RetrogeneDB ID:

retro_hsap_736

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:121443046..121443280(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232823
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TXN
Ensembl ID:ENSG00000136810
Aliases:TXN, TRDX, TRX, TRX1
Description:thioredoxin [Source:HGNC Symbol;Acc:12435]


Retrocopy-Parental alignment summary:






>retro_hsap_736
ATGGTGAAGCAAATTGAGAGCAAGGTTGCTTTTCAGGAAGGCTTGGAGGCTGCAGGTGATAAATTTGTCATGGTTGACTT
CTCAGCCACGTGGTATGGGCCTTGCAAAAAGATCAAGCTTTTCTTTCATTCCCTCTCTGAAAAGTATTCCAACATGGTAT
TCTTTGAAGTACATGTGGCTGACTGTCAGGATGTTGCTTCAGAATGTGAAGTCAAATGCATGCCAACCTTCCAG

ORF - retro_hsap_736 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 74.29 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECE
MVKQIESK.AFQE.L.AAGDK.V.VDFSATW.GPCK.IK.FFHSLSEKYSN..F.EV.V.DCQDVASECE
RetrocopyMVKQIESKVAFQEGLEAAGDKFVMVDFSATWYGPCKKIKLFFHSLSEKYSNMVFFEVHVADCQDVASECE
ParentalVKCMPTFQ
VKCMPTFQ
RetrocopyVKCMPTFQ

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 71 .04 RPM
bodymap2_adrenal 0 .10 RPM 60 .38 RPM
bodymap2_brain 0 .00 RPM 54 .36 RPM
bodymap2_breast 0 .00 RPM 69 .94 RPM
bodymap2_colon 0 .00 RPM 110 .68 RPM
bodymap2_heart 0 .00 RPM 24 .28 RPM
bodymap2_kidney 0 .00 RPM 124 .19 RPM
bodymap2_liver 0 .00 RPM 86 .59 RPM
bodymap2_lung 0 .00 RPM 155 .57 RPM
bodymap2_lymph_node 0 .00 RPM 67 .10 RPM
bodymap2_ovary 0 .02 RPM 59 .91 RPM
bodymap2_prostate 0 .00 RPM 105 .74 RPM
bodymap2_skeletal_muscle 0 .00 RPM 13 .15 RPM
bodymap2_testis 0 .06 RPM 47 .28 RPM
bodymap2_thyroid 0 .00 RPM 57 .59 RPM
bodymap2_white_blood_cells 0 .00 RPM 58 .89 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_736 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_736 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_736 retrocopy 5' end.

Lab - click to see more details

retro_hsap_736 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_736 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_524
Gorilla gorilla retro_ggor_620
Parental genes homology:
Parental genes homology involve 22 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000130183 retrocopies
retro_acar_112, retro_acar_121, retro_acar_122,
Choloepus hoffmanni ENSCHOG0000001150610 retrocopies
retro_chof_1111, retro_chof_127, retro_chof_1557, retro_chof_1680, retro_chof_1696, retro_chof_240, retro_chof_2424, retro_chof_317, retro_chof_617, retro_chof_82,
Callithrix jacchus ENSCJAG000000173215 retrocopies
retro_cjac_1407, retro_cjac_2536, retro_cjac_2733, retro_cjac_3010, retro_cjac_69,
Cavia porcellus ENSCPOG000000153485 retrocopies
retro_cpor_1048, retro_cpor_49, retro_cpor_54, retro_cpor_55, retro_cpor_74,
Dasypus novemcinctus ENSDNOG0000001920520 retrocopies
retro_dnov_100, retro_dnov_1047, retro_dnov_1122, retro_dnov_1222, retro_dnov_1353, retro_dnov_1403, retro_dnov_1404, retro_dnov_1628, retro_dnov_1634, retro_dnov_1646, retro_dnov_1949, retro_dnov_1996, retro_dnov_2069, retro_dnov_2197, retro_dnov_2239, retro_dnov_290, retro_dnov_466, retro_dnov_593, retro_dnov_843, retro_dnov_852,
Echinops telfairi ENSETEG0000000306513 retrocopies
retro_etel_1173, retro_etel_1256, retro_etel_1672, retro_etel_1725, retro_etel_1807, retro_etel_1831, retro_etel_1932, retro_etel_1956, retro_etel_320, retro_etel_389, retro_etel_737, retro_etel_903, retro_etel_926,
Homo sapiens ENSG00000136810 7 retrocopies
retro_hsap_1713, retro_hsap_206, retro_hsap_2330, retro_hsap_3052, retro_hsap_3614, retro_hsap_405, retro_hsap_736 ,
Gorilla gorilla ENSGGOG000000069256 retrocopies
retro_ggor_1283, retro_ggor_1769, retro_ggor_2440, retro_ggor_35, retro_ggor_401, retro_ggor_620,
Loxodonta africana ENSLAFG000000128562 retrocopies
retro_lafr_372, retro_lafr_93,
Macropus eugenii ENSMEUG000000035158 retrocopies
retro_meug_1198, retro_meug_1204, retro_meug_1603, retro_meug_192, retro_meug_2170, retro_meug_2175, retro_meug_539, retro_meug_840,
Microcebus murinus ENSMICG000000021282 retrocopies
retro_mmur_118, retro_mmur_717,
Macaca mulatta ENSMMUG000000103221 retrocopy
retro_mmul_167,
Mus musculus ENSMUSG000000283672 retrocopies
retro_mmus_3063, retro_mmus_432,
Otolemur garnettii ENSOGAG000000091656 retrocopies
retro_ogar_1573, retro_ogar_2763, retro_ogar_3141, retro_ogar_3205, retro_ogar_727, retro_ogar_851,
Ochotona princeps ENSOPRG0000001380511 retrocopies
retro_opri_1132, retro_opri_1172, retro_opri_220, retro_opri_309, retro_opri_468, retro_opri_643, retro_opri_681, retro_opri_738, retro_opri_81, retro_opri_887, retro_opri_89,
Procavia capensis ENSPCAG000000140111 retrocopy
retro_pcap_311,
Pongo abelii ENSPPYG000000194912 retrocopies
retro_pabe_1428, retro_pabe_2965,
Pan troglodytes ENSPTRG000000212457 retrocopies
retro_ptro_1158, retro_ptro_1703, retro_ptro_1988, retro_ptro_2444, retro_ptro_309, retro_ptro_339, retro_ptro_524,
Rattus norvegicus ENSRNOG000000120811 retrocopy
retro_rnor_616,
Sarcophilus harrisii ENSSHAG000000067391 retrocopy
retro_shar_329,
Ictidomys tridecemlineatus ENSSTOG000000206684 retrocopies
retro_itri_6, retro_itri_714, retro_itri_823, retro_itri_884,
Tupaia belangeri ENSTBEG000000111932 retrocopies
retro_tbel_1293, retro_tbel_3405,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .03 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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