RetrogeneDB ID:

retro_hsap_2207

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:213696857..213697649(+)
Located in intron of:ENSG00000236193
Retrocopy
information
Ensembl ID:ENSG00000231254
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PCED1A
Ensembl ID:ENSG00000132635
Aliases:PCED1A, C20orf81, FAM113A, bA12M19.1
Description:PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]


Retrocopy-Parental alignment summary:






>retro_hsap_2207
CGCCCTGCCTCCGCCGCCATGGCCCAGCTGCGAGCCTGCGAAGTCCGGCAGCTGCTGCACAACAAGTTCGTGGTGGTCAT
GGGGGACTCGGTCCAGCTGGCCGTGTACAAGGACCTGGTGCTCCTGCTTCAGAAGGACTGCCTGCTGTCCTCCAGTCAGC
TGAAGGCCAAGGGCGAACTGAGCTTCGAGCGCGACATGCTGCTGGTGGGCTGCAGCAGTGGCCGCATGCACTACGACCGC
CACTACCGCGAGGTGCGCCAGTTCCGCTCGGGCCACCACCTGGTGCGCTTCTACTTCCTCACGCGCGTGTATTCGCACTA
CGCGGAGCGCGTCGTGGAGGAGCTGCGTAGGGCCGAGCCCGCCCCGGACGTGGTGGTCATGAACTCCTGCCTCTGGGACC
TCGCCAGGGATGGCCGGGGCTTCCCCAGGAGCTACCGGCGTGACGTGGAGAGCCTGTTCGTGCGGTTGGACTGGGCGCTG
CCCACGTCCTGCCTTCTGTTGTGGAACACGGCCATGCCCGTGGCCGAGACCATCTCGGGAAGCTGCCTCCCATGCGCGCG
CCAGCTCCGCCGCGCCCGCCTGCGCGAAGACGTGATGGAGGCCAACTTCTACAGCTCCGCCGAGGCGGCGAGGCGCGGCT
TTGACGTGCTGGACCTGCATTTCCACTTCCGCCACGCCACGCGGCACCGGCTCCCCGACGGCGTGCACTGGGACGAGCGC
GCGCACCGCCACCTTTCCCAGCTGCTGCTGGCCCACCTGGCAGACGCCTGGGGCGTGGACCTGCCCCGCCGC

ORF - retro_hsap_2207 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.16 %
Parental protein coverage: 58.37 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRPLRSDMVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAG
RP....M....A.EV.QLLHNKFVV..GDS.Q.AVYKDLVLLLQKD.LL...QLKAKGELSFE.D.L..G
RetrocopyRPASAAMAQLRACEVRQLLHNKFVVVMGDSVQLAVYKDLVLLLQKDCLLSSSQLKAKGELSFERDMLLVG
ParentalGQLGELHNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYG-PAPDLVIINSCLWDLSRYG
...G..H....YREVRQF...SGHHLVRFYFLTRVYS.Y.E.V.EEL....PAPD.V..NSCLWDL.R.G
RetrocopyCSSGRMHYDRHYREVRQF--RSGHHLVRFYFLTRVYSHYAERVVEELRRAEPAPDVVVMNSCLWDLARDG
ParentalRCSMESYRENLERVFVRMDQVLPDSCLLVWNMAMPLGERITGGFLLPELQPLAGSLRRDVVEGNFYSATL
R....SYR...E..FVR.D..LP.SCLL.WN.AMP..E.I.G..L....Q.....LR.DV.E.NFYS...
RetrocopyRGFPRSYRRDVESLFVRLDWALPTSCLLLWNTAMPVAETISGSCLPCARQLRRARLREDVMEANFYSSAE
ParentalAGDHCFDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKR
A....FDVLDLHFHFRHA..HR..DGVHWD..AHRHLS.LLL.H.ADAWGV.LP.R
RetrocopyAARRGFDVLDLHFHFRHATRHRLPDGVHWDERAHRHLSQLLLAHLADAWGVDLPRR

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 .00 RPM 10 .63 RPM
bodymap2_adrenal 0 .00 RPM 21 .68 RPM
bodymap2_brain 0 .00 RPM 9 .26 RPM
bodymap2_breast 0 .00 RPM 10 .19 RPM
bodymap2_colon 0 .00 RPM 6 .34 RPM
bodymap2_heart 0 .00 RPM 2 .95 RPM
bodymap2_kidney 0 .00 RPM 10 .48 RPM
bodymap2_liver 0 .00 RPM 5 .17 RPM
bodymap2_lung 0 .00 RPM 12 .03 RPM
bodymap2_lymph_node 0 .00 RPM 27 .65 RPM
bodymap2_ovary 0 .00 RPM 17 .68 RPM
bodymap2_prostate 0 .00 RPM 14 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .93 RPM
bodymap2_testis 0 .72 RPM 9 .58 RPM
bodymap2_thyroid 0 .00 RPM 34 .63 RPM
bodymap2_white_blood_cells 0 .00 RPM 7 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2207 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2207 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2207 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2207 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2207 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2080
Macaca mulatta retro_mmul_341
Mus musculus retro_mmus_332
Parental genes homology:
Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000038631 retrocopy
retro_btau_182,
Cavia porcellus ENSCPOG000000254752 retrocopies
retro_cpor_343, retro_cpor_79,
Equus caballus ENSECAG000000164971 retrocopy
retro_ecab_87,
Felis catus ENSFCAG000000028861 retrocopy
retro_fcat_18,
Homo sapiens ENSG00000132635 2 retrocopies
retro_hsap_2207 , retro_hsap_82,
Microcebus murinus ENSMICG000000165782 retrocopies
retro_mmur_163, retro_mmur_278,
Myotis lucifugus ENSMLUG000000286622 retrocopies
retro_mluc_222, retro_mluc_647,
Macaca mulatta ENSMMUG000000052002 retrocopies
retro_mmul_333, retro_mmul_341,
Mus musculus ENSMUSG000000377732 retrocopies
retro_mmus_1001, retro_mmus_332,
Otolemur garnettii ENSOGAG000000047011 retrocopy
retro_ogar_81,
Pongo abelii ENSPPYG000000108332 retrocopies
retro_pabe_192, retro_pabe_2080,
Pan troglodytes ENSPTRG000000131851 retrocopy
retro_ptro_105,
Pteropus vampyrus ENSPVAG000000068341 retrocopy
retro_pvam_9,
Sus scrofa ENSSSCG000000071681 retrocopy
retro_sscr_23,
Ictidomys tridecemlineatus ENSSTOG000000163562 retrocopies
retro_itri_1190, retro_itri_783,
Tursiops truncatus ENSTTRG000000034641 retrocopy
retro_ttru_16,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .03 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 .00 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 .07 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 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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