RetrogeneDB ID:

retro_hsap_4198

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:99672357..99672537(+)
Located in intron of:ENSG00000196312
Retrocopy
information
Ensembl ID:ENSG00000269907
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTMA
Ensembl ID:ENSG00000187514
Aliases:PTMA, TMSA
Description:prothymosin, alpha [Source:HGNC Symbol;Acc:9623]


Retrocopy-Parental alignment summary:






>retro_hsap_4198
ATGTCAGATGCAGCTGTAGACACCAGCTCTGAAATCATTGCCAAGGACTTAAAGGAGAAGAAGGAAGTTGTGAAAGAGGC
GGAAAATGGAAGAGACGCCCCTGCTAACGGGAATGCTAATGAGGAAAATGGGGAGCAGGAGGCTGACAAGGAGGTAGATG
AAGAAGGGGAAGAAAGTGGG

ORF - retro_hsap_4198 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90. %
Parental protein coverage: 56.07 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDAAVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNANEENGEQEADNEVDEEEEEGG
MSDAAVDTSSEI..KDLKEKKEVV.EAENGRDAPANGNANEENGEQEAD.EVDEE.EE.G
RetrocopyMSDAAVDTSSEIIAKDLKEKKEVVKEAENGRDAPANGNANEENGEQEADKEVDEEGEESG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .02 RPM 521 .70 RPM
bodymap2_adrenal 0 .04 RPM 745 .89 RPM
bodymap2_brain 0 .02 RPM 198 .00 RPM
bodymap2_breast 0 .00 RPM 297 .01 RPM
bodymap2_colon 0 .33 RPM 618 .53 RPM
bodymap2_heart 0 .02 RPM 69 .84 RPM
bodymap2_kidney 0 .06 RPM 297 .74 RPM
bodymap2_liver 0 .00 RPM 142 .33 RPM
bodymap2_lung 0 .00 RPM 665 .07 RPM
bodymap2_lymph_node 0 .15 RPM 567 .65 RPM
bodymap2_ovary 0 .04 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 - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4198 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4198 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4198 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4198 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4198 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000025492 retrocopies
retro_btau_1034, retro_btau_143,
Canis familiaris ENSCAFG000000325964 retrocopies
retro_cfam_113, retro_cfam_1570, retro_cfam_282, retro_cfam_78,
Callithrix jacchus ENSCJAG000000136119 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 ENSFCAG000000047801 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 ENSGGOG000000098744 retrocopies
retro_ggor_1551, retro_ggor_2149, retro_ggor_2981, retro_ggor_952,
Myotis lucifugus ENSMLUG000000026282 retrocopies
retro_mluc_131, retro_mluc_26,
Macaca mulatta ENSMMUG000000121401 retrocopy
retro_mmul_196,
Mus musculus ENSMUSG000000262384 retrocopies
retro_mmus_3135, retro_mmus_3136, retro_mmus_414, retro_mmus_55,
Nomascus leucogenys ENSNLEG000000141352 retrocopies
retro_nleu_30, retro_nleu_96,
Rattus norvegicus ENSRNOG000000185841 retrocopy
retro_rnor_69,
Sus scrofa ENSSSCG000000236901 retrocopy
retro_sscr_895,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.33 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .21 RPM
CEU_NA12751 0 .22 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .14 RPM
CEU_NA12873 0 .29 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .11 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .11 RPM
GBR_HG00099 0 .15 RPM
GBR_HG00111 0 .13 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .19 RPM
GBR_HG00131 0 .23 RPM
GBR_HG00133 0 .27 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .25 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .19 RPM
TSI_NA20518 0 .22 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .17 RPM
TSI_NA20765 0 .33 RPM
TSI_NA20771 0 .17 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .24 RPM
YRI_NA18907 0 .28 RPM
YRI_NA18916 0 .19 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .22 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .30 RPM

Indel association:

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



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