RetrogeneDB ID:

retro_hsap_4837

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:53483313..53483975(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235416
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TIPIN
Ensembl ID:ENSG00000075131
Aliases:None
Description:TIMELESS interacting protein [Source:HGNC Symbol;Acc:30750]


Retrocopy-Parental alignment summary:






>retro_hsap_4837
ATGCTAGAATCACAGGAGAATGGCATGATTGACCTTCCAGATTATGAGCATGTAGAAGATGAAACTTTTCCTCCTTTCCC
ACCTCCAGCCTCTCCAGAGAGACAAGATGATGAAGGAGCTGAACCTGATAGTCAGGAAGTGGAGCACTTGTTCCTGTACC
TCCAAAGAGAGCAGTTAAAAGAAATATATCCGAGCTGGATGCTCACAGATTAATTTCAGAGAGAGGGCTTCCAGCCTTAA
GGCATGTATTTGATAAGGCAAAATTCAAAGGTAAAAGTCATGAGGCTGAAGACTTAAAGATGCTAATCAGACACATGGAA
CACTGGGCACGTAGGCGATTCCCTAAACTGCAGTTTGAGGATTTTATTGACAGAGTTGAATACCTGAGAAATAAAAAGGA
AATTCAGACCTGTTTAAAATGAATTCGACTTGATCTCCCTATTTTACATGAATATGTTGTTAGCAATAATGAGGAAGTTG
GGGAAAATAATGGACATTGTGTAACTGCTACTGAATTAGATCCCTTTCTGACAAACTCATCTGAAAGTGAGATGTTTGCT
TCTGAGTCAAGTAGAAGCCTAACAGATGAGCAACAACAAAGGATTGAGAGAAATAAACAACCGGCTTTGGAAAGAAGGCA
GGCAAAGCTGCTGAGTAATAGT

ORF - retro_hsap_4837 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.82 %
Parental protein coverage: 75.51 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLEPQENGVIDLPDYEHVEDETFPPFPPPASPERQDGEGTEPDEE-SGNGAPVRVPPKRTVKRNIPKLDA
MLE.QENG.IDLPDYEHVEDETFPPF.PP.................SG.GA.V.VPPKR.VKRNI..LDA
RetrocopyMLESQENGMIDLPDYEHVEDETFPPF-PPPASPERQDDEGAEPDS<SGSGALVPVPPKRAVKRNISELDA
ParentalQRLISERGLPALRHVFDKAKFKGKGHEAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEYLGSKKEVQTC
.RLISERGLPALRHVFDKAKFKGK.HEAEDLKMLIRHMEHWA.R.FPKLQFEDFIDRVEYL..KKE.QTC
RetrocopyHRLISERGLPALRHVFDKAKFKGKSHEAEDLKMLIRHMEHWARRRFPKLQFEDFIDRVEYLRNKKEIQTC
ParentalLKRIRLDLPILHEDFVSNNDEVAENNEHDVTSTELDPFLTNLSESEMFASELSRSLTEEQQQRIERNKQL
LK.IRLDLPILHE..VSNN.EV.ENN.H.VT.TELDPFLTN.SESEMFASE.SRSLT.EQQQRIERNKQ.
RetrocopyLK*IRLDLPILHEYVVSNNEEVGENNGHCVTATELDPFLTNSSESEMFASESSRSLTDEQQQRIERNKQP
ParentalALERRQAKLLSNS
ALERRQAKLLSNS
RetrocopyALERRQAKLLSNS

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 2 .52 RPM
bodymap2_adrenal 0 .02 RPM 7 .35 RPM
bodymap2_brain 0 .00 RPM 5 .20 RPM
bodymap2_breast 0 .00 RPM 4 .38 RPM
bodymap2_colon 0 .00 RPM 2 .17 RPM
bodymap2_heart 0 .00 RPM 1 .11 RPM
bodymap2_kidney 0 .00 RPM 3 .10 RPM
bodymap2_liver 0 .00 RPM 2 .53 RPM
bodymap2_lung 0 .00 RPM 1 .69 RPM
bodymap2_lymph_node 0 .00 RPM 3 .62 RPM
bodymap2_ovary 0 .00 RPM 8 .67 RPM
bodymap2_prostate 0 .00 RPM 5 .47 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .76 RPM
bodymap2_testis 0 .00 RPM 22 .13 RPM
bodymap2_thyroid 0 .00 RPM 4 .54 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .46 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4837 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4837 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4837 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4837 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4837 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3220
Parental genes homology:
Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000048601 retrocopy
retro_chof_223,
Dasypus novemcinctus ENSDNOG000000031773 retrocopies
retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens ENSG00000075131 1 retrocopy
retro_hsap_4837 ,
Gorilla gorilla ENSGGOG000000000613 retrocopies
retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana ENSLAFG000000260161 retrocopy
retro_lafr_1104,
Microcebus murinus ENSMICG000000043862 retrocopies
retro_mmur_155, retro_mmur_255,
Macaca mulatta ENSMMUG000000036951 retrocopy
retro_mmul_1582,
Nomascus leucogenys ENSNLEG000000129091 retrocopy
retro_nleu_1336,
Pan troglodytes ENSPTRG000000071922 retrocopies
retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus ENSRNOG000000430681 retrocopy
retro_rnor_364,

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 = 0.02 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 .02 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:

The presence of retro_hsap_4837 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_4837 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. X:53478158..53491600 96.94 96.99 99.32 98.02 98.78 98.9 100 100 100 100 97.95 100 100 100

Indel #1, located at the genomic coordinates X:53478158..53491600.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 98.02 % Puerto Ricansfrom Puerto Rico PUR 98.78 % Colombians fromMedellin, Colombia CLM 98.9 % Americans of AfricanAncestry in SW USA ASW 96.94 % Yoruba in Ibadan,Nigeria YRI 96.99 % Luhya in Webuye,Kenya LWK 99.32 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 97.95 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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