RetrogeneDB ID:

retro_hsap_82

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:47628846..47630145(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179715
Aliases:PCED1B, FAM113B
Status:KNOWN_PROTEIN_CODING
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_82
ATGATCCTTCTGCGGGCCTCCGAAGTGCGGCAGCTGCTTCACAATAAGTTCGTGGTCATCCTGGGGGACTCTGTGCATAG
GGCAGTATACAAGGACCTGGTGCTTCTGCTGCAGAAGGACCGCCTGCTCACTCCCGGGCAGCTTAGAGCAAGGGGGGAGC
TGAACTTCGAACAAGATGAGCTGGTGGACGGAGGCCAGCGGGGCCACATGCACAACGGCCTTAACTACCGTGAGGTCCGC
GAGTTCCGCTCCGACCACCATCTGGTACGTTTTTACTTCCTCACCCGCGTGTACTCCGATTACCTCCAGACCATCTTGAA
AGAGCTGCAGTCGGGCGAGCACGCCCCCGACCTGGTCATCATGAATTCCTGCCTCTGGGACATCTCCAGGTATGGTCCGA
ACTCCTGGAGAAGCTACCTGGAGAACCTGGAGAACCTGTTCCAGTGCCTGGGCCAGGTGCTGCCCGAGTCTTGCCTCCTG
GTGTGGAACACGGCCATGCCTGTGGGCGAGGAAGTCACCGGGGGTTTTCTTCCGCCCAAGCTCCGGCGGCAGAAGGCCAC
CTTCCTGAAAAACGAAGTGGTCAAAGCCAACTTCCACAGCGCCACCGAGGCACGTAAACATAACTTCGATGTACTGGACT
TGCATTTCCACTTCCGCCACGCGAGGGAGAACCTGCACTGGGACGGGGTGCACTGGAATGGACGTGTGCACCGCTGCCTC
TCCCAGCTGCTGCTGGCCCACGTGGCCGACGCCTGGGGTGTGGAGCTGCCCCACCGCCACCCCGTGGGCGAGTGGATCAA
GAAGAAAAAACCTGGCCCGAGAGTCGAAGGGCCGCCCCAGGCCAACAGAAATCACCCGGCCTTACCTCTGTCCCCACCCT
TACCTTCCCCCACATACCGCCCCCTGCTTGGGTTCCCACCCCAGCGCTTGCCGCTGCTCCCGCTCCTGTCCCCACAGCCT
CCTCCTCCCATTCTCCATCACCAGGGAATGCCCCGGTTCCCACAGGGTCCCCCAGATGCCTGTTTTTCCTCAGACCATAC
TTTCCAGTCGGATCAATTCTATTGCCATTCAGATGTCCCCTCATCAGCCCATGCAGGTTTCTTCGTCGAAGACAATTTTA
TGGTTGGTCCTCAGCTGCCTATGCCCTTCTTCCCCACACCCCGTTATCAGCGGCCTGCCCCAGTGGTACATAGGGGTTTT
GGCAGGTATCGTCCCCGTGGCCCCTATACGCCCTGGGGACAGCGGCCTCGACCTTCAAAGAGAAGGGCCCCAGCCAATCC
TGAGCCAAGGCCTCAATAG

ORF - retro_hsap_82 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.04 %
Parental protein coverage: 59.03 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
M....ASEV.QLLHNKFVVILGDS..RAVYKDLVLLLQKD.LLT..QL.A.GEL.FEQD.LV.GGQ.G..
RetrocopyMILLRASEVRQLLHNKFVVILGDSVHRAVYKDLVLLLQKDRLLTPGQLRARGELNFEQDELVDGGQRGHM
ParentalHNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYGRCSMES
HNG..YREVR.F...S.HHLVRFYFLTRVYS.YL...L.EL..G..APDLVI.NSCLWD.SRYG..S..S
RetrocopyHNGLNYREVREF--RSDHHLVRFYFLTRVYSDYLQTILKELQSGEHAPDLVIMNSCLWDISRYGPNSWRS
ParentalYRENLERVFVRMDQVLPDSCLLVWNMAMPLGERITGGFLLPEL-QPLAGSLRRDVVEGNFYSATLAGDHC
Y.ENLE..F....QVLP.SCLLVWN.AMP.GE..TGGFL.P.L....A..L...VV..NF.SAT.A..H.
RetrocopyYLENLENLFQCLGQVLPESCLLVWNTAMPVGEEVTGGFLPPKLRRQKATFLKNEVVKANFHSATEARKHN
ParentalFDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKRGYPPDPWIE
FDVLDLHFHFRHA....H.DGVHW....HR.LS.LLL.HVADAWGVELP.R..P...WI.
RetrocopyFDVLDLHFHFRHARENLHWDGVHWNGRVHRCLSQLLLAHVADAWGVELPHR-HPVGEWIK

