RetrogeneDB ID: retro_mmus_3136

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:55552812..55553098(+)
• Located in intron of: None

Retrocopy information

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

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_3136
ATGCCAGATAGGGCAGTAGACACCGGCTCAGAGATCACTATCGAGGACTTAAAGGAGGAGAAAGAAGTTGTGGAGGAGGC
AGAGAATGGAAGAGAAGAACCTGCCAATGGGAATGGTGATTAGGAAAATGGGGAGCAGGATGCTGACAATGAGGTAGATG
TAGAAGAGGAAGAAGGTGGTGAGGAAGTTGAGAAGAAAAATGAGGAAACTGAGGCTTGACGGGAAGCAGGTAGCTAAGGA
TGATGAGGATGAGGATGTTGACAGGAAGAGGTAGAAGACTGATGAG

Alignment

ORF - retro_mmus_3136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.86 %
• Parental protein coverage: 85.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDAAVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNAQNEENGEQEADNEVDEEEEEGGEE-EEEEEE
          M.D.AVDT.SEIT..DLKE.KEVVEEAENGR..PANGN....ENGEQ.ADNEVD.EEEEGGEE.E...EE
Retrocopy MPDRAVDTGSEITIEDLKEEKEVVEEAENGREEPANGNG-D*ENGEQDADNEVDVEEEEGGEEVEKKNEE

Parental  GDGEEEDGD-EDEEAEAPTGKRVAEDD
          .....E.G...D.E.E....KR...D.
Retrocopy TEA*REAGS>KDDEDEDVDRKR*KTDE

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

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3136 was not detected

EST

No EST(s) were mapped for retro_mmus_3136 retrocopy.

TSS

No TSS is located nearby retro_mmus_3136 retrocopy 5' end.

Lab

retro_mmus_3136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3136 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,