RetrogeneDB ID:

retro_hsap_4158

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:37885889..37886384(+)
Located in intron of:ENSG00000255872
Retrocopy
information
Ensembl ID:ENSG00000213839
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMX2
Ensembl ID:ENSG00000213593
Aliases:TMX2, PDIA12, PIG26, TXNDC14
Description:thioredoxin-related transmembrane protein 2 [Source:HGNC Symbol;Acc:30739]


Retrocopy-Parental alignment summary:






>retro_hsap_4158
TATATGGGCCCTGAGTATATCAAGTACTTCAATGATAAAACCATTGATGAGGAACTAGAACGGGACAACAGGGTCACTTG
GATTGTGGAGTTCTTTGCCAATTGGTCTAATGACTGCCAATCATTTGCCCCTATCTATGCTGACCTCTCCCTTAAGTACA
ACTGTACAGGGCTAAATTTTGGGACGGTGGATGCTGGACGCTATACTGATGTTAGTACGCGGTACAAAGTGAGCACATCA
CCCCTCACCAATCAACTCCCTACCCTGATCCTGTTCCAAGGTGGCAAGAAGGTAATGCGGCAGCCACAGACTGACAAGAA
AGGACGGGCTGTCTCATGGACCTTCTCTGAGGAGAATGTGATCCGAGAATTTAACTTAAATGAGCTATACCAGCGGGCCA
AGAAGCTATCAAAGGCTGGAGACAATATCCCTGAGGAGCAGCCTGTGGCTTCAACCCCCACCACAGTGTCAGATGGGGAA
AGCAAGAAGGATAAA

ORF - retro_hsap_4158 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.55 %
Parental protein coverage: 63.95 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYMGPEYIKYFNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFGKVDVGRYTD
YMGPEYIKYFNDKTIDEELERD.RVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFG.VD.GRYTD
RetrocopyYMGPEYIKYFNDKTIDEELERDNRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCTGLNFGTVDAGRYTD
ParentalVSTRYKVSTSPLTKQLPTLILFQGGKEAMRRPQIDKKGRAVSWTFSEENVIREFNLNELYQRAKKLSKAG
VSTRYKVSTSPLT.QLPTLILFQGGK..MR.PQ.DKKGRAVSWTFSEENVIREFNLNELYQRAKKLSKAG
RetrocopyVSTRYKVSTSPLTNQLPTLILFQGGKKVMRQPQTDKKGRAVSWTFSEENVIREFNLNELYQRAKKLSKAG
ParentalDNIPEEQPVASTPTTVSDGENKKDK
DNIPEEQPVASTPTTVSDGE.KKDK
RetrocopyDNIPEEQPVASTPTTVSDGESKKDK

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 5 .01 RPM 29 .46 RPM
bodymap2_adrenal 3 .81 RPM 62 .62 RPM
bodymap2_brain 2 .95 RPM 71 .75 RPM
bodymap2_breast 8 .11 RPM 53 .62 RPM
bodymap2_colon 2 .65 RPM 39 .75 RPM
bodymap2_heart 2 .07 RPM 48 .29 RPM
bodymap2_kidney 3 .39 RPM 101 .89 RPM
bodymap2_liver 0 .66 RPM 78 .09 RPM
bodymap2_lung 2 .00 RPM 52 .11 RPM
bodymap2_lymph_node 4 .64 RPM 54 .99 RPM
bodymap2_ovary 4 .38 RPM 76 .36 RPM
bodymap2_prostate 1 .59 RPM 60 .64 RPM
bodymap2_skeletal_muscle 1 .25 RPM 26 .45 RPM
bodymap2_testis 3 .41 RPM 43 .95 RPM
bodymap2_thyroid 2 .50 RPM 95 .04 RPM
bodymap2_white_blood_cells 5 .65 RPM 46 .60 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4158 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4158 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4158 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4158 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4158 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2827
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000354261 retrocopy
retro_cjac_3263,
Homo sapiens ENSG00000213593 1 retrocopy
retro_hsap_4158 ,
Monodelphis domestica ENSMODG000000201121 retrocopy
retro_mdom_924,
Mus musculus ENSMUSG000000500431 retrocopy
retro_mmus_154,
Pan troglodytes ENSPTRG000000337021 retrocopy
retro_ptro_2827,

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 = 3.55 RPM Legend:


Library Retrogene expression
CEU_NA11831 2 .44 RPM
CEU_NA11843 0 .77 RPM
CEU_NA11930 3 .39 RPM
CEU_NA12004 2 .01 RPM
CEU_NA12400 1 .93 RPM
CEU_NA12751 1 .87 RPM
CEU_NA12760 1 .71 RPM
CEU_NA12827 1 .79 RPM
CEU_NA12872 2 .80 RPM
CEU_NA12873 2 .46 RPM
FIN_HG00183 1 .67 RPM
FIN_HG00277 2 .48 RPM
FIN_HG00315 1 .96 RPM
FIN_HG00321 2 .75 RPM
FIN_HG00328 1 .87 RPM
FIN_HG00338 1 .92 RPM
FIN_HG00349 1 .54 RPM
FIN_HG00375 2 .15 RPM
FIN_HG00377 1 .51 RPM
FIN_HG00378 2 .78 RPM
GBR_HG00099 3 .52 RPM
GBR_HG00111 1 .42 RPM
GBR_HG00114 2 .08 RPM
GBR_HG00119 2 .32 RPM
GBR_HG00131 2 .99 RPM
GBR_HG00133 2 .48 RPM
GBR_HG00134 2 .31 RPM
GBR_HG00137 1 .21 RPM
GBR_HG00142 2 .03 RPM
GBR_HG00143 2 .01 RPM
TSI_NA20512 1 .44 RPM
TSI_NA20513 2 .66 RPM
TSI_NA20518 2 .64 RPM
TSI_NA20532 3 .09 RPM
TSI_NA20538 2 .21 RPM
TSI_NA20756 2 .01 RPM
TSI_NA20765 3 .07 RPM
TSI_NA20771 2 .24 RPM
TSI_NA20786 2 .17 RPM
TSI_NA20798 1 .65 RPM
YRI_NA18870 3 .55 RPM
YRI_NA18907 1 .87 RPM
YRI_NA18916 2 .27 RPM
YRI_NA19093 2 .37 RPM
YRI_NA19099 2 .58 RPM
YRI_NA19114 3 .20 RPM
YRI_NA19118 1 .80 RPM
YRI_NA19213 2 .49 RPM
YRI_NA19214 2 .31 RPM
YRI_NA19223 2 .69 RPM

Indel association:

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



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