RetrogeneDB ID:

retro_hsap_403

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:68627439..68628773(-)
Located in intron of:ENSG00000116729
Retrocopy
information
Ensembl ID:ENSG00000234383
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CTBP2
Ensembl ID:ENSG00000175029
Aliases:None
Description:C-terminal binding protein 2 [Source:HGNC Symbol;Acc:2495]


Retrocopy-Parental alignment summary:






>retro_hsap_403
ATGGCCCTTGTGGATAAGCACAAAGTCAAGAGACAGCAATTGGACAGAATTTGTGAAGGTATCCGCCCCCAGATCATGAA
CGGCCCCCTGCACTCCTGCCCCCTGGTGGCGCTGCTGGACGGCCGCGACTGCACTGTGGAGATGCCCATCCTGAAAGACC
TGGCCACTGTGGCCTTCTGTGACGCGCAGTCCACGCAGGAAATCCACGAGAAGGTTCTAACGAAGCCATGGGTACCATGA
TGTACCACACCATCATCCTCACCAGGGAGGACCTAGAAAAGTTTAAGGCCCCGAGAGTGATCGTGCAGATAGGCAGTGGC
TACGATAACGTGGACATCAAGGCTGCCAGCGAGCTCGGAATTGCTGTGTGCAATATCCCGTCTGCAGCCGTGGAAGAGAC
ACCGGACTCTACCATCTGCCACATCCTCAATCTGTACCAGAGGAACACATGGCTGTACCAAGCACTGCGGTAAGGCACAC
GGGTTCAGAGCATGGAGCAGAACCGCGAGTTGGCCTCGGGATCGGCCAGCATCCGTGGGGAAATGCTGGGCCTCATCGGC
TTTGATCGCAGGGGGTAGGCGGTTGCAGTTCGAGCCAAGGCCTTTGGATTCAGCGTCATATTTTATGACCCCTACTTGCA
GGATGGGATCGAGCGATCCCTGGGCGTGCAGAGGGTCTACACTCTGTAGGATTTGCTGTATCAGAGCGACTGCGTCTCCT
TGCACTGCAATCTCAACGAACATAACCACCACCTCATCAATGACTTTACCATAAAGCAGATGAGGCAGGGAGCATTCCTT
GTGAACGCACCCCGTGGTGGCCTGGTGGACGAGAAAGCCTTAGCACAAGCTCTCAAGGAGGGCAGGATACGAGGGGCAGC
CCTCTATGTGCGTGAGTCGGAGCCCTTTAGCTTTGCTCAGGGTCCGTTGAAAGATGCACCGAATCTTATCTGCACTCCTC
ACACTGCCTGGTACAGCAAGCAGGCGTCACTGGAGATGAGGGAGGCAGCTGCCACTGAGATCCGCCGAGCCATCACAGGT
CACATCCCAGAAAGCTTAAGAAACTGTGTGAACAAGGAATTCTCTGTCACATCAGCGCCTTGGTCAGTAATAGACCAGCA
AGCAATTCATCCTGAGCTCAATGGTGCCACATACAGATATCCGCCAGGCATCGTGGGCGTGGCTCCAGGAGGACTTCCTG
CAGCCGTGGAAGGGATCATCCCTGGAGGCATCCCAGTGACTCACAACCTCCCAACAGTGGCACATCCTTCCCAGGCGCCC
TCTCCCAACCAGCCCACAAAACACGGGGACAATCGAGAGCACTCCAACGAGCAA

ORF - retro_hsap_403 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMALVDKHKVKRQRLDRICEGIRPQIMNGPLHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHE
MALVDKHKVKRQ.LDRICEGIRPQIMNGPLH..PLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHE
RetrocopyMALVDKHKVKRQQLDRICEGIRPQIMNGPLHSCPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHE
ParentalKVL-NEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTI
KVL.NEA.G.MMYHTI.LTREDLEKFKA.RVIV.IGSGYDNVDIKAA.ELGIAVCNIPSAAVEET.DSTI
RetrocopyKVL<NEAMGTMMYHTIILTREDLEKFKAPRVIVQIGSGYDNVDIKAASELGIAVCNIPSAAVEETPDSTI
ParentalCHILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFY
CHILNLY.RNTWLYQALR.GTRVQS.EQ.RE.ASG.A.IRGE.LGLIGF.R.G.AVAVRAKAFGFSVIFY
RetrocopyCHILNLYQRNTWLYQALR*GTRVQSMEQNRELASGSASIRGEMLGLIGFDRRG*AVAVRAKAFGFSVIFY
ParentalDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEK
DPYLQDGIERSLGVQRVYTL.DLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNA.RGGLVDEK
RetrocopyDPYLQDGIERSLGVQRVYTL*DLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAPRGGLVDEK
ParentalALAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRI
ALAQALKEGRIRGAAL.V.ESEPFSFAQGPLKDAPNLICTPHTAWYS.QASLEMREAAATEIRRAITG.I
RetrocopyALAQALKEGRIRGAALYVRESEPFSFAQGPLKDAPNLICTPHTAWYSKQASLEMREAAATEIRRAITGHI
ParentalPESLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPT
PESLRNCVNKEF.VTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAA.EGIIPGGIPVTHNLPT
RetrocopyPESLRNCVNKEFSVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAVEGIIPGGIPVTHNLPT
ParentalVAHPSQAPSPNQPTKHGDNREHPNEQ
VAHPSQAPSPNQPTKHGDNREH.NEQ
RetrocopyVAHPSQAPSPNQPTKHGDNREHSNEQ

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 .02 RPM 38 .30 RPM
bodymap2_adrenal 0 .16 RPM 24 .87 RPM
bodymap2_brain 0 .16 RPM 16 .36 RPM
bodymap2_breast 0 .10 RPM 31 .01 RPM
bodymap2_colon 0 .00 RPM 74 .81 RPM
bodymap2_heart 0 .00 RPM 19 .29 RPM
bodymap2_kidney 0 .06 RPM 69 .01 RPM
bodymap2_liver 0 .02 RPM 4 .03 RPM
bodymap2_lung 0 .11 RPM 68 .51 RPM
bodymap2_lymph_node 0 .00 RPM 32 .27 RPM
bodymap2_ovary 0 .50 RPM 73 .73 RPM
bodymap2_prostate 0 .26 RPM 66 .58 RPM
bodymap2_skeletal_muscle 0 .00 RPM 20 .88 RPM
bodymap2_testis 0 .53 RPM 57 .41 RPM
bodymap2_thyroid 0 .09 RPM 84 .01 RPM
bodymap2_white_blood_cells 0 .08 RPM 55 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_403 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_403 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_403 retrocopy 5' end.

Lab - click to see more details

retro_hsap_403 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_403 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000127751 retrocopy
retro_cfam_1868,
Callithrix jacchus ENSCJAG000000125392 retrocopies
retro_cjac_1866, retro_cjac_2528,
Homo sapiens ENSG00000175029 1 retrocopy
retro_hsap_403 ,
Oryctolagus cuniculus ENSOCUG000000070761 retrocopy
retro_ocun_378,
Pongo abelii ENSPPYG0000000274610 retrocopies
retro_pabe_1706, retro_pabe_1710, retro_pabe_1711, retro_pabe_1719, retro_pabe_1737, retro_pabe_1750, retro_pabe_1773, retro_pabe_3228, retro_pabe_3230, retro_pabe_3587,

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 ) 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 .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 .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:

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





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