RetrogeneDB ID:

retro_hsap_2623

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:27674545..27675208(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213846
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM4
Ensembl ID:ENSG00000167460
Aliases:TPM4, HEL-S-108
Description:tropomyosin 4 [Source:HGNC Symbol;Acc:12013]


Retrocopy-Parental alignment summary:






>retro_hsap_2623
GCGCAGGGCCTGCAGCGGGAGCTGGGCGGTGAGTGTGAGCGGCGCGAGAAAGCTAAAGGTGATGTGGCCGCCCTCAACCG
ACGCATCCAGCTCGTTGAGGAGAAGTTGGACAGGGCTCAGGAAAGACTGGCCACGGCCCCGCAGAAGCTGGAGGAGGCAG
AAAAAGCTGCAGATGAGAGTGAGAGAGGAATGAAGGTGATAGAAAACCGGGCCATGAAGGATGAGGAGAAGATGGAAATT
CAGGAGCTGCAGCTCAAAGAGGCCAAGCACATTGCGGAAGAGGCTGACCGCAAATACTGGGAGGTAGCTCGTAAGCTGGT
CTTCCTGGAGGGTGAGCTGGAGAGGGCAGAGGAGCGTGTGGAGGTGTCTGAACTAAAATGTGGTGACCTTGAAGAAGAAC
TCAAGAATGTTACTAACAATCTGAAATCTCTGGAGGCTGCGTCTGAAAAGTATTCTGAAAAGGAGGACAAATGTGAAGAA
GAAATTAAACTTCTGTGTGACAAACTGAAAGAGGCTGAGACCCGTGCTGAATTTGCAGAGAGAACGGTTGCAAAACTGGA
AAAGACAATTGATGACCTGGAAGAGAAACTTGCCCAGGCCAAAGAAGAGAACGTGGGCTTACATCAGACACTGGATCAGA
CACTAAACGAGCTTAACTGTATA

ORF - retro_hsap_2623 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.02 %
Parental protein coverage: 89.11 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENR
AQGLQREL.GE.ERREKA.GDVAALNRRIQLVEE.LDRAQERLATA.QKLEEAEKAADESERGMKVIENR
RetrocopyAQGLQRELGGECERREKAKGDVAALNRRIQLVEEKLDRAQERLATAPQKLEEAEKAADESERGMKVIENR
ParentalAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAEVSELKCGDLEEELKNVTNN
AMKDEEKMEIQE.QLKEAKHIAEEADRKY.EVARKLV.LEGELERAEER.EVSELKCGDLEEELKNVTNN
RetrocopyAMKDEEKMEIQELQLKEAKHIAEEADRKYWEVARKLVFLEGELERAEERVEVSELKCGDLEEELKNVTNN
ParentalLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTVAKLEKTIDDLEEKLAQAKEENVGLHQT
LKSLEAASEKYSEKEDK.EEEIKLL.DKLKEAETRAEFAERTVAKLEKTIDDLEEKLAQAKEENVGLHQT
RetrocopyLKSLEAASEKYSEKEDKCEEEIKLLCDKLKEAETRAEFAERTVAKLEKTIDDLEEKLAQAKEENVGLHQT
ParentalLDQTLNELNCI
LDQTLNELNCI
RetrocopyLDQTLNELNCI

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 1 .07 RPM 717 .16 RPM
bodymap2_adrenal 2 .01 RPM 529 .36 RPM
bodymap2_brain 0 .77 RPM 154 .12 RPM
bodymap2_breast 0 .93 RPM 317 .96 RPM
bodymap2_colon 0 .85 RPM 542 .29 RPM
bodymap2_heart 0 .18 RPM 107 .68 RPM
bodymap2_kidney 3 .27 RPM 295 .73 RPM
bodymap2_liver 0 .13 RPM 50 .80 RPM
bodymap2_lung 0 .58 RPM 1591 .70 RPM
bodymap2_lymph_node 0 .22 RPM 419 .69 RPM
bodymap2_ovary 3 .08 RPM 886 .43 RPM
bodymap2_prostate 2 .49 RPM 516 .99 RPM
bodymap2_skeletal_muscle 0 .24 RPM 56 .67 RPM
bodymap2_testis 5 .84 RPM 440 .37 RPM
bodymap2_thyroid 1 .45 RPM 210 .46 RPM
bodymap2_white_blood_cells 0 .04 RPM 316 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2623 in 9 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 3:27674192..27674711
ENCFF002CFX POLR2A 3:27674199..27674715
ENCFF002CHO POLR2A 3:27674268..27674644
ENCFF002CUP POLR2A 3:27674260..27674576
ENCFF002DAE POLR2A 3:27674346..27674656
ENCFF002DAH POLR2A 3:27674406..27674690
ENCFF002DBO POLR2A 3:27674351..27674598
ENCFF002DBP POLR2A 3:27674383..27674713
ENCFF002DBQ POLR2A 3:27674602..27674972

EST - click to see more details

No EST(s) were mapped for retro_hsap_2623 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_133967413 libraries532 libraries727 libraries127 libraries30 libraries

The graphical summary, for retro_hsap_2623 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_2623 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2623 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000141351 retrocopy
retro_cjac_206,
Homo sapiens ENSG000001435499 retrocopies
retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Homo sapiens ENSG00000167460 2 retrocopies
retro_hsap_2623 , retro_hsap_3969,
Gorilla gorilla ENSGGOG000000145104 retrocopies
retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Oryctolagus cuniculus ENSOCUG000000098841 retrocopy
retro_ocun_1652,

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 = 0.61 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .26 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .46 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .22 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 0 .25 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .37 RPM
FIN_HG00377 0 .18 RPM
FIN_HG00378 0 .21 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .14 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .31 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 0 .61 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .32 RPM
TSI_NA20765 0 .35 RPM
TSI_NA20771 0 .28 RPM
TSI_NA20786 0 .37 RPM
TSI_NA20798 0 .41 RPM
YRI_NA18870 0 .61 RPM
YRI_NA18907 0 .59 RPM
YRI_NA18916 0 .19 RPM
YRI_NA19093 0 .34 RPM
YRI_NA19099 0 .32 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 0 .23 RPM
YRI_NA19213 0 .48 RPM
YRI_NA19214 0 .27 RPM
YRI_NA19223 0 .18 RPM

Indel association:

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



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