RetrogeneDB ID:

retro_hsap_4851

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:69157012..69157867(-)
Located in intron of:ENSG00000158813
Retrocopy
information
Ensembl ID:ENSG00000233229
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CNOT7
Ensembl ID:ENSG00000198791
Aliases:CNOT7, CAF1, Caf1a, hCAF-1
Description:CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]


Retrocopy-Parental alignment summary:






>retro_hsap_4851
ATGCCAGCAGCAACTGTACATCATAGCCAAAGAATTTGTGAAGTTTGGGCTTGCAACGTGGATGAAGAGATGAAGAAAAT
TCATCAAGTTATCCGAAAATATAATTACGTTGCTATGGACACCGAGTTTCCAGGTGTGGTTGCAAGACCCACTGGAGGAT
TCAGGAGCAATGCTGACTATCAATACCAACTATTGCGGTGTAATGTAGACTTGTTAAAGATAATTCAGCTAGGACTGACA
TTTATAAATGAGCAAGGAGAATACCCTCCAGGAACTTCAACTTGGCAGTTTAATTTTAAATTTAATTTGACAGAGGACAT
GTATGCCCAGAACTCTATAGAGCTACTAACAACATCTGGTATCCAGTTTAAAAAACATGATGAGGAAGGAATTGAGACCC
AGTACTTTGCAGAACTTCTTATGACTTCAGGAGTGGTCCTCTGTGAAGGGGTCAAATGGTTGTCATTTCACAGCAGTTAC
AACTTTGGCTATTTAATCAAAATGCTGACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTGAGATCCTTCGATT
GTTTTTACCTGTCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAACATCTCAAAGATGGATTACAGGAGGTGGCAG
AACAGTTAGAGCTGGCATAGATAGGACCACCACATCAGGCAGGATCTAAATCATTGCTGACAGGAATGGCCTTTTTCAAA
ATGAGAGGAATGTTCTTTGAAGATCATACTGATGATGCCAAATATTGTGGTCATTTGTATGGCCTTGGTTCTGGTTCATC
CTATGTACAGAATGGCACAGGGAATGCATATGAAGAAGAAGCCAACAAGCAGTCA

ORF - retro_hsap_4851 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.98 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD
MPAATV.HSQRICEVWACN.DEEMKKI.QVIRKYNYVAMDTEFPGVVARP.G.FRSNADYQYQLLRCNVD
RetrocopyMPAATVHHSQRICEVWACNVDEEMKKIHQVIRKYNYVAMDTEFPGVVARPTGGFRSNADYQYQLLRCNVD
ParentalLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL
LLKIIQLGLTF.NEQGEYPPGTSTWQFNFKFNLTEDMYAQ.SIELLTTSGIQFKKH.EEGIETQYFAELL
RetrocopyLLKIIQLGLTFINEQGEYPPGTSTWQFNFKFNLTEDMYAQNSIELLTTSGIQFKKHDEEGIETQYFAELL
ParentalMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQ
MTSGVVLCEGVKWLSFHS.Y.FGYLIK.LTNSNLPEEELDFFEILRLF.PVIYDVKYLMKSCK.LK.GLQ
RetrocopyMTSGVVLCEGVKWLSFHSSYNFGYLIKMLTNSNLPEEELDFFEILRLFLPVIYDVKYLMKSCKHLKDGLQ
ParentalEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEEE
EVAEQLEL..IGP.HQAGS.SLLTGMAFFKMR.MFFEDH.DDAKYCGHLYGLGSGSSYVQNGTGNAYEEE
RetrocopyEVAEQLELA*IGPPHQAGSKSLLTGMAFFKMRGMFFEDHTDDAKYCGHLYGLGSGSSYVQNGTGNAYEEE
ParentalANKQS
ANKQS
RetrocopyANKQS

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 54 .33 RPM
bodymap2_adrenal 0 .00 RPM 74 .59 RPM
bodymap2_brain 0 .00 RPM 80 .89 RPM
bodymap2_breast 0 .00 RPM 77 .20 RPM
bodymap2_colon 0 .00 RPM 77 .65 RPM
bodymap2_heart 0 .00 RPM 51 .75 RPM
bodymap2_kidney 0 .15 RPM 85 .24 RPM
bodymap2_liver 0 .00 RPM 35 .07 RPM
bodymap2_lung 0 .00 RPM 59 .95 RPM
bodymap2_lymph_node 0 .00 RPM 73 .79 RPM
bodymap2_ovary 0 .00 RPM 103 .21 RPM
bodymap2_prostate 0 .00 RPM 80 .28 RPM
bodymap2_skeletal_muscle 0 .00 RPM 80 .70 RPM
bodymap2_testis 0 .00 RPM 110 .78 RPM
bodymap2_thyroid 0 .00 RPM 117 .79 RPM
bodymap2_white_blood_cells 0 .00 RPM 136 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4851 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4851 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4851 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4851 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4851 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3771
Macaca mulatta retro_mmul_2592
Parental genes homology:
Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000006774 retrocopies
retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus ENSCJAG000000117951 retrocopy
retro_cjac_720,
Felis catus ENSFCAG000000005911 retrocopy
retro_fcat_1889,
Homo sapiens ENSG00000198791 2 retrocopies
retro_hsap_211, retro_hsap_4851 ,
Macaca mulatta ENSMMUG000000018731 retrocopy
retro_mmul_2592,
Mustela putorius furoENSMPUG000000179721 retrocopy
retro_mputfur_1596,
Nomascus leucogenys ENSNLEG000000024892 retrocopies
retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus ENSOCUG000000145891 retrocopy
retro_ocun_118,
Otolemur garnettii ENSOGAG000000063242 retrocopies
retro_ogar_1883, retro_ogar_505,
Pongo abelii ENSPPYG000000183852 retrocopies
retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii ENSSHAG000000118282 retrocopies
retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus ENSSTOG000000091752 retrocopies
retro_itri_1729, retro_itri_1730,

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 .02 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 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 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 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 .02 RPM

Indel association:

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





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