSOGAG00000001860	1 retrocopy	retro_ogar_3308,
Pongo abelii	ENSPPYG00000015167	1 retrocopy	retro_pabe_329,
Pan troglodytes	ENSPTRG00000023618	2 retrocopies	retro_ptro_294, retro_ptro_3035,
Rattus norvegicus	ENSRNOG00000014188	3 retrocopies	retro_rnor_2309, retro_rnor_845, retro_rnor_846,
Sorex araneus	ENSSARG00000003780	1 retrocopy	retro_sara_168,
Ictidomys tridecemlineatus	ENSSTOG00000024763	3 retrocopies	retro_itri_1085, retro_itri_1372, retro_itri_715,
Tupaia belangeri	ENSTBEG00000017224	7 retrocopies	retro_tbel_168, retro_tbel_2196, retro_tbel_2345, retro_tbel_2474, retro_tbel_3235, retro_tbel_3987, retro_tbel_4393,
Tarsius syrichta	ENSTSYG00000008284	1 retrocopy	retro_tsyr_686,