RetrogeneDB ID:

retro_hsap_3840

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:39608974..39609797(-)
Located in intron of:ENSG00000241127
Retrocopy
information
Ensembl ID:ENSG00000236015
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMX1
Ensembl ID:ENSG00000139921
Aliases:None
Description:thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]


Retrocopy-Parental alignment summary:






>retro_hsap_3840
ATGGCACCCTCCAGGAGTCTTGCAGTTCCGCTGGCAGTCCTGGTACTGTTGCTTGGGGGTGCTCCCTGGACCCACAGGCG
GCAGAGCAACGTACGCATCATCACAGACAAGAACTGGAGAGAGCTGCTGGAAGGAGGCTGGATGATACAATTTTATGCCC
CGTGGTGCCCTGCTTGTCAAAACCATTAACCGGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTGAGGTTAATGTTG
TGAAAGTAGATGTCACAGAGCAGCCAGGACTGACTGGACAGTTTACAATAACTGTTCTTCCTACTATTTATCATTGTAAA
GATGGTGAATTTAGGCATCCTCAGGGTCCAAGGACTCAGAAGGACTTCATAAACTTTATAAGTGATAAAGAGTGGAAGAG
TATTGAACCCGTTTCATCATGGTTTGTTTCAGGTTCTGTTCAGATGAGTAGTACGTCAGCACTCTTTCAGCTATCTACGT
GGATCAGGACTTGCCATAACTACTTTATTGAAGACATTGGATTGCCAGTGTGGGGATCATATGCTGTTTTTCCTTTAGCA
ACTCTGCATTCTGGACTGTTACTAGGACTCTGTATGATATTTGTGGCAGGTTGCCTTTGTCCTTCAGAAAGGCACACACC
ACAGCCATACCCTTCAAAAAAATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACAAGAGGCGGATAAAG
AAGATGTTTCAGAAGAAGAAGCCAAAAGTAAAGAAGGAACAAAGACTTTCCACAGAATGCCATAACACAACACTCTCTGG
GTCCATCACTGGTCACAGATAAA

ORF - retro_hsap_3840 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.99 %
Parental protein coverage: 99.64 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAPSGSLAVPLAVLVLLLWGAPWTHGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEWESFA
MAPS.SLAVPLAVLVLLL.GAPWTH.R.SNVR.ITD.NWRELLEG.WMI.FYAPWCPACQN..PEWESFA
RetrocopyMAPSRSLAVPLAVLVLLLGGAPWTHRRQSNVRIITDKNWRELLEGGWMIQFYAPWCPACQNH*PEWESFA
ParentalEWGEDL-EVNIAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVS
EWGEDL.EVN..KVDVTEQPGL.G.F.IT.LPTIYHCKDGEFR..QGPRT.KDFINFISDKEWKSIEPVS
RetrocopyEWGEDL<EVNVVKVDVTEQPGLTGQFTITVLPTIYHCKDGEFRHPQGPRTQKDFINFISDKEWKSIEPVS
ParentalSWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFALATLFSGLLLGLCMIFVADCLCPS
SWF..GSV.MSS.SALFQLS.WIRTCHNYFIED.GLPVWGSY.VF.LATL.SGLLLGLCMIFVA.CLCPS
RetrocopySWFVSGSVQMSSTSALFQLSTWIRTCHNYFIEDIGLPVWGSYAVFPLATLHSGLLLGLCMIFVAGCLCPS
ParentalKRRRPQPYPYPSKKLLSESAQPLKKVEEEQEADEEDVSEEEAESKEGTNKDF-PQNAIRQRSLGPSLATD
.R..PQ..PYPSKKL.SESAQPLKK.EEEQEAD.EDVSEEEA.SKEGT.K.F.PQNAI.Q.SLGPSL.TD
RetrocopyERHTPQ--PYPSKKL-SESAQPLKKLEEEQEADKEDVSEEEAKSKEGT-KTF<PQNAITQHSLGPSLVTD
ParentalK
K
RetrocopyK

