RetrogeneDB ID:

retro_hsap_449

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:146675152..146676513(-)
Located in intron of:ENSG00000237188
Retrocopy
information
Ensembl ID:ENSG00000226015
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT8
Ensembl ID:ENSG00000156261
Aliases:CCT8, C21orf112, Cctq, D21S246, PRED71
Description:chaperonin containing TCP1, subunit 8 (theta) [Source:HGNC Symbol;Acc:1623]


Retrocopy-Parental alignment summary:






>retro_hsap_449
ATGGCGCTTCAAGTTCCCAAGGCTCCGGGCTTCGCCCAGATGCTCAAGGAGGGAGCGAAACACTTTTCAGAATTAGAAGA
GGCTGTGTATAGAAACATACAAGCTTGCAAGGAGCTTGCCCAAACCACTCGTACAGCATATGGACGAAATGGAATGAAAA
AAATGGTTATCAACTACTTGGAGAAGTTGTTTGTGACAAATGATGCAGCGACTATTTTAAGAGAACTAGAAGTACAGCAT
CCTGCTGCAAAAATGACTGTAATGGCTTCTCATATGCAAGAGCAAGAAGTTGGAGATGGCACAAACATTGTTCTGGTATT
TGCTGGAGCTCTCCTGGAATTAGCTGAAGAACTTCTGAGGATTGGCCTGTCAGTTTCAGAGGTCATAGAAGGTTATGAAA
TAGCTTGCAGAAAAGCTCATGAGATTCTTCCTAATTTGGTACGTTGTTCTGCAAAAAACCTTCGAGATGTTGATGAAGTC
TCATCTCTACTTCGTACCTCTGTAATGTGTAAACAATATGGTAATGAAGTATTTCTGGCCAAGCTTATTGTTCAGGCATG
CGTATCTATTTTTCCTGATTCTGGCCATTTCAAAGTTGATAACATCAGAGTTTGTAAAATTCTGGGCTGTGGTATCACTT
CCTCTTCAGTATTGCATGGCATGGTTTTTAAGAAGGAAACAGAAGGTGATGTACATCTGTCAAAGATGCAAAAATAGCAG
TGTACTCTTGTCCTTTTGATGGCATGATAACAGAAACTAAGGGAACAGTGTTGATAAAGACTGATGAAGAATTGATGAAT
TTAAGTAAGGGAGAAGAAAATCTCATGGATGCATAAGTCAAAGCTATTGCTGATACTGGTGCAAATGTTGTAGTAACAGG
TGGCAAAGTGGCAGACATGGCTCTTCATTATGCAAACAAATATAATATGATGTTAGTGAAGCTAAACTCAAAATGGGATG
TCTGAAGACTCTGTAAAACAGTTGGTGCTACAGCTCTTCCTAGATTGACACCTCCTGTCCTTGAAGAAATGGGACACTGA
GACAGTGTTTACCTCTCAGAAGTTGGAGATACTCAGGTGGTGGTTTTTAAGCATGAAAAGGAAGATGGCATCATTTCTAC
CATAGTACTTCAGGGCTCTACAGACAATCTGATGGATGACATAGAAAGGGCAGTAGATGATGGTGTTAATACTTTCAAAG
TTCTTACAAGGGATAAACGTCTTGTACCCGGAGGTGGAGCAACAGAAATTGAATTAGCCAAACAGATCACATCATATGGA
GAGACATGTCCTGGACTTGAACAGTACGCTATTAAGAAGTTTGCTGAGGCGTTTGAAGCTATTCCCCGTGCACTGGCAGA
A

ORF - retro_hsap_449 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.29 %
Parental protein coverage: 82.85 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMALHVPKAPGFAQMLKEGAKHFSGLEEAVYRNIQACKELAQTTRTAYGPNGMNKMVINHLEKLFVTNDAA
MAL.VPKAPGFAQMLKEGAKHFS.LEEAVYRNIQACKELAQTTRTAYG.NGM.KMVIN.LEKLFVTNDAA
RetrocopyMALQVPKAPGFAQMLKEGAKHFSELEEAVYRNIQACKELAQTTRTAYGRNGMKKMVINYLEKLFVTNDAA
ParentalTILRELEVQHPAAKMIVMASHMQEQEVGDGTNFVLVFAGALLELAEELLRIGLSVSEVIEGYEIACRKAH
TILRELEVQHPAAKM.VMASHMQEQEVGDGTN.VLVFAGALLELAEELLRIGLSVSEVIEGYEIACRKAH
RetrocopyTILRELEVQHPAAKMTVMASHMQEQEVGDGTNIVLVFAGALLELAEELLRIGLSVSEVIEGYEIACRKAH
ParentalEILPNLVCCSAKNLRDIDEVSSLLRTSIMSKQYGNEVFLAKLIAQACVSIFPDSGHFNVDNIRVCKILGS
EILPNLV.CSAKNLRD.DEVSSLLRTS.M.KQYGNEVFLAKLI.QACVSIFPDSGHF.VDNIRVCKILG.
RetrocopyEILPNLVRCSAKNLRDVDEVSSLLRTSVMCKQYGNEVFLAKLIVQACVSIFPDSGHFKVDNIRVCKILGC
ParentalGISSSSVLHGMVFKKETEGDV-TSVKDAKIAVYSCPFDGMITETKGTVLIKTAEELMNFSKGEENLMDAQ
GI.SSSVLHGMVFKKETEGDV.TSVKDAKIAVYSCPFDGMITETKGTVLIKT.EELMN.SKGEENLMDA.
RetrocopyGITSSSVLHGMVFKKETEGDV<TSVKDAKIAVYSCPFDGMITETKGTVLIKTDEELMNLSKGEENLMDA*
ParentalVKAIADTGANVVVTGGKVADMALHYANKYNIMLVRLNSKWDLRRLCKTVGATALPRLTPPVLEEMGHCDS
VKAIADTGANVVVTGGKVADMALHYANKYN.MLV.LNSKWD..RLCKTVGATALPRLTPPVLEEMGH.DS
RetrocopyVKAIADTGANVVVTGGKVADMALHYANKYNMMLVKLNSKWDV*RLCKTVGATALPRLTPPVLEEMGH*DS
ParentalVYLSEVGDTQVVVFKHEKEDGAISTIVLRGSTDNLMDDIERAVDDGVNTFKVLTRDKRLVPGGGATEIEL
VYLSEVGDTQVVVFKHEKEDG.ISTIVL.GSTDNLMDDIERAVDDGVNTFKVLTRDKRLVPGGGATEIEL
RetrocopyVYLSEVGDTQVVVFKHEKEDGIISTIVLQGSTDNLMDDIERAVDDGVNTFKVLTRDKRLVPGGGATEIEL
ParentalAKQITSYGETCPGLEQYAIKKFAEAFEAIPRALAE
AKQITSYGETCPGLEQYAIKKFAEAFEAIPRALAE
RetrocopyAKQITSYGETCPGLEQYAIKKFAEAFEAIPRALAE

