RetrogeneDB ID:

retro_hsap_944

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:133993721..133994222(-)
Located in intron of:ENSG00000166086
Retrocopy
information
Ensembl ID:ENSG00000254481
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A2
Ensembl ID:ENSG00000184007
Aliases:PTP4A2, HH13, HH7-2, HU-PP-1, OV-1, PRL-2, PRL2, PTP4A, PTPCAAX2, ptp-IV1a, ptp-IV1b
Description:protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]


Retrocopy-Parental alignment summary:






>retro_hsap_944
ATGAACCGTCCAGCCCCTGTGGAGATTTCCTGTGAGAACATGCGTTTTCTTGTAACTCACAACCCTACCAGTGCTACTCT
CAACGAGTTCCCAGAGGAACTTAAGAAGTATGGAGTGATGACTTTGGTTCGAGTTTGTGATGCTACGTATGATAAAGCTC
CAGTTGAAAAAGAAGGAATCCACCTTCTAGATTGGCCATTTGATGATGGAGCTCCACCCCCTAATCAGATAGTAGATGAT
TGGTTAAACCTGTTATAAACCAAATTCTGTGAAGAGCCAGGTGGCTGTGTTGCAGTGCCTTGTGTTGCGGGATTGGGAAG
GGCACCTGTGCTGGTTGCACTTGCTTTGATTGAATATGGAATGAAGTACGAAGATGCAGTTCAGTTTATAACACAAAAAA
GAAGGGGGGCCTTCAATTCCAAACAGCTGCTTTACTTGGAGAAATACTGACCTAAGATGTGATTACGCTTCAGAGATACC
AACGGGCACTGCTGTGTTCAG

ORF - retro_hsap_944 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.02 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
MNRPAPVEIS.ENMRFL.THNPT.ATLN.F.EELKKYGV.TLVRVCDATYDKAPVEKEGIH.LDWPFDDG
RetrocopyMNRPAPVEISCENMRFLVTHNPTSATLNEFPEELKKYGVMTLVRVCDATYDKAPVEKEGIHLLDWPFDDG
ParentalAPPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
APPPNQIVDDWLNLL.TKF.EEPG.CVAV.CVAGLGRAPVLVALALIE.GMKYEDAVQFI.QKRRGAFNS
RetrocopyAPPPNQIVDDWLNLL*TKFCEEPGGCVAVPCVAGLGRAPVLVALALIEYGMKYEDAVQFITQKRRGAFNS
ParentalKQLLYLEKYRPKMRLRFRDTNGHCCVQ
KQLLYLEKY.PKM.LRFRDTNGHCCVQ
RetrocopyKQLLYLEKY*PKM*LRFRDTNGHCCVQ

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 .10 RPM 574 .21 RPM
bodymap2_adrenal 0 .59 RPM 318 .20 RPM
bodymap2_brain 0 .42 RPM 334 .61 RPM
bodymap2_breast 0 .08 RPM 434 .95 RPM
bodymap2_colon 0 .00 RPM 272 .98 RPM
bodymap2_heart 0 .09 RPM 189 .34 RPM
bodymap2_kidney 0 .00 RPM 186 .85 RPM
bodymap2_liver 0 .00 RPM 104 .10 RPM
bodymap2_lung 0 .35 RPM 295 .96 RPM
bodymap2_lymph_node 0 .00 RPM 311 .00 RPM
bodymap2_ovary 0 .25 RPM 426 .92 RPM
bodymap2_prostate 0 .29 RPM 332 .86 RPM
bodymap2_skeletal_muscle 0 .04 RPM 538 .11 RPM
bodymap2_testis 0 .13 RPM 264 .30 RPM
bodymap2_thyroid 0 .36 RPM 390 .94 RPM
bodymap2_white_blood_cells 2 .05 RPM 654 .97 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_944 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_944 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_119391452 libraries306 libraries68 libraries1 library2 libraries

The graphical summary, for retro_hsap_944 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_944 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_944 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_654
Gorilla gorilla retro_ggor_763
Pongo abelii retro_pabe_808
Macaca mulatta retro_mmul_1132
Parental genes homology:
Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000391211 retrocopy
retro_btau_638,
Callithrix jacchus ENSCJAG000000065392 retrocopies
retro_cjac_3257, retro_cjac_566,
Homo sapiens ENSG000001122455 retrocopies
retro_hsap_2171, retro_hsap_3212, retro_hsap_479, retro_hsap_4798, retro_hsap_807,
Homo sapiens ENSG00000184007 4 retrocopies
retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944 ,
Mus musculus ENSMUSG000000287882 retrocopies
retro_mmus_1894, retro_mmus_2432,
Nomascus leucogenys ENSNLEG000000021373 retrocopies
retro_nleu_2880, retro_nleu_2956, retro_nleu_3015,
Oryctolagus cuniculus ENSOCUG000000020601 retrocopy
retro_ocun_1673,
Otolemur garnettii ENSOGAG000000296031 retrocopy
retro_ogar_3341,
Pongo abelii ENSPPYG000000016063 retrocopies
retro_pabe_1507, retro_pabe_808, retro_pabe_890,
Rattus norvegicus ENSRNOG000000500441 retrocopy
retro_rnor_305,
Sus scrofa ENSSSCG000000036051 retrocopy
retro_sscr_1186,
Ictidomys tridecemlineatus ENSSTOG000000027752 retrocopies
retro_itri_1165, retro_itri_152,
Tupaia belangeri ENSTBEG000000067901 retrocopy
retro_tbel_4601,
Tursiops truncatus ENSTTRG000000165712 retrocopies
retro_ttru_1396, retro_ttru_1402,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .03 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 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .14 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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