RetrogeneDB ID: retro_sscr_895

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:16909294..16909567(+)
• Located in intron of: ENSSSCG00000001080

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTMA
• Ensembl ID: ENSSSCG00000023690
• Aliases: None
• Description: prothymosin, alpha [Source:HGNC Symbol;Acc:9623]

Sequence

>retro_sscr_895
AAGGAGTTAAAGGAGAAGAAGGAAGTTGTTGAGGAGGTGAGCATGGAAGAGGTATAACTACGAAGGGGAAGGCTAAGGAG
GACAATGGGGTGCAGGAAGCTGTCACTGATGTAGAAGAAGGGGGGAGGGAGTGGAGGAGGAGGAAGAAGGTGATGGTGAA
GAAAAGGATGAAATGAAGATGAGGGGGCTGAGGCAGCTTTGGGTGGTGGGCAGCTGAAGGTGACAAGGGTGATGATGTTG
ACACCGAAGAACAAGAAGACCGATGAGGATGAC

Alignment

ORF - retro_sscr_895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KDLKEKKEVVEEA-ENGREAPANGNANEENGEQEADNEVDEEEEEGGEE-EEEEEEGDGEEEDG-DEDEE
          K.LKEKKEVVEE..E.GR.....G.A.E.NG.QEA...V....EEGG.E..EEEEEGDGEE.D...EDE.
Retrocopy KELKEKKEVVEEV<EHGRGITTKGKAKEDNGVQEAVTDV----EEGGRE<VEEEEEGDGEEKDE<NEDEG

Parental  AEAATGKR-AAEDDEDDDVDTKKQ-KTDEDD
          AEAA.G...AAE.D..DDVDT..Q.KTDEDD
Retrocopy AEAALGGG<AAEGDKGDDVDTEEQ>KTDEDD

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
SRP014902_placenta	0.00 RPM	109.10 RPM
SRP014902_testis	0.00 RPM	129.42 RPM
SRP018288_heart	0.03 RPM	45.26 RPM
SRP018288_kidney	0.00 RPM	178.10 RPM
SRP018288_liver	0.00 RPM	199.25 RPM
SRP018288_lung	0.00 RPM	169.74 RPM
SRP018856_adipose	0.00 RPM	775.85 RPM
SRP035408_brain	0.32 RPM	660.49 RPM
SRP035408_liver	0.09 RPM	873.45 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_895 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_895 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_895 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1570

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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 ,