RetrogeneDB ID:

retro_hsap_3722

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:42834504..42835781(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229161
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TCP1
Ensembl ID:ENSG00000120438
Aliases:TCP1, CCT-alpha, CCT1, CCTa, D6S230E, TCP-1-alpha
Description:t-complex 1 [Source:HGNC Symbol;Acc:11655]


Retrocopy-Parental alignment summary:






>retro_hsap_3722
ATGGAGAGGCCTTTGTCCGTGTTTGGGGACCGCAGCACTGGGGAGGCGATCTGCTCCCAGAACGTTATGGCTGCAGCTTT
GATTGCCAATACTGTAAAAAGTTCTCTTGGTCCAGTTGGCTTGGTTAAAATGTTGGTGGATGATATTGGTGATGTATCCA
TTACTAACGGTGGTGCACCATCCTGAAGTTACTGGAGGTAGAACATCCTGCAGCTAAAGTTCTTTGTGAGCTGGCTGATC
TGCAAGACAAAGAAGTTGGAGATGGAACTACCTCCGTGGTTATTATTGCAGCAGAACTCCTAAAAAATGAAGATGAATTA
GTCAAACAGAAAATTCATCCCACGTCAGTTATTAGTGGCTATGGACTTGCTTGCAAGGAAGCAGTGCGTTATATCAATGA
AAACCTAATTGTTAACACAGATAAAGTGGGAAGAGATTGCCTGATTAATGCTGCCAAGACATCCACGTCTTCCAAAATCA
TTGGAATAAATGGCGATTTCTTTGCTAACATGGTAGTAGATGCTGTATTTGCTATTAAATACACAGACATAAGAGGCCAG
CCATGCTATCCAGTCAATTCTGTTAATATTTTGAAAGCCCATGGGAAAAGTCAAACAGAGAGTATGCTCATCAGTGGCTA
TGCACTCAACTGTGTGGTGGGATCCCAGGGCATACCCAAGAGAATTGTAAATGCAAAAATTGCTTGCCTTGACTTTGGCC
TGCAAAAAACAAAAATGAAGCTTGGTATACAGGTGGTCATTACAGACCCTGAAAAACTGGACCAAATTAGACAGAGAGAA
TCAGATATTACCAAGGAGAGAATTCAGAAGATCCTGGTAACTGGTGCCAGCATTATTCTAACCACTGGTGGAATTGATGA
TATGTGTCTGAAGTATTTTGTGGAGGCTGGTGCTACGGCAGTTAGAAGAGTTTTTAAAAGGGACCTTAAACGCATTCCGA
AAGCTTCTGGAGCAACTATTCTGTCAACTCTGGCCAATTTGAAAGGTAAAGAAACTTTTGAAGCTGCAGTGTTGGGGCAG
GCAGAAGAAGTGGTATAGCAGAGAATTTGTGATGATGAGCTGATCTTAATCAAAAACACTAACCCTCATACATTTGCATC
GATTATCTTACGTGGGACAAATGATTACATGTGTGATGAGATGAAGCATTCTTTACATGATGCTTTTTGTGTAGTGAAGA
TAGTTTTGGTGTCAAAATCTGTGGTTCCAGGTGTGGGTGCTGTAGAAGTAGCCCTTTCTATATACCTTGAAAACTAT

