RetrogeneDB ID:

retro_hsap_132

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:28065731..28065947(+)
Located in intron of:ENSG00000009780
Retrocopy
information
Ensembl ID:ENSG00000231344
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TXNDC17
Ensembl ID:ENSG00000129235
Aliases:TXNDC17, TRP14, TXNL5
Description:thioredoxin domain containing 17 [Source:HGNC Symbol;Acc:28218]


Retrocopy-Parental alignment summary:






>retro_hsap_132
ATGCTGAACCAGGGGCTGAAGCATGTTAGTGAAGGATGTGTGTTCGCCTACTGCCAAGTAGAAGAAAAGCCTTATTGGAA
AGATCCAAATAATGACTTCAGAAAAAACTTGGAAGTAACCACAGTGCCTACACTACTTAAATATGGAACACCTCAAAAAC
TGGTAGAATCTTAGTGTCTTCAGGCCAACCTCGTGGAAATGTTTTTCTCTAAGGAT

ORF - retro_hsap_132 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 58.54 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVVREGLKHISEGCVFIYCQVGEKPYWKDPNNDFRKNLKVTAVPTLLKYGTPQKLVESECLQANLVEMLFS
....GLKH.SEGCVF.YCQV.EKPYWKDPNNDFRKNL.VT.VPTLLKYGTPQKLVES.CLQANLVEM.FS
RetrocopyMLNQGLKHVSEGCVFAYCQVEEKPYWKDPNNDFRKNLEVTTVPTLLKYGTPQKLVES*CLQANLVEMFFS
ParentalED
.D
RetrocopyKD

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 7 .20 RPM
bodymap2_adrenal 0 .10 RPM 12 .16 RPM
bodymap2_brain 0 .12 RPM 9 .42 RPM
bodymap2_breast 0 .56 RPM 11 .85 RPM
bodymap2_colon 0 .00 RPM 12 .59 RPM
bodymap2_heart 0 .02 RPM 8 .75 RPM
bodymap2_kidney 0 .00 RPM 23 .95 RPM
bodymap2_liver 0 .04 RPM 26 .49 RPM
bodymap2_lung 0 .00 RPM 9 .62 RPM
bodymap2_lymph_node 0 .13 RPM 13 .72 RPM
bodymap2_ovary 0 .04 RPM 10 .39 RPM
bodymap2_prostate 0 .16 RPM 15 .83 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .53 RPM
bodymap2_testis 0 .02 RPM 16 .10 RPM
bodymap2_thyroid 0 .21 RPM 14 .46 RPM
bodymap2_white_blood_cells 0 .00 RPM 15 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_132 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_132 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_132 retrocopy 5' end.

Lab - click to see more details

retro_hsap_132 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_132 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_137
Gorilla gorilla retro_ggor_230
Pongo abelii retro_pabe_485
Macaca mulatta retro_mmul_365
Callithrix jacchus retro_cjac_2887
Parental genes homology:
Parental genes homology involve 27 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070384 retrocopies
retro_amel_1181, retro_amel_1267, retro_amel_148, retro_amel_344,
Callithrix jacchus ENSCJAG000000111504 retrocopies
retro_cjac_2775, retro_cjac_2877, retro_cjac_2887, retro_cjac_3048,
Cavia porcellus ENSCPOG000000028871 retrocopy
retro_cpor_116,
Equus caballus ENSECAG000000250061 retrocopy
retro_ecab_430,
Echinops telfairi ENSETEG000000019051 retrocopy
retro_etel_14,
Felis catus ENSFCAG000000241431 retrocopy
retro_fcat_1128,
Homo sapiens ENSG00000129235 2 retrocopies
retro_hsap_132 , retro_hsap_2218,
Gorilla gorilla ENSGGOG000000030552 retrocopies
retro_ggor_1750, retro_ggor_230,
Macropus eugenii ENSMEUG000000089461 retrocopy
retro_meug_1771,
Microcebus murinus ENSMICG000000066202 retrocopies
retro_mmur_1093, retro_mmur_766,
Macaca mulatta ENSMMUG000000037882 retrocopies
retro_mmul_365, retro_mmul_932,
Mustela putorius furoENSMPUG000000113382 retrocopies
retro_mputfur_518, retro_mputfur_564,
Mus musculus ENSMUSG000000208033 retrocopies
retro_mmus_2817, retro_mmus_2818, retro_mmus_488,
Nomascus leucogenys ENSNLEG000000092302 retrocopies
retro_nleu_2262, retro_nleu_2516,
Oryctolagus cuniculus ENSOCUG000000165571 retrocopy
retro_ocun_297,
Ochotona princeps ENSOPRG000000005092 retrocopies
retro_opri_575, retro_opri_8,
Procavia capensis ENSPCAG000000037491 retrocopy
retro_pcap_180,
Pongo abelii ENSPPYG000000078801 retrocopy
retro_pabe_485,
Pan troglodytes ENSPTRG000000086442 retrocopies
retro_ptro_137, retro_ptro_1683,
Pteropus vampyrus ENSPVAG000000023991 retrocopy
retro_pvam_1187,
Rattus norvegicus ENSRNOG000000140721 retrocopy
retro_rnor_1700,
Sorex araneus ENSSARG000000065011 retrocopy
retro_sara_20,
Ictidomys tridecemlineatus ENSSTOG000000219862 retrocopies
retro_itri_197, retro_itri_574,
Tupaia belangeri ENSTBEG000000005391 retrocopy
retro_tbel_3760,
Tarsius syrichta ENSTSYG000000109962 retrocopies
retro_tsyr_1058, retro_tsyr_982,
Tursiops truncatus ENSTTRG000000120721 retrocopy
retro_ttru_1252,
Vicugna pacos ENSVPAG000000015541 retrocopy
retro_vpac_501,

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 = 0.2 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .09 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .10 RPM

Indel association:

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



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