RetrogeneDB ID:

retro_hsap_4014

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:146220271..146220927(+)
Located in intron of:ENSG00000196922
Retrocopy
information
Ensembl ID:ENSG00000254618
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMED10
Ensembl ID:ENSG00000170348
Aliases:TMED10, P24(DELTA), S31I125, S31III125, TMP21, Tmp-21-I, p23
Description:transmembrane emp24-like trafficking protein 10 (yeast) [Source:HGNC Symbol;Acc:16998]


Retrocopy-Parental alignment summary:






>retro_hsap_4014
ATGTCTGGTTTGTCTGGCCCACCAGCCCGGCATGGCCCTTGTCCATCGGCGTTGCTGCTTTTGTTCCTGCTGGGCCCCAG
CTTGGTCCTCGCCATCTCCTTCCATCTGTCCATTAATTCTCACAACTGCTTCCATGAGGAGATCCACAAGGACCTACTAG
TGACTGGCACATACGAGATCTCTGACCAGTCTGGGGGCACTGGTGGCCTGTGCAGCCACCTCAAGATCACAGATTCTGCT
GGCCATATTTTCTACTCCAAAAAGAATACAACCAAGGGGAAATTTGCCTTTACCACTGAAGATTATGACATGTTTGAAGT
GTGTTTTGAGAGCAAGGAAACAGGGCAGATACCTGACCAACTTGTGATCCTAGACATGAAGCATGGAGTGGAGGTGAAAA
ATTACAGAGAGATTGCAAAAGTTGAGAAGCTCAAACCATTAGAGGTGAAGCTGCGACACCTAGAAGACCTTTCAGAATCT
ATTGTTAATGATTTTGCCTACATGAAGAAGAGAGAAGAGGAGATGGTGATACCAGTGAGTCAACAAACACTTGGGTCCTA
CACTTCAGCATCTTTTCAATGTTCTGCCTCACTGGACTAGCCACCTGGCAGGTCTTCTACCTGTGATGCTTCTTCAAGGC
TAAGAAGTTGATTGAG

ORF - retro_hsap_4014 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.36 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGLSGPPARRGPFPLALLLLFLLGPRLVLAISFHLPINSRKCLREEIHKDLLVTGAYEISDQSGGAGGL
MSGLSGPPAR.GP.P.ALLLLFLLGP.LVLAISFHL.INS..C..EEIHKDLLVTG.YEISDQSGG.GGL
RetrocopyMSGLSGPPARHGPCPSALLLLFLLGPSLVLAISFHLSINSHNCFHEEIHKDLLVTGTYEISDQSGGTGGL
ParentalRSHLKITDSAGHILYSKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEEIAK
.SHLKITDSAGHI.YSK...TKGKFAFTTEDYDMFEVCFESK.TG.IPDQLVILDMKHGVE.KNY.EIAK
RetrocopyCSHLKITDSAGHIFYSKKNTTKGKFAFTTEDYDMFEVCFESKETGQIPDQLVILDMKHGVEVKNYREIAK
ParentalVEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEM-RDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLR
VEKLKPLEV.LR.LEDLSESIVNDFAYMKKREEEM..DT.ESTNT.VL.FSIFSMFCL.GLATWQVFYL.
RetrocopyVEKLKPLEVKLRHLEDLSESIVNDFAYMKKREEEM<GDTSESTNTWVLHFSIFSMFCLTGLATWQVFYL*
ParentalRFFKAKKLIE
.FFKAKKLIE
RetrocopyCFFKAKKLIE

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 .44 RPM 308 .15 RPM
bodymap2_adrenal 0 .10 RPM 243 .91 RPM
bodymap2_brain 0 .23 RPM 222 .61 RPM
bodymap2_breast 0 .64 RPM 368 .62 RPM
bodymap2_colon 0 .41 RPM 332 .38 RPM
bodymap2_heart 0 .68 RPM 233 .79 RPM
bodymap2_kidney 0 .35 RPM 333 .97 RPM
bodymap2_liver 0 .36 RPM 347 .93 RPM
bodymap2_lung 0 .05 RPM 346 .41 RPM
bodymap2_lymph_node 0 .37 RPM 283 .75 RPM
bodymap2_ovary 0 .44 RPM 502 .16 RPM
bodymap2_prostate 0 .33 RPM 312 .13 RPM
bodymap2_skeletal_muscle 0 .15 RPM 340 .55 RPM
bodymap2_testis 0 .55 RPM 383 .34 RPM
bodymap2_thyroid 0 .51 RPM 362 .92 RPM
bodymap2_white_blood_cells 0 .20 RPM 338 .97 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4014 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4014 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_182574904 libraries108 libraries365 libraries315 libraries137 libraries

The graphical summary, for retro_hsap_4014 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_4014 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4014 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2724
Pongo abelii retro_pabe_3296
Macaca mulatta retro_mmul_2316
Parental genes homology:
Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000168991 retrocopy
retro_acar_187,
Callithrix jacchus ENSCJAG000000206272 retrocopies
retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus ENSDNOG000000198511 retrocopy
retro_dnov_1225,
Echinops telfairi ENSETEG000000106071 retrocopy
retro_etel_1798,
Homo sapiens ENSG00000170348 2 retrocopies
retro_hsap_2701, retro_hsap_4014 ,
Gorilla gorilla ENSGGOG000000074531 retrocopy
retro_ggor_2696,
Myotis lucifugus ENSMLUG000000171252 retrocopies
retro_mluc_2079, retro_mluc_2093,
Macaca mulatta ENSMMUG000000151682 retrocopies
retro_mmul_2316, retro_mmul_885,
Mus musculus ENSMUSG000000212482 retrocopies
retro_mmus_1093, retro_mmus_649,
Nomascus leucogenys ENSNLEG000000164532 retrocopies
retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus ENSOCUG000000046691 retrocopy
retro_ocun_875,
Pongo abelii ENSPPYG000000293891 retrocopy
retro_pabe_3296,
Pan troglodytes ENSPTRG000000065522 retrocopies
retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus ENSRNOG000000079012 retrocopies
retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus ENSSTOG000000073921 retrocopy
retro_itri_362,
Vicugna pacos ENSVPAG000000030891 retrocopy
retro_vpac_573,

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 = 0.47 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .39 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .39 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .24 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .30 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .33 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .34 RPM
GBR_HG00099 0 .29 RPM
GBR_HG00111 0 .24 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .12 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .24 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .28 RPM
GBR_HG00143 0 .22 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .27 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .15 RPM
TSI_NA20765 0 .46 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .47 RPM
YRI_NA18907 0 .28 RPM
YRI_NA18916 0 .34 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .16 RPM
YRI_NA19118 0 .33 RPM
YRI_NA19213 0 .33 RPM
YRI_NA19214 0 .37 RPM
YRI_NA19223 0 .26 RPM

Indel association:

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



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