RetrogeneDB ID: retro_hsap_1863

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:74647716..74648015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTMA
• Ensembl ID: ENSG00000187514
• Aliases: PTMA, TMSA
• Description: prothymosin, alpha [Source:HGNC Symbol;Acc:9623]

Sequence

>retro_hsap_1863
ATGTCAGATGCAGCCATAGACACCAGCTCCGAGATCACCACCAAGGACTTAAAGGAGAAGAAGGAAGTTGTGGAGGAGGC
GGAAATGGAAGAGATGCCTCTGCTAATGGGAACACTAATGAGGAAAATTGGGAGCAGGAGGTTGACAATGAGGTAGATGA
AGAAGAGGAAGAAGGTGATGGTGAGGAAGAGGATGGAGATGAAGACGAGGAAGCTGAGTTTGCTATGGGCAAGTGAGTAG
CTGAAGATGATAAGGATGATGATGTCCATACCAAGAAGCAGAAGATTGATGAGGACAAC

Alignment

ORF - retro_hsap_1863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDAAVDTSSEITTKDLKEKKEVVEEAE-NGRDAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEEEG
          MSDAA.DTSSEITTKDLKEKKEVVEEAE.NGRDA.....AN....E.....EVD.E.....EEEEE....
Retrocopy MSDAAIDTSSEITTKDLKEKKEVVEEAE<NGRDA----SANGNTNEENWEQEVDNEVD---EEEEEGDGE

Parental  DEDGDEDEEAESATGKRAAEDDEDDDVDTKKQKTDEDD
          .EDGDEDEEAE.A.GK..AEDD.DDDV.TKKQK.DED.
Retrocopy EEDGDEDEEAEFAMGK*VAEDDKDDDVHTKKQKIDEDN

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
bodymap2_adipose	0.00 RPM	521.70 RPM
bodymap2_adrenal	0.02 RPM	745.89 RPM
bodymap2_brain	0.00 RPM	198.00 RPM
bodymap2_breast	0.00 RPM	297.01 RPM
bodymap2_colon	0.00 RPM	618.53 RPM
bodymap2_heart	0.00 RPM	69.84 RPM
bodymap2_kidney	0.00 RPM	297.74 RPM
bodymap2_liver	0.00 RPM	142.33 RPM
bodymap2_lung	0.00 RPM	665.07 RPM
bodymap2_lymph_node	0.00 RPM	567.65 RPM
bodymap2_ovary	0.06 RPM	481.42 RPM
bodymap2_prostate	0.00 RPM	527.14 RPM
bodymap2_skeletal_muscle	0.00 RPM	86.08 RPM
bodymap2_testis	0.00 RPM	324.27 RPM
bodymap2_thyroid	0.00 RPM	434.32 RPM
bodymap2_white_blood_cells	0.00 RPM	541.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1863 was not detected

EST

No EST(s) were mapped for retro_hsap_1863 retrocopy.

TSS

No TSS is located nearby retro_hsap_1863 retrocopy 5' end.

Lab

retro_hsap_1863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1863 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2149

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).