RetrogeneDB ID:

retro_hsap_3629

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:87831413..87832406(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215477
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RCN1
Ensembl ID:ENSG00000049449
Aliases:RCN1, HEL-S-84, PIG20, RCAL, RCN
Description:reticulocalbin 1, EF-hand calcium binding domain [Source:HGNC Symbol;Acc:9934]


Retrocopy-Parental alignment summary:






>retro_hsap_3629
ATGGCGCGCGGTGGCCGCAGCCGCCGCCTGGGGCTAGTCCTCGGGCTCGTCCTGGAGATGCTGCTGGCGCTGGTGCTGGC
CTGCGGGCGCTGCGGGCCAAGCCCACCGTGCGCAAGGAGCGCGTGGTGCGGCCTGACTCGGAGCTGGGCGAGCGGCTTCC
AGAGGTCAACCGGAGCTTCCGGTACCGCCATGAGGCCTTCCTGGGCAAGGAGGACTCTAAGACCTTCGACCAGCTCACCC
CGGACAAGAGCAAGGAGAGGCTGGGGAAGATTGTTGATCGAATCAACAATGATGGAGATGGCTTTGGCACTACTGAGGAG
CTGAAAACCTGGATCAAACGGGTGCAGAAAAGATACATCTTCGATGATGTCGCCAAAGTCTGGCGGGATTACGATAGGGA
CAAGGATGATAAAATTTACTAGGAAGAATACAAACAAGCCACCTATGACCTAGGAAACCCCGCGGAGTTTCATGATTCTT
CAGATCATTACACCTTTAAAAAGATGCTGCCGCGTGACGAGAGAAGATTCAAAGCTGCAGACCTCGATGGCGCCCTGACA
GCCACTCGGGAGGAGTTCACTGCCTTTCTGCATACCGAAGAGTTTGAGCATATGAAGGAAATTGTGGTTTTGGAAACCCT
GGAGGACAACGACAAGAACGGTGATGGGTTTGTGGATCAGGATGAATATATTGTGGTTATGTTTTCCCATGAGAATGGCT
CTGAGCCAGACTGGGTTTTATCAGAACTGGAGCAATTTAACGAATTCCGGGATCTGAACAAGGACCGGAAGTTGGACAAA
GACGAGATTCGCCACTGGATCCTCTCTCAAGATTATGATCATGCACAGGGTGAGGCCAGGCATCTAGTATATATGAGTCA
GACAAAAACAAGAATCAGAGGCTAAAGAGGAAATATTGGAGAACTGGAACATGTTTGTTGGAAGCCAAACTACCAATTAT
GGGGAAGATCCCACAAAAAATCATGATGAGCTT

ORF - retro_hsap_3629 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.27 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMARGGRGRRLGLALG----LLLALVLAP-RVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLG
MARGGR.RRLGL.LG.....LLALVLA..R.LRAKPTVRKERVVRPDSELGER.PE.N.SF.Y.HEAFLG
RetrocopyMARGGRSRRLGLVLGLVLEMLLALVLAC<RALRAKPTVRKERVVRPDSELGERLPEVNRSFRYRHEAFLG
ParentalKEDSKTFDQLTPDESKERLGKIVDRIDNDGDGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDKI
KEDSKTFDQLTPD.SKERLGKIVDRI.NDGDGF.TTEELKTWIKRVQKRYIFD.VAKVW.DYDRDKDDKI
RetrocopyKEDSKTFDQLTPDKSKERLGKIVDRINNDGDGFGTTEELKTWIKRVQKRYIFDDVAKVWRDYDRDKDDKI
ParentalSWEEYKQATYGYYLGNPAEFHDSSDHHTFKKMLPRDERRFKAADLNGDLTATREEFTAFLHPEEFEHMKE
..EEYKQATY...LGNPAEFHDSSDH.TFKKMLPRDERRFKAADL.G.LTATREEFTAFLH.EEFEHMKE
RetrocopyY*EEYKQATYD--LGNPAEFHDSSDHYTFKKMLPRDERRFKAADLDGALTATREEFTAFLHTEEFEHMKE
ParentalIVVLETLEDIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILP
IVVLETLED.DKNGDGFVDQDEYI..MFSH.ENG.EPDWVLSE.EQFNEFRDLNKD.KLDKDEIRHWIL.
RetrocopyIVVLETLEDNDKNGDGFVDQDEYIVVMFSH-ENGSEPDWVLSELEQFNEFRDLNKDRKLDKDEIRHWILS
ParentalQDYDHAQAEARHLVYESD-KNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL
QDYDHAQ.EARHLVY.S...........E.ILENWNMFVGSQ.TNYGED.TKNHDEL
RetrocopyQDYDHAQGEARHLVYMSQ>QKQESEAKEE-ILENWNMFVGSQTTNYGEDPTKNHDEL

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 166 .62 RPM
bodymap2_adrenal 0 .00 RPM 156 .06 RPM
bodymap2_brain 0 .00 RPM 50 .54 RPM
bodymap2_breast 0 .00 RPM 102 .80 RPM
bodymap2_colon 0 .00 RPM 151 .48 RPM
bodymap2_heart 0 .00 RPM 35 .96 RPM
bodymap2_kidney 0 .00 RPM 98 .38 RPM
bodymap2_liver 0 .00 RPM 67 .68 RPM
bodymap2_lung 0 .00 RPM 113 .40 RPM
bodymap2_lymph_node 0 .00 RPM 95 .00 RPM
bodymap2_ovary 0 .00 RPM 239 .25 RPM
bodymap2_prostate 0 .00 RPM 128 .97 RPM
bodymap2_skeletal_muscle 0 .00 RPM 27 .94 RPM
bodymap2_testis 0 .25 RPM 137 .82 RPM
bodymap2_thyroid 0 .00 RPM 151 .84 RPM
bodymap2_white_blood_cells 0 .00 RPM 16 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3629 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3629 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_168241929 libraries661 libraries233 libraries4 libraries2 libraries

The graphical summary, for retro_hsap_3629 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_3629 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3629 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2976
Parental genes homology:
Parental genes homology involve 3 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000049449 2 retrocopies
retro_hsap_1259, retro_hsap_3629 ,
Pongo abelii ENSPPYG000000033851 retrocopy
retro_pabe_2976,
Rattus norvegicus ENSRNOG0000001345228 retrocopies
retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353, retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409, retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797,

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 ) 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 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 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 .00 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 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 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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