RetrogeneDB ID: retro_mmus_55

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:89146746..89147247(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094790
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ptma
• Ensembl ID: ENSMUSG00000026238
• Aliases: Ptma, Thym
• Description: prothymosin alpha [Source:MGI Symbol;Acc:MGI:97803]

Sequence

>retro_mmus_55
CCCACTGGCTGCTCCGAAAAGCCATCTTTGCATTGTTCCCGGGTTGTGCTCTGCGCTCGCTGCAGCCACCTTTGCTGCCC
ACCGCCTCCTCCAGCGGAGTCCTGCAGCTCTCTCGCCAGAGTCCTCGAACTCGACTTTAATTCCCTCACTCGCGGTATTG
GACCACCGGCGTGCCCCTCCATGTTAGACGCGGACACCAGCTCCAAGATCACCACCAAGGTCTTGAAGGAGAAGAAGGAA
GTTGTGGAGGAGGCAGAGAATGGAAGAGATGTACCTGCCAATGGGAATGCTCAAAATAAGGAAAATGGGGAGCAGGAGGC
TGACAATGAGGTAGATGAAGAAGAGGAAGAAGGTGGAGAGGAAGAGGAGGAGGAGGAGGAGGAGGAAGGTGACGATGAGG
AAGAGGATGGAGATGAAGATGTGGAAGCTGAGGCTCCTACGGGCAAGCAGGTGGCTGAAGATGTGGACACCAAGAAGAAG
AAGACCGAGAAGGATGACTAG

Alignment

ORF - retro_mmus_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 88.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DTSSEITTKDLKEKKEVVEEAENGRDAPANGNAQNEENGEQEADNEVDEEEEEGGEEEEEEEE--GDGEE
          DTSS.ITTK.LKEKKEVVEEAENGRD.PANGNAQN.ENGEQEADNEVDEEEEEGGEEEEEEEE..GD.EE
Retrocopy DTSSKITTKVLKEKKEVVEEAENGRDVPANGNAQNKENGEQEADNEVDEEEEEGGEEEEEEEEEEGDDEE

Parental  EDGDEDEEAEAPTGKRVAEDDEDDDVDTKK
          EDGDED.EAEAPTGK.VAED.......T.K
Retrocopy EDGDEDVEAEAPTGKQVAEDVDTKKKKTEK

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	66.05 RPM
SRP007412_cerebellum	0.00 RPM	120.54 RPM
SRP007412_heart	0.00 RPM	97.94 RPM
SRP007412_kidney	0.08 RPM	233.71 RPM
SRP007412_liver	0.00 RPM	95.06 RPM
SRP007412_testis	0.09 RPM	65.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_55 was not detected

EST

No EST(s) were mapped for retro_mmus_55 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_145192	96 libraries	100 libraries	667 libraries	186 libraries	23 libraries

The graphical summary, for retro_mmus_55 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_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_55 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002549	2 retrocopies	retro_btau_1034, retro_btau_143,
Canis familiaris	ENSCAFG00000032596	4 retrocopies	retro_cfam_113, retro_cfam_1570, retro_cfam_282, retro_cfam_78,
Callithrix jacchus	ENSCJAG00000013611	9 retrocopies	retro_cjac_1484, retro_cjac_1976, retro_cjac_2318, retro_cjac_2507, retro_cjac_2611, retro_cjac_3035, retro_cjac_3151, retro_cjac_421, retro_cjac_647,
Felis catus	ENSFCAG00000004780	1 retrocopy	retro_fcat_1682,
Homo sapiens	ENSG00000187514	6 retrocopies	retro_hsap_1863, retro_hsap_2690, retro_hsap_3447, retro_hsap_4198, retro_hsap_4288, retro_hsap_4787,
Gorilla gorilla	ENSGGOG00000009874	4 retrocopies	retro_ggor_1551, retro_ggor_2149, retro_ggor_2981, retro_ggor_952,
Myotis lucifugus	ENSMLUG00000002628	2 retrocopies	retro_mluc_131, retro_mluc_26,
Macaca mulatta	ENSMMUG00000012140	1 retrocopy	retro_mmul_196,
Mus musculus	ENSMUSG00000026238	4 retrocopies	retro_mmus_3135, retro_mmus_3136, retro_mmus_414, retro_mmus_55 ,
Nomascus leucogenys	ENSNLEG00000014135	2 retrocopies	retro_nleu_30, retro_nleu_96,
Rattus norvegicus	ENSRNOG00000018584	1 retrocopy	retro_rnor_69,
Sus scrofa	ENSSSCG00000023690	1 retrocopy	retro_sscr_895,