RetrogeneDB ID:

retro_hsap_4034

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:30189479..30189793(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000253346
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GTF2A2
Ensembl ID:ENSG00000140307
Aliases:GTF2A2, HsT18745, TF2A2, TFIIA
Description:general transcription factor IIA, 2, 12kDa [Source:HGNC Symbol;Acc:4647]


Retrocopy-Parental alignment summary:






>retro_hsap_4034
ATGGCATATCAGTTATACAGAAATACCGCTTTGGGAAACAGTCTTCAGGTGAGCCTAGATGAGCTCATACAGTCTCAACA
GACCACCTACAAGTTCTACTTCAGTTTGATAAGGCTATAAATTCAGCATTGGCTCAGAGGGTTAGGAACAGAGTCAATTT
CAGGAGCTTTCTAAATATGTACAGATTCTGTGATAATCTGTGGACTTTCGTATTGAATGATGTTGAATTCAGAGAAGTGA
CAAAATTTATTAAAGTGGATGAAGCAAAAATAGTAGACTGTGATGGTAAAAATACTGGCTCCAATACTACAGAA

ORF - retro_hsap_4034 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAYQLYRNTTLGNSLQESLDELIQSQQIT-PQLALQVLLQFDKAINAALAQRVRNRVNFRGSLNTYRFCD
MAYQLYRNT.LGNSLQ.SLDELIQSQQ.T..Q..LQ.......A.......RV....NFR..LN.YRFCD
RetrocopyMAYQLYRNTALGNSLQVSLDELIQSQQTT<LQVLLQFDKAINSALAQRVRNRV----NFRSFLNMYRFCD
ParentalNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE
N.WTFVLNDVEFREVT..IKVD..KIV.CDGKNTGSNTTE
RetrocopyNLWTFVLNDVEFREVTKFIKVDEAKIVDCDGKNTGSNTTE

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 .00 RPM 20 .85 RPM
bodymap2_adrenal 0 .00 RPM 33 .28 RPM
bodymap2_brain 0 .00 RPM 22 .57 RPM
bodymap2_breast 0 .00 RPM 27 .74 RPM
bodymap2_colon 0 .00 RPM 37 .05 RPM
bodymap2_heart 0 .00 RPM 25 .96 RPM
bodymap2_kidney 0 .00 RPM 38 .78 RPM
bodymap2_liver 0 .00 RPM 19 .20 RPM
bodymap2_lung 0 .00 RPM 22 .29 RPM
bodymap2_lymph_node 0 .00 RPM 23 .68 RPM
bodymap2_ovary 0 .00 RPM 35 .20 RPM
bodymap2_prostate 0 .00 RPM 37 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 14 .91 RPM
bodymap2_testis 0 .02 RPM 121 .36 RPM
bodymap2_thyroid 0 .00 RPM 36 .61 RPM
bodymap2_white_blood_cells 0 .00 RPM 32 .54 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4034 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4034 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4034 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4034 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4034 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2734
Parental genes homology:
Parental genes homology involve 16 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000102981 retrocopy
retro_btau_1649,
Canis familiaris ENSCAFG000000166652 retrocopies
retro_cfam_786, retro_cfam_912,
Cavia porcellus ENSCPOG000000008161 retrocopy
retro_cpor_525,
Dipodomys ordii ENSDORG000000078673 retrocopies
retro_dord_377, retro_dord_385, retro_dord_695,
Homo sapiens ENSG00000140307 1 retrocopy
retro_hsap_4034 ,
Macaca mulatta ENSMMUG000000184281 retrocopy
retro_mmul_2303,
Monodelphis domestica ENSMODG000000116361 retrocopy
retro_mdom_1563,
Otolemur garnettii ENSOGAG000000070611 retrocopy
retro_ogar_1752,
Ochotona princeps ENSOPRG000000128411 retrocopy
retro_opri_908,
Pan troglodytes ENSPTRG000000071291 retrocopy
retro_ptro_2734,
Rattus norvegicus ENSRNOG000000110622 retrocopies
retro_rnor_1021, retro_rnor_1141,
Sorex araneus ENSSARG000000122282 retrocopies
retro_sara_607, retro_sara_734,
Sus scrofa ENSSSCG000000045833 retrocopies
retro_sscr_545, retro_sscr_934, retro_sscr_935,
Ictidomys tridecemlineatus ENSSTOG000000040103 retrocopies
retro_itri_1631, retro_itri_440, retro_itri_925,
Tupaia belangeri ENSTBEG000000010539 retrocopies
retro_tbel_1162, retro_tbel_1207, retro_tbel_123, retro_tbel_1394, retro_tbel_1439, retro_tbel_257, retro_tbel_2655, retro_tbel_2737, retro_tbel_513,
Xenopus tropicalis ENSXETG000000220021 retrocopy
retro_xtro_18,

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 ) Legend:


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 .00 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 .00 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 .00 RPM

Indel association:

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





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