RetrogeneDB ID:

retro_hsap_106

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:188923961..188924894(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179059
Aliases:ZFP42, REX1, ZNF754
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:YY1
Ensembl ID:ENSG00000100811
Aliases:None
Description:YY1 transcription factor [Source:HGNC Symbol;Acc:12856]


Retrocopy-Parental alignment summary:






>retro_hsap_106
ATGAGCCAGCAACTGAAGAAACGGGCAAAGACAAGACACCAGAAAGGCCTGGGTGGAAGAGCCCCCAGTGGGGCTAAGCC
CAGGCAAGGCAAGTCAAGCCAAGACCTGCAGGCGGAAATAGAACCTGTCAGCGCGGTGTGGGCCTTATGTGATGGCTATG
TGTGCTATGAGCCTGGCCCTCAGGCTCTCGGAGGGGATGATTTCTCAGACTGTTACATAGAATGCGTCATAAGGGGTGAG
TTTTCTCAACCCATCCTGGAAGAGGACTCACTTTTTGAGTCCTTGGAATACCTAAAGAAAGGATCAGAACAACAGCTTTC
TCAAAAGGTTTTCGAAGCAAGCTCCCTTGAATGTTCTTTGGAATACATGAAAAAAGGGGTAAAGAAAGAGCTTCCACAAA
AGATAGTTGGAGAGAATTCGCTTGAGTATTCTGAGTACATGACAGGCAAGAAGCTTCCGCCTGGAGGAATACCTGGCATT
GACCTATCAGATCCTAAACAGCTCGCAGAATTTGCTAGAAAGAAGCCCCCCATAAATAAAGAATATGACAGTCTGAGCGC
AATCGCTTGTCCTCAGAGTGGATGCACTAGGAAGTTGAGGAATAGAGCTGCCCTGAGAAAGCATCTCCTCATTCATGGTC
CCCGAGACCACGTCTGTGCGGAATGTGGGAAAGCGTTCGTTGAGAGCTCAAAACTAAAGAGACATTTCCTGGTTCATACT
GGAGAGAAGCCGTTTCGGTGCACTTTTGAAGGGTGCGGAAAGCGCTTCTCTCTGGACTTTAATTTGCGTACGCACGTGCG
CATCCACACGGGGGAGAAACGTTTCGTGTGTCCCTTTCAAGGCTGCAACAGGAGGTTTATTCAGTCAAATAACCTGAAAG
CCCACATCCTAACGCATGCAAATACGAACAAGAATGAACAAGAGGGAAAGTAG

ORF - retro_hsap_106 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.04 %
Parental protein coverage: 51.21 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKKWEQKQVQIKTLEGEFSVTMWSSDEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSD
KK....Q...K..E...S........KK....E......I.GENS...YSEYMTGKKLPPGGIPGIDLSD
RetrocopyKKGSEQQLSQKVFEAS-SLECSLEYMKKGVKKE--LPQKIVGENSL-EYSEYMTGKKLPPGGIPGIDLSD
ParentalPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKR
PKQLAEFAR.KP...KE.D....IACP..GCT...R...A.RKHL..HGPR.HVCAECGKAFVESSKLKR
RetrocopyPKQLAEFARKKPPINKEYDSLSAIACPQSGCTRKLRNRAALRKHLLIHGPRDHVCAECGKAFVESSKLKR
ParentalHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKN
H.LVHTGEKPF.CTFEGCGKRFSLDFNLRTHVRIHTG....VCPF.GCN..F.QS.NLK.HILTHA....
RetrocopyHFLVHTGEKPFRCTFEGCGKRFSLDFNLRTHVRIHTGEKRFVCPFQGCNRRFIQSNNLKAHILTHANTNK
ParentalNQ
N.
RetrocopyNE

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 94 .06 RPM
bodymap2_adrenal 0 .00 RPM 114 .34 RPM
bodymap2_brain 0 .00 RPM 90 .36 RPM
bodymap2_breast 0 .06 RPM 109 .69 RPM
bodymap2_colon 0 .00 RPM 145 .12 RPM
bodymap2_heart 0 .00 RPM 76 .08 RPM
bodymap2_kidney 0 .02 RPM 104 .39 RPM
bodymap2_liver 0 .00 RPM 67 .34 RPM
bodymap2_lung 0 .00 RPM 124 .17 RPM
bodymap2_lymph_node 0 .00 RPM 162 .40 RPM
bodymap2_ovary 0 .00 RPM 130 .12 RPM
bodymap2_prostate 0 .00 RPM 130 .21 RPM
bodymap2_skeletal_muscle 0 .13 RPM 109 .93 RPM
bodymap2_testis 1 .89 RPM 123 .98 RPM
bodymap2_thyroid 0 .00 RPM 123 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 224 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_106 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_106 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1427571747 libraries53 libraries27 libraries2 libraries0 libraries

The graphical summary, for retro_hsap_106 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_106 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_106 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_45
Gorilla gorilla retro_ggor_190
Pongo abelii retro_pabe_145
Equus caballus retro_ecab_97
Parental genes homology:
Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111461 retrocopy
retro_amel_2,
Bos taurus ENSBTAG000000208191 retrocopy
retro_btau_91,
Callithrix jacchus ENSCJAG000000168532 retrocopies
retro_cjac_1931, retro_cjac_4045,
Cavia porcellus ENSCPOG000000208092 retrocopies
retro_cpor_1220, retro_cpor_1522,
Equus caballus ENSECAG000000058051 retrocopy
retro_ecab_97,
Homo sapiens ENSG00000100811 2 retrocopies
retro_hsap_106 , retro_hsap_97,
Gorilla gorilla ENSGGOG000000263322 retrocopies
retro_ggor_190, retro_ggor_2,
Mustela putorius furoENSMPUG000000029311 retrocopy
retro_mputfur_867,
Mus musculus ENSMUSG000000212641 retrocopy
retro_mmus_190,
Nomascus leucogenys ENSNLEG000000009993 retrocopies
retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus ENSOCUG000000269381 retrocopy
retro_ocun_1871,
Otolemur garnettii ENSOGAG000000069554 retrocopies
retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii ENSPPYG000000259493 retrocopies
retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes ENSPTRG000000067173 retrocopies
retro_ptro_3093, retro_ptro_45, retro_ptro_494,

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 = 0.07 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 .03 RPM
FIN_HG00183 0 .00 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 .00 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 .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 .07 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 .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).





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