RetrogeneDB ID:

retro_hsap_1259

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:45964488..45965468(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214455
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_1259
CGCGGTGGCCGCCTGGGGTTAGCCCTGGGGCTGCTGCTGGCGCTGGTGCTGGCGCCGCGGGTTCTGCGGGCCAAGCCCAC
GGTGCGCAAAGAGCGCGTGGTGCGGCCCGACTCGGAGCTGGGCGAGCGGCCCCCTGAGGACAACCAGAGCTTCCAGTACG
ACCACGAGGCCTTCCTGGGCAAGGAGGACTCCAAGAACTTCGACGAGCTCACCCCGGACGAGAGCAAGGAGAGGCTAGGG
AAGATTGTTGATCGAATCGACAATGATGGGTATGGCTTTGTCACTACTGAGGAGCTGAAAACCTGGATCAAACGGGTGCA
GAAAAGATACATCTTTGATAATGTCGCCAAAGTCTGGAAGGATTATGATAGGGACAAGGATGATAACATTTCCTGGGAAG
AATACAAACAAGCCACCTATGGTTACTATACCTAGGAAACCCCGCAGAGTTTCATGATTCTTCAGATCATCACACCTTTA
AAAAGATGCTGCCACGTGATGAGAGAAGATTCAAAGCTGCAGACCTCAATGGTGACCTGACAGCTACTCCGGAGGAGTTC
ACTGCCTTTCTGCATCCTGAAGAGTTTGAACATATGAAGGAAATTGTGGCTTTGGAAACCCTGGAGGACATCGACAAGAA
CGGGGATGGGTTTGTGGATCAGGATGAGTATATTGCGGATATGTTTTCCCATGAGGAGAATGGCCCTGAGCCAGACTGGG
TTTTATCAGAACGGGAGCAGTTTAACGAATTCCGGGATCTGAACAAGGACGGGAAGTTAGACAAAGATGAGATTCGCCAC
TGGATCCTCCCTCAAGATTATGATCATGCACAGGCTGAGGCCAGGCATCTGGTATATGAGTCAGACAAAAACAAGGATGA
GAAGCTAACTAAAGAGGAAATATTGGAGAACTGGAACATGTTTGTTGGAAGCCAAGCTACCAATTACGGGGAAGATCTCA
CAAAAAATCATGATGAGCTT

ORF - retro_hsap_1259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.73 %
Parental protein coverage: 98.49 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRGRRLGLALGLLLALVLAPRVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQL
RG.RLGLALGLLLALVLAPRVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSK.FD.L
RetrocopyRGGRLGLALGLLLALVLAPRVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKNFDEL
ParentalTPDESKERLGKIVDRIDNDGDGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDKISWEEYKQATY
TPDESKERLGKIVDRIDNDG.GFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDD.ISWEEYKQATY
RetrocopyTPDESKERLGKIVDRIDNDGYGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDNISWEEYKQATY
ParentalGYYL-GNPAEF-HDSSDHHTFKKMLPRDERRFKAADLNGDLTATREEFTAFLHPEEFEHMKEIVVLETLE
GYY....P..F.HDSSDHHTFKKMLPRDERRFKAADLNGDLTAT.EEFTAFLHPEEFEHMKEIV.LETLE
RetrocopyGYYT*ETPQSF<HDSSDHHTFKKMLPRDERRFKAADLNGDLTATPEEFTAFLHPEEFEHMKEIVALETLE
ParentalDIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQA
DIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQA
RetrocopyDIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQA
ParentalEARHLVYESDKNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL
EARHLVYESDKNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL
RetrocopyEARHLVYESDKNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL

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 27 .01 RPM 166 .62 RPM
bodymap2_adrenal 2 .29 RPM 156 .06 RPM
bodymap2_brain 6 .00 RPM 50 .54 RPM
bodymap2_breast 9 .69 RPM 102 .80 RPM
bodymap2_colon 9 .78 RPM 151 .48 RPM
bodymap2_heart 3 .30 RPM 35 .96 RPM
bodymap2_kidney 8 .89 RPM 98 .38 RPM
bodymap2_liver 4 .60 RPM 67 .68 RPM
bodymap2_lung 5 .47 RPM 113 .40 RPM
bodymap2_lymph_node 6 .19 RPM 95 .00 RPM
bodymap2_ovary 4 .47 RPM 239 .25 RPM
bodymap2_prostate 8 .83 RPM 128 .97 RPM
bodymap2_skeletal_muscle 1 .04 RPM 27 .94 RPM
bodymap2_testis 4 .73 RPM 137 .82 RPM
bodymap2_thyroid 11 .49 RPM 151 .84 RPM
bodymap2_white_blood_cells 0 .65 RPM 16 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1259 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1259 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_332851487 libraries327 libraries13 libraries1 library1 library

The graphical summary, for retro_hsap_1259 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_1259 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1259 has 0 orthologous retrocopies within eutheria group .

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 ) > 0 RPM = 11.95 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .09 RPM
CEU_NA11843 5 .74 RPM
CEU_NA11930 5 .80 RPM
CEU_NA12004 5 .36 RPM
CEU_NA12400 4 .00 RPM
CEU_NA12751 6 .27 RPM
CEU_NA12760 3 .32 RPM
CEU_NA12827 5 .90 RPM
CEU_NA12872 3 .81 RPM
CEU_NA12873 5 .33 RPM
FIN_HG00183 4 .56 RPM
FIN_HG00277 7 .51 RPM
FIN_HG00315 6 .10 RPM
FIN_HG00321 6 .26 RPM
FIN_HG00328 3 .91 RPM
FIN_HG00338 2 .64 RPM
FIN_HG00349 3 .19 RPM
FIN_HG00375 7 .36 RPM
FIN_HG00377 3 .76 RPM
FIN_HG00378 3 .89 RPM
GBR_HG00099 3 .05 RPM
GBR_HG00111 5 .82 RPM
GBR_HG00114 5 .26 RPM
GBR_HG00119 6 .97 RPM
GBR_HG00131 5 .58 RPM
GBR_HG00133 5 .67 RPM
GBR_HG00134 5 .09 RPM
GBR_HG00137 8 .36 RPM
GBR_HG00142 11 .95 RPM
GBR_HG00143 3 .45 RPM
TSI_NA20512 4 .69 RPM
TSI_NA20513 4 .57 RPM
TSI_NA20518 6 .00 RPM
TSI_NA20532 5 .75 RPM
TSI_NA20538 5 .57 RPM
TSI_NA20756 4 .10 RPM
TSI_NA20765 5 .97 RPM
TSI_NA20771 5 .25 RPM
TSI_NA20786 1 .83 RPM
TSI_NA20798 4 .68 RPM
YRI_NA18870 4 .06 RPM
YRI_NA18907 2 .53 RPM
YRI_NA18916 2 .84 RPM
YRI_NA19093 2 .45 RPM
YRI_NA19099 4 .31 RPM
YRI_NA19114 1 .65 RPM
YRI_NA19118 5 .26 RPM
YRI_NA19213 3 .44 RPM
YRI_NA19214 3 .66 RPM
YRI_NA19223 2 .81 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017