RetrogeneDB ID:

retro_hsap_1219

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:79483058..79484679(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230584
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT5
Ensembl ID:ENSG00000150753
Aliases:CCT5, CCT-epsilon, CCTE, HEL-S-69, TCP-1-epsilon
Description:chaperonin containing TCP1, subunit 5 (epsilon) [Source:HGNC Symbol;Acc:1618]


Retrocopy-Parental alignment summary:






>retro_hsap_1219
GCGTCTATGGGGACCCTCGCCTTTGATTGATATGGGCCCCCTTTCCTTATCATCAAAGATCAGGACCGCAAGTCCCGCCT
TATGGGACTTGAGGCCCTCAAGTCTCATATAATGGTGGCAAATGCTGTAGCACATGCGACAAGAACATCACTTGGACCAA
AGGGGCTTCATAAGATGGTGGTGGATAAGGATGGCGATGTGACTGTAACTAATGATGGGGTCACCATCTTAAGCGTGATG
GATGTCAGTCATCAGATTGCCCAGTTTGATGGTGGAAATGTCTAAGTCTCAGGATGATGAAATTGGAGATGGAACCACAG
GTGTGGTTGTCCTGGCTGGTGCCTTGTTAGAAGAAGCCCAGGAGTTGCCAGACCGAAGTATTCATCCAATCAGAATAGCA
GATGGCTATGAGCAGGCTGCCTGCTTTGCTGTGGAACACCTGGACAAGATCAGTGACAGCATCCTTGTTGACATAAAAGA
CACCAAACCCCTGATTCAGACTGCAAAAACCACGCTGGGCTCCAAAGTGGTCAACAATTGTTACCGACAAATGGCTGAGA
TTGCTGTGAATGCCATCCTCCCTTAACAGATATGGAGCAGAGAGGTGTTGACTTTGAGCTTATCAAAGTAGAAAGCAAAG
TGGGTGGCAGCCTGGAGGACAATAAACGGATTAAGGGTGTGATTGTGGACAAGTATTTCAGTCACCCACAGATGCCAAAA
AAAGTGGAAGATGCCAAGATTGTAATTCTCACATGTCCATTTGAACTACCCAAACCAAAAGCAAAGCATAAGCTGGATGT
GACCTCTGTAGAAGATTATAAAGCCCTTCAGAAATATGAAAAGGAGAAATTTTAAGAGATGATTCAACAAATTAAAGAGA
CTGGTGCTAACCTAGAAATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTACTTCTTCAGAACAACTTGCCTGCG
GTTTGCTAGGTAGGAGGACCTGAAATTGAACTGATTGCCATCACAACAGGAGGGCAGATCATCACCAAGTTCTCAGAGCT
CATGGCCAGGAAGCTGGGCTTTGCTGGTCTTGTACAGGAGATCTCATTTTGGACAACTAAGGATAAAATGCTGGTCATCG
AGCAGTGTAAGAACTCCAGAGCTATAACCATTTTTATGAGAAGAAGAAATAAGATGATTATTGAGGAGGCAAAACAATCC
CTTCACGGTGCTTTGTGTGTCATCTGGAACCTCATCCGTGATAATCATGTGGTGTATGGAGGAGGGGCTGCTGAGATATC
CTGTGCTCTGCCAGTTAGCCAAGAGGTGGATAAGTGCCCCACCTTAGAACAGTATGCCATGAGAGCGCTTGCCAACACGT
TGGAGGTCATCCCCAAGGCCCTTTCTGAAAACGGTGGCATGAATCCTATCCAGAGTATGACCAAAGTCTGAGCCAGCCAA
GTGAAGGAGATGAACCTTGCTCTTGGCATCGACTGTTTGCACAAGGGGACAAATTATATGAAGCAATAACGTGTCACAGA
AACCTCGATTGGCAAAAAAGCAACAGATATCTCTTGCAACACAAATGGTTAGAATGATTTTGAAGAATGACAACATTCAT
AAGACTGGAGAATCTGAAGAA

