RetrogeneDB ID:

retro_hsap_4044

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:37604856..37605522(-)
Located in intron of:ENSG00000147475
Retrocopy
information
Ensembl ID:ENSG00000233170
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CXorf56
Ensembl ID:ENSG00000018610
Aliases:None
Description:chromosome X open reading frame 56 [Source:HGNC Symbol;Acc:26239]


Retrocopy-Parental alignment summary:






>retro_hsap_4044
ATGCCGAAAGTAGTGTCTCGGTCAGTAGTCTGCTCTGACACTCGGGACCGGGAGGAATATGACGACGGCGAGAAGCCCCT
CCATGTGTACTACTGTTTGTGCGGCCAGGTGGTCCTAGTGCTGGACTGTCAGTTAGAGAAATTGCCCATGAGGCCCCGGG
ACCGGTCCCGTGTGATTGATGCTGCCAAACATGCCCATAAGTTTTGTAACACAGAAGACGAAGAGACTATGTATCTGCGG
AGACCTGAAGGCATTGAACTACAGTACAGAAAGAAATGTGCAAAGTGTGGACTGCTGCTCTTCTACCAATCCCAGCCGAA
GAATGCTCCCGTTACCTTCATTGTGGATGGAGCAGTCGTCAAGTTTGGCCAGGGCTTTGGGAAAACGAACATATATACTC
AGAAACAAGAGCCTCCTAAGAAGGTGATGATGACCAAACGGACCAAAGACATGGGCAAGTTCAGTTCTGTCACTGTGTCT
ACCATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCGTATGCACAGAATGCCAAAGTGATTGAAAA
ACAGCTGGAGCGCAAAGGCATGAGCAAGAGGCCACTGCAAGAGCTGGCTGAATGGGAAGCCAAGAAAGTGAAAATGAAGG
GGACCTTGATTGACAACCAGTTCAAA

ORF - retro_hsap_4044 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQ.VLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
RetrocopyMPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQVVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
ParentalTEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
TEDEETMYLRRPEGIE.QYRKKCAKCGL.LFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
RetrocopyTEDEETMYLRRPEGIELQYRKKCAKCGLLLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
ParentalKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA
KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKR.LQELAE.EAKK.
RetrocopyKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRPLQELAEWEAKKV
ParentalKMKGTLIDNQFK
KMKGTLIDNQFK
RetrocopyKMKGTLIDNQFK

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 .24 RPM 17 .95 RPM
bodymap2_adrenal 0 .61 RPM 24 .58 RPM
bodymap2_brain 0 .94 RPM 19 .50 RPM
bodymap2_breast 0 .78 RPM 24 .65 RPM
bodymap2_colon 0 .17 RPM 15 .95 RPM
bodymap2_heart 0 .59 RPM 8 .66 RPM
bodymap2_kidney 1 .24 RPM 18 .70 RPM
bodymap2_liver 0 .25 RPM 3 .49 RPM
bodymap2_lung 0 .07 RPM 10 .02 RPM
bodymap2_lymph_node 0 .24 RPM 13 .08 RPM
bodymap2_ovary 1 .37 RPM 21 .59 RPM
bodymap2_prostate 0 .24 RPM 18 .62 RPM
bodymap2_skeletal_muscle 0 .29 RPM 7 .18 RPM
bodymap2_testis 2 .55 RPM 19 .89 RPM
bodymap2_thyroid 1 .49 RPM 30 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 21 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_4044 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 8:37605327..37605757
ENCFF002CJE POLR2A 8:37605452..37605611
ENCFF002CQC POLR2A 8:37605300..37605780
ENCFF002CQG POLR2A 8:37605276..37605800

EST - click to see more details

No EST(s) were mapped for retro_hsap_4044 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_184444706 libraries737 libraries377 libraries8 libraries1 library

The graphical summary, for retro_hsap_4044 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_4044 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4044 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_104
Gorilla gorilla retro_ggor_2711
Pongo abelii retro_pabe_177
Parental genes homology:
Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000051111 retrocopy
retro_cjac_311,
Homo sapiens ENSG00000018610 1 retrocopy
retro_hsap_4044 ,
Gorilla gorilla ENSGGOG000000133241 retrocopy
retro_ggor_2711,
Latimeria chalumnae ENSLACG000000124681 retrocopy
retro_lcha_59,
Myotis lucifugus ENSMLUG000000157511 retrocopy
retro_mluc_72,
Macaca mulatta ENSMMUG000000226651 retrocopy
retro_mmul_2333,
Mus musculus ENSMUSG000000064231 retrocopy
retro_mmus_1715,
Nomascus leucogenys ENSNLEG000000148621 retrocopy
retro_nleu_2057,
Otolemur garnettii ENSOGAG000000124741 retrocopy
retro_ogar_145,
Pongo abelii ENSPPYG000000206701 retrocopy
retro_pabe_177,
Pan troglodytes ENSPTRG000000222241 retrocopy
retro_ptro_104,
Sorex araneus ENSSARG000000031631 retrocopy
retro_sara_5,
Sarcophilus harrisii ENSSHAG000000063191 retrocopy
retro_shar_16,
Ictidomys tridecemlineatus ENSSTOG000000115791 retrocopy
retro_itri_103,
Tursiops truncatus ENSTTRG000000131012 retrocopies
retro_ttru_231, retro_ttru_77,

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 = 0.49 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .36 RPM
CEU_NA11843 0 .40 RPM
CEU_NA11930 0 .49 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .28 RPM
CEU_NA12751 0 .24 RPM
CEU_NA12760 0 .40 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .27 RPM
CEU_NA12873 0 .41 RPM
FIN_HG00183 0 .30 RPM
FIN_HG00277 0 .30 RPM
FIN_HG00315 0 .39 RPM
FIN_HG00321 0 .27 RPM
FIN_HG00328 0 .26 RPM
FIN_HG00338 0 .28 RPM
FIN_HG00349 0 .43 RPM
FIN_HG00375 0 .39 RPM
FIN_HG00377 0 .48 RPM
FIN_HG00378 0 .28 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .47 RPM
GBR_HG00119 0 .36 RPM
GBR_HG00131 0 .46 RPM
GBR_HG00133 0 .43 RPM
GBR_HG00134 0 .41 RPM
GBR_HG00137 0 .38 RPM
GBR_HG00142 0 .31 RPM
GBR_HG00143 0 .38 RPM
TSI_NA20512 0 .31 RPM
TSI_NA20513 0 .36 RPM
TSI_NA20518 0 .33 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .26 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .37 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .17 RPM
YRI_NA18907 0 .42 RPM
YRI_NA18916 0 .36 RPM
YRI_NA19093 0 .16 RPM
YRI_NA19099 0 .35 RPM
YRI_NA19114 0 .34 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .24 RPM
YRI_NA19214 0 .47 RPM
YRI_NA19223 0 .30 RPM

Indel association:

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





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