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 .20 RPM 133 .78 RPM
bodymap2_adrenal 1 .45 RPM 157 .02 RPM
bodymap2_brain 0 .66 RPM 132 .32 RPM
bodymap2_breast 0 .78 RPM 110 .84 RPM
bodymap2_colon 0 .27 RPM 199 .16 RPM
bodymap2_heart 0 .66 RPM 93 .27 RPM
bodymap2_kidney 1 .37 RPM 155 .41 RPM
bodymap2_liver 3 .40 RPM 75 .92 RPM
bodymap2_lung 0 .40 RPM 135 .67 RPM
bodymap2_lymph_node 0 .27 RPM 139 .76 RPM
bodymap2_ovary 0 .71 RPM 181 .47 RPM
bodymap2_prostate 0 .71 RPM 151 .78 RPM
bodymap2_skeletal_muscle 0 .33 RPM 129 .68 RPM
bodymap2_testis 0 .51 RPM 247 .37 RPM
bodymap2_thyroid 1 .45 RPM 179 .59 RPM
bodymap2_white_blood_cells 0 .53 RPM 163 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_449 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_449 retrocopy
EST ID Start End Identity Match Mis-match Score
BG471324 146675084 146675794 98.8 700 9 690
CB155944 146675321 146675898 99.5 574 3 571

TSS - click to see more details

No TSS is located nearby retro_hsap_449 retrocopy 5' end.

Lab - click to see more details

retro_hsap_449 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_449 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_435
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000156261 1 retrocopy
retro_hsap_449 ,
Gorilla gorilla ENSGGOG000000063441 retrocopy
retro_ggor_435,
Pongo abelii ENSPPYG000000113181 retrocopy
retro_pabe_1759,

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 = 0.76 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .43 RPM
CEU_NA11843 0 .40 RPM
CEU_NA11930 0 .55 RPM
CEU_NA12004 0 .49 RPM
CEU_NA12400 0 .42 RPM
CEU_NA12751 0 .46 RPM
CEU_NA12760 0 .76 RPM
CEU_NA12827 0 .52 RPM
CEU_NA12872 0 .27 RPM
CEU_NA12873 0 .29 RPM
FIN_HG00183 0 .44 RPM
FIN_HG00277 0 .37 RPM
FIN_HG00315 0 .41 RPM
FIN_HG00321 0 .54 RPM
FIN_HG00328 0 .40 RPM
FIN_HG00338 0 .21 RPM
FIN_HG00349 0 .65 RPM
FIN_HG00375 0 .34 RPM
FIN_HG00377 0 .28 RPM
FIN_HG00378 0 .49 RPM
GBR_HG00099 0 .23 RPM
GBR_HG00111 0 .28 RPM
GBR_HG00114 0 .37 RPM
GBR_HG00119 0 .34 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .27 RPM
GBR_HG00134 0 .33 RPM
GBR_HG00137 0 .47 RPM
GBR_HG00142 0 .61 RPM
GBR_HG00143 0 .32 RPM
TSI_NA20512 0 .23 RPM
TSI_NA20513 0 .27 RPM
TSI_NA20518 0 .69 RPM
TSI_NA20532 0 .54 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .23 RPM
TSI_NA20765 0 .56 RPM
TSI_NA20771 0 .28 RPM
TSI_NA20786 0 .34 RPM
TSI_NA20798 0 .25 RPM
YRI_NA18870 0 .34 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .25 RPM
YRI_NA19093 0 .29 RPM
YRI_NA19099 0 .37 RPM
YRI_NA19114 0 .24 RPM
YRI_NA19118 0 .27 RPM
YRI_NA19213 0 .24 RPM
YRI_NA19214 0 .37 RPM
YRI_NA19223 0 .40 RPM

Indel association:

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



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