ORF - retro_hsap_1219 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.53 %
Parental protein coverage: 99.82 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalASMGTLAFDEYGRPFLIIKDQDRKSRLMGLEALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVTVT
ASMGTLAFD.YG.PFLIIKDQDRKSRLMGLEALKSHIM.A.AVA...RTSLGP.GL.KM.VDKDGDVTVT
RetrocopyASMGTLAFD*YGPPFLIIKDQDRKSRLMGLEALKSHIMVANAVAHATRTSLGPKGLHKMVVDKDGDVTVT
ParentalNDGATILSMMDVDHQIAK-LMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQA
NDG.TILS.MDV.HQIA..LMVE.SKSQDDEIGDGTTGVVVLAGALLEEA..L.DR.IHPIRIADGYEQA
RetrocopyNDGVTILSVMDVSHQIAQ>LMVEMSKSQDDEIGDGTTGVVVLAGALLEEAQELPDRSIHPIRIADGYEQA
ParentalARVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVNSCHRQMAEIAVNAVLT-VADMERRDVDFELI
A..A.EHLDKISDS.LVDIKDT.PLIQTAKTTLGSKVVN.C.RQMAEIAVNA.L....DME.R.VDFELI
RetrocopyACFAVEHLDKISDSILVDIKDTKPLIQTAKTTLGSKVVNNCYRQMAEIAVNAILP<LTDMEQRGVDFELI
ParentalKVEGKVGGRLEDTKLIKGVIVDKDFSHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKALQK
KVE.KVGG.LED.K.IKGVIVDK.FSHPQMPKKVEDAKI.ILTCPFE.PKPK.KHKLDVTSVEDYKALQK
RetrocopyKVESKVGGSLEDNKRIKGVIVDKYFSHPQMPKKVEDAKIVILTCPFELPKPKAKHKLDVTSVEDYKALQK
ParentalYEKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVPRFSELT
YEKEKF.EMIQQIKETGANL.ICQWGFDDEANHLLLQNNLPAV..VGGPEIELIAI.TGG.I...FSEL.
RetrocopyYEKEKF*EMIQQIKETGANLEICQWGFDDEANHLLLQNNLPAVC*VGGPEIELIAITTGGQIITKFSELM
ParentalAEKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIRDNRVV
A.KLGFAGLVQEISF.TTKDKMLVIEQCKNSRA.TIF.R..NKMIIEEAK.SLH.ALCVI.NLIRDN.VV
RetrocopyARKLGFAGLVQEISFWTTKDKMLVIEQCKNSRAITIFMRRRNKMIIEEAKQSLHGALCVIWNLIRDNHVV
ParentalYGGGAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIPMALSENSGMNPIQTMTEVRARQVKEMNPAL
YGGGAAEISCAL.VSQE.DKCPTLEQYAMRA.A..LEVIP.ALSEN.GMNPIQ.MT.V.A.QVKEMN.AL
RetrocopyYGGGAAEISCALPVSQEVDKCPTLEQYAMRALANTLEVIPKALSENGGMNPIQSMTKV*ASQVKEMNLAL
ParentalGIDCLHKGTNDMKQQHVIETLIG-KKQQISLATQMVRMILKIDDIRKPGESEE
GIDCLHKGTN.MKQ..V.ET.IG.KKQQISLATQMVRMILK.D.I.K.GESEE
RetrocopyGIDCLHKGTNYMKQ*RVTETSIG>KKQQISLATQMVRMILKNDNIHKTGESEE

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 83 .47 RPM
bodymap2_adrenal 0 .00 RPM 111 .54 RPM
bodymap2_brain 0 .00 RPM 60 .29 RPM
bodymap2_breast 0 .00 RPM 82 .61 RPM
bodymap2_colon 0 .00 RPM 104 .59 RPM
bodymap2_heart 0 .00 RPM 49 .25 RPM
bodymap2_kidney 0 .00 RPM 122 .02 RPM
bodymap2_liver 0 .00 RPM 59 .12 RPM
bodymap2_lung 0 .00 RPM 78 .66 RPM
bodymap2_lymph_node 0 .00 RPM 95 .90 RPM
bodymap2_ovary 0 .00 RPM 106 .27 RPM
bodymap2_prostate 0 .00 RPM 77 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 107 .82 RPM
bodymap2_testis 0 .00 RPM 196 .13 RPM
bodymap2_thyroid 0 .00 RPM 120 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 121 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1219 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1219 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1219 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1219 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1219 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_834
Pongo abelii retro_pabe_1012
Macaca mulatta retro_mmul_1294
Parental genes homology:
Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000089771 retrocopy
retro_cjac_516,
Homo sapiens ENSG00000150753 2 retrocopies
retro_hsap_1219 , retro_hsap_3230,
Gorilla gorilla ENSGGOG000000240641 retrocopy
retro_ggor_2197,
Macaca mulatta ENSMMUG000000201122 retrocopies
retro_mmul_1294, retro_mmul_2033,
Monodelphis domestica ENSMODG000000023561 retrocopy
retro_mdom_861,
Pan troglodytes ENSPTRG000000167252 retrocopies
retro_ptro_2182, retro_ptro_834,
Tupaia belangeri ENSTBEG000000012012 retrocopies
retro_tbel_1618, retro_tbel_4389,

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 = 0.04 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 .04 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 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 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 .03 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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