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 77 .84 RPM
bodymap2_adrenal 1 .23 RPM 66 .24 RPM
bodymap2_brain 0 .66 RPM 32 .51 RPM
bodymap2_breast 0 .12 RPM 68 .29 RPM
bodymap2_colon 0 .52 RPM 70 .36 RPM
bodymap2_heart 0 .13 RPM 18 .85 RPM
bodymap2_kidney 0 .39 RPM 74 .10 RPM
bodymap2_liver 0 .21 RPM 25 .92 RPM
bodymap2_lung 0 .25 RPM 47 .35 RPM
bodymap2_lymph_node 1 .08 RPM 67 .45 RPM
bodymap2_ovary 0 .87 RPM 61 .92 RPM
bodymap2_prostate 0 .45 RPM 53 .81 RPM
bodymap2_skeletal_muscle 0 .02 RPM 18 .35 RPM
bodymap2_testis 0 .21 RPM 68 .25 RPM
bodymap2_thyroid 0 .26 RPM 80 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 111 .81 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3840 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3840 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3840 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3840 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3840 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2522
Gorilla gorilla retro_ggor_2587
Pongo abelii retro_pabe_3058
Macaca mulatta retro_mmul_1618
Parental genes homology:
Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000150411 retrocopy
retro_amel_719,
Canis familiaris ENSCAFG000000146261 retrocopy
retro_cfam_796,
Choloepus hoffmanni ENSCHOG000000113051 retrocopy
retro_chof_1249,
Callithrix jacchus ENSCJAG000000068931 retrocopy
retro_cjac_1453,
Dasypus novemcinctus ENSDNOG000000164961 retrocopy
retro_dnov_78,
Felis catus ENSFCAG000000027801 retrocopy
retro_fcat_333,
Homo sapiens ENSG00000139921 2 retrocopies
retro_hsap_3840 , retro_hsap_3970,
Gorilla gorilla ENSGGOG000000097681 retrocopy
retro_ggor_2587,
Loxodonta africana ENSLAFG000000132511 retrocopy
retro_lafr_1214,
Macaca mulatta ENSMMUG000000019011 retrocopy
retro_mmul_1618,
Nomascus leucogenys ENSNLEG000000123622 retrocopies
retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus ENSOCUG000000039801 retrocopy
retro_ocun_571,
Pongo abelii ENSPPYG000000058102 retrocopies
retro_pabe_3058, retro_pabe_3264,
Pan troglodytes ENSPTRG000000063392 retrocopies
retro_ptro_2522, retro_ptro_2695,

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 = 1.64 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .34 RPM
CEU_NA11843 0 .60 RPM
CEU_NA11930 0 .42 RPM
CEU_NA12004 0 .57 RPM
CEU_NA12400 0 .70 RPM
CEU_NA12751 0 .83 RPM
CEU_NA12760 0 .49 RPM
CEU_NA12827 0 .47 RPM
CEU_NA12872 0 .90 RPM
CEU_NA12873 0 .57 RPM
FIN_HG00183 1 .13 RPM
FIN_HG00277 1 .04 RPM
FIN_HG00315 0 .50 RPM
FIN_HG00321 1 .12 RPM
FIN_HG00328 0 .71 RPM
FIN_HG00338 0 .45 RPM
FIN_HG00349 0 .57 RPM
FIN_HG00375 0 .93 RPM
FIN_HG00377 0 .40 RPM
FIN_HG00378 0 .53 RPM
GBR_HG00099 0 .20 RPM
GBR_HG00111 0 .60 RPM
GBR_HG00114 0 .47 RPM
GBR_HG00119 1 .03 RPM
GBR_HG00131 1 .21 RPM
GBR_HG00133 0 .77 RPM
GBR_HG00134 0 .92 RPM
GBR_HG00137 0 .91 RPM
GBR_HG00142 1 .64 RPM
GBR_HG00143 0 .45 RPM
TSI_NA20512 0 .34 RPM
TSI_NA20513 0 .82 RPM
TSI_NA20518 0 .72 RPM
TSI_NA20532 0 .85 RPM
TSI_NA20538 0 .83 RPM
TSI_NA20756 0 .38 RPM
TSI_NA20765 0 .81 RPM
TSI_NA20771 0 .26 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .53 RPM
YRI_NA18870 0 .71 RPM
YRI_NA18907 0 .35 RPM
YRI_NA18916 0 .67 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .37 RPM
YRI_NA19114 0 .37 RPM
YRI_NA19118 0 .37 RPM
YRI_NA19213 0 .67 RPM
YRI_NA19214 0 .30 RPM
YRI_NA19223 0 .90 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017