ORF - retro_hsap_3722 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.46 %
Parental protein coverage: 98.38 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEGPLSVFGDRSTGETIRSQNVMAAASIANIVKSSLGPVGLDKMLVDDIGDVTITNDGA-TILKLLEVEH
ME.PLSVFGDRSTGE.I.SQNVMAAA.IAN.VKSSLGPVGL.KMLVDDIGDV.ITN.GA.TILKLLEVEH
RetrocopyMERPLSVFGDRSTGEAICSQNVMAAALIANTVKSSLGPVGLVKMLVDDIGDVSITNGGA<TILKLLEVEH
ParentalPAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENLIVN
PAAKVLCELADLQDKEVGDGTTSVVIIAAELLKN.DELVKQKIHPTSVISGY.LACKEAVRYINENLIVN
RetrocopyPAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNEDELVKQKIHPTSVISGYGLACKEAVRYINENLIVN
ParentalTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTDIRGQPRYPVNSVNILKAHGRSQMESM
TD..GRDCLINAAKTS.SSKIIGINGDFFANMVVDAV.AIKYTDIRGQP.YPVNSVNILKAHG.SQ.ESM
RetrocopyTDKVGRDCLINAAKTSTSSKIIGINGDFFANMVVDAVFAIKYTDIRGQPCYPVNSVNILKAHGKSQTESM
ParentalLISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQKIL
LISGYALNCVVGSQG.PKRIVNAKIACLDF.LQKTKMKLG.QVVITDPEKLDQIRQRESDITKERIQKIL
RetrocopyLISGYALNCVVGSQGIPKRIVNAKIACLDFGLQKTKMKLGIQVVITDPEKLDQIRQRESDITKERIQKIL
ParentalATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGATILSTLANLEGEETFEAAMLGQAE
.TGA..ILTTGGIDDMCLKYFVEAGA.AVRRV.KRDLKRI.KASGATILSTLANL.G.ETFEAA.LGQAE
RetrocopyVTGASIILTTGGIDDMCLKYFVEAGATAVRRVFKRDLKRIPKASGATILSTLANLKGKETFEAAVLGQAE
ParentalEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAAL
EVV..RICDDELILIKNT...T.ASIILRG.ND.MCDEM..SLHDA.CVVK.VL.SKSVVPG.GAVE.AL
RetrocopyEVV*QRICDDELILIKNTNPHTFASIILRGTNDYMCDEMKHSLHDAFCVVKIVLVSKSVVPGVGAVEVAL
ParentalSIYLENY
SIYLENY
RetrocopySIYLENY

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 195 .42 RPM
bodymap2_adrenal 0 .00 RPM 176 .79 RPM
bodymap2_brain 0 .00 RPM 155 .48 RPM
bodymap2_breast 0 .02 RPM 164 .98 RPM
bodymap2_colon 0 .00 RPM 234 .76 RPM
bodymap2_heart 0 .00 RPM 117 .28 RPM
bodymap2_kidney 0 .00 RPM 198 .78 RPM
bodymap2_liver 0 .00 RPM 111 .41 RPM
bodymap2_lung 0 .02 RPM 144 .27 RPM
bodymap2_lymph_node 0 .00 RPM 203 .51 RPM
bodymap2_ovary 0 .00 RPM 257 .38 RPM
bodymap2_prostate 0 .02 RPM 157 .06 RPM
bodymap2_skeletal_muscle 0 .02 RPM 166 .69 RPM
bodymap2_testis 0 .00 RPM 348 .91 RPM
bodymap2_thyroid 0 .09 RPM 252 .47 RPM
bodymap2_white_blood_cells 0 .00 RPM 131 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3722 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3722 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3722 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3722 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3722 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2617
Gorilla gorilla retro_ggor_2514
Macaca mulatta retro_mmul_1696
Parental genes homology:
Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000154051 retrocopy
retro_amel_828,
Callithrix jacchus ENSCJAG000000117922 retrocopies
retro_cjac_1867, retro_cjac_2193,
Equus caballus ENSECAG000000179531 retrocopy
retro_ecab_798,
Homo sapiens ENSG00000120438 1 retrocopy
retro_hsap_3722 ,
Gorilla gorilla ENSGGOG000000140631 retrocopy
retro_ggor_2514,
Microcebus murinus ENSMICG000000079981 retrocopy
retro_mmur_795,
Macaca mulatta ENSMMUG000000128461 retrocopy
retro_mmul_1696,
Oryctolagus cuniculus ENSOCUG000000138471 retrocopy
retro_ocun_1577,
Pongo abelii ENSPPYG000000171461 retrocopy
retro_pabe_3135,
Pan troglodytes ENSPTRG000000187601 retrocopy
retro_ptro_2617,
Pteropus vampyrus ENSPVAG000000053161 retrocopy
retro_pvam_522,
Sorex araneus ENSSARG000000024631 retrocopy
retro_sara_624,
Sarcophilus harrisii ENSSHAG000000151281 retrocopy
retro_shar_830,
Ictidomys tridecemlineatus ENSSTOG000000055721 retrocopy
retro_itri_1274,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 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 .14 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 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).





Copyright © RetrogeneDB 2014-2017