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 3 .60 RPM 10 .63 RPM
bodymap2_adrenal 12 .92 RPM 21 .68 RPM
bodymap2_brain 0 .42 RPM 9 .26 RPM
bodymap2_breast 3 .83 RPM 10 .19 RPM
bodymap2_colon 1 .64 RPM 6 .34 RPM
bodymap2_heart 0 .46 RPM 2 .95 RPM
bodymap2_kidney 0 .60 RPM 10 .48 RPM
bodymap2_liver 0 .42 RPM 5 .17 RPM
bodymap2_lung 4 .10 RPM 12 .03 RPM
bodymap2_lymph_node 20 .38 RPM 27 .65 RPM
bodymap2_ovary 10 .74 RPM 17 .68 RPM
bodymap2_prostate 3 .85 RPM 14 .06 RPM
bodymap2_skeletal_muscle 0 .33 RPM 1 .93 RPM
bodymap2_testis 3 .94 RPM 9 .58 RPM
bodymap2_thyroid 0 .85 RPM 34 .63 RPM
bodymap2_white_blood_cells 22 .56 RPM 7 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_82 was not detected

EST - click to see more details

8 EST(s) were mapped to retro_hsap_82 retrocopy
EST ID Start End Identity Match Mis-match Score
BF798708 47629601 47629742 98.6 139 0 135
BF798709 47629602 47629742 95.7 136 1 129
CD636379 47628942 47629509 99.9 566 1 565
CD636381 47629222 47629716 99.4 490 2 486
CD636382 47628945 47629571 98.6 599 6 574
CD636383 47629274 47629721 99.1 438 3 430
CD636384 47628942 47629538 96.5 585 4 567
CV027149 47628846 47629433 99.5 577 2 573

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_253481699 libraries 88 libraries 25 libraries 12 libraries 5 libraries
TSS #2 TSS_253491775 libraries 47 libraries 6 libraries 0 libraries 1 library

The graphical summary, for retro_hsap_82 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_82 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_82 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_105
Pongo abelii retro_pabe_192
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 = 16.91 RPM Legend:


Library Retrogene expression
CEU_NA11831 15 .71 RPM
CEU_NA11843 8 .50 RPM
CEU_NA11930 3 .62 RPM
CEU_NA12004 7 .29 RPM
CEU_NA12400 8 .66 RPM
CEU_NA12751 9 .28 RPM
CEU_NA12760 13 .61 RPM
CEU_NA12827 8 .40 RPM
CEU_NA12872 14 .48 RPM
CEU_NA12873 4 .40 RPM
FIN_HG00183 1 .43 RPM
FIN_HG00277 8 .43 RPM
FIN_HG00315 8 .69 RPM
FIN_HG00321 7 .56 RPM
FIN_HG00328 9 .52 RPM
FIN_HG00338 7 .41 RPM
FIN_HG00349 5 .04 RPM
FIN_HG00375 6 .99 RPM
FIN_HG00377 9 .91 RPM
FIN_HG00378 8 .12 RPM
GBR_HG00099 6 .39 RPM
GBR_HG00111 7 .63 RPM
GBR_HG00114 8 .94 RPM
GBR_HG00119 3 .98 RPM
GBR_HG00131 4 .20 RPM
GBR_HG00133 7 .55 RPM
GBR_HG00134 9 .46 RPM
GBR_HG00137 4 .65 RPM
GBR_HG00142 7 .11 RPM
GBR_HG00143 9 .16 RPM
TSI_NA20512 9 .13 RPM
TSI_NA20513 3 .24 RPM
TSI_NA20518 7 .74 RPM
TSI_NA20532 2 .69 RPM
TSI_NA20538 8 .25 RPM
TSI_NA20756 11 .84 RPM
TSI_NA20765 8 .02 RPM
TSI_NA20771 3 .18 RPM
TSI_NA20786 4 .55 RPM
TSI_NA20798 8 .17 RPM
YRI_NA18870 14 .69 RPM
YRI_NA18907 8 .87 RPM
YRI_NA18916 16 .19 RPM
YRI_NA19093 14 .55 RPM
YRI_NA19099 16 .91 RPM
YRI_NA19114 8 .81 RPM
YRI_NA19118 13 .42 RPM
YRI_NA19213 13 .42 RPM
YRI_NA19214 15 .32 RPM
YRI_NA19223 8 .36 RPM

Indel association:

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



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