RetrogeneDB ID:

retro_hsap_50

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:73524101..73524602(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000187969
Aliases:ZCCHC13, CNBP2, ZNF9L
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CNBP
Ensembl ID:ENSG00000169714
Aliases:CNBP, CNBP1, DM2, PROMM, RNF163, ZCCHC22, ZNF9
Description:CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]


Retrocopy-Parental alignment summary:






>retro_hsap_50
ATGAGCAGTAAGGATTTCTTCGCGTGTGGACACTCTGGCCATTGGGCTCGGGGATGCCCTAGAGGAGGAGCTGGAGGGCG
AAGAGGTGGAGGCCATGGCAGAGGTTCTCAATGTGGTTCCACCACCCTATCTTACACCTGTTACTGCTGTGGTGAGTCCG
GTCGTAATGCTAAGAACTGTGTCCTTCTCGGAAACATCTGCTACAACTGTGGGAGAAGCGGCCACATCGCCAAAGACTGT
AAGGATCCTAAACGAGAGAGACGCCAACACTGTTATACCTGCGGCAGACTAGGACATCTGGCTCGTGACTGTGATCGTCA
GAAAGAGCAGAAATGCTACTCTTGCGGCAAACTTGGGCACATTCAGAAAGACTGCGCCCAGGTCAAGTGTTACCGATGCG
GCGAGATTGGCCACGTGGCCATCAATTGCAGCAAGGCGAGGCCAGGTCAACTGCTACCGCTGCGGCAAATCCCGACATCT
AGCCAAGGAATGTCCCAGTGA

ORF - retro_hsap_50 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.28 %
Parental protein coverage: 85.29 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDACYNC
MSS...F.CG.SGHWAR.CP.GG..GR.....GRG.Q..S..L...CY.CGESG..AK.C.L....CYNC
RetrocopyMSSKDFFACGHSGHWARGCPRGGAGGRRGGGHGRGSQCGSTTLSYTCYCCGESGRNAKNCVLLGNICYNC
ParentalGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVA
GR.GHIAKDCK.PKRER.Q.CY.CG..GHLARDCD...EQKCYSCG..GHIQKDC..VKCYRCGE.GHVA
RetrocopyGRSGHIAKDCKDPKRERRQHCYTCGRLGHLARDCDRQKEQKCYSCGKLGHIQKDCAQVKCYRCGEIGHVA
ParentalINCSK
INCSK
RetrocopyINCSK

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 341 .52 RPM
bodymap2_adrenal 0 .00 RPM 419 .42 RPM
bodymap2_brain 0 .00 RPM 307 .18 RPM
bodymap2_breast 0 .00 RPM 305 .86 RPM
bodymap2_colon 0 .00 RPM 486 .35 RPM
bodymap2_heart 0 .00 RPM 390 .77 RPM
bodymap2_kidney 0 .00 RPM 225 .13 RPM
bodymap2_liver 0 .00 RPM 210 .60 RPM
bodymap2_lung 0 .00 RPM 606 .40 RPM
bodymap2_lymph_node 0 .00 RPM 353 .87 RPM
bodymap2_ovary 0 .00 RPM 413 .37 RPM
bodymap2_prostate 0 .00 RPM 608 .89 RPM
bodymap2_skeletal_muscle 0 .00 RPM 778 .15 RPM
bodymap2_testis 4 .94 RPM 379 .46 RPM
bodymap2_thyroid 0 .00 RPM 497 .30 RPM
bodymap2_white_blood_cells 0 .00 RPM 495 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_50 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_50 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_2011961825 libraries1 library1 library2 libraries0 libraries
TSS #2 TSS_2011971824 libraries2 libraries1 library2 libraries0 libraries

The graphical summary, for retro_hsap_50 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_50 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_50 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3658
Equus caballus retro_ecab_1072
Parental genes homology:
Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000153342 retrocopies
retro_amel_1285, retro_amel_1773,
Canis familiaris ENSCAFG000000043202 retrocopies
retro_cfam_1272, retro_cfam_23,
Cavia porcellus ENSCPOG000000128162 retrocopies
retro_cpor_424, retro_cpor_94,
Dipodomys ordii ENSDORG000000029191 retrocopy
retro_dord_569,
Echinops telfairi ENSETEG000000084085 retrocopies
retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus ENSFCAG000000280422 retrocopies
retro_fcat_1922, retro_fcat_2001,
Homo sapiens ENSG00000169714 1 retrocopy
retro_hsap_50 ,
Gorilla gorilla ENSGGOG000000100851 retrocopy
retro_ggor_2926,
Macropus eugenii ENSMEUG000000116991 retrocopy
retro_meug_55,
Myotis lucifugus ENSMLUG000000125541 retrocopy
retro_mluc_141,
Macaca mulatta ENSMMUG000000115851 retrocopy
retro_mmul_2505,
Mustela putorius furoENSMPUG000000173153 retrocopies
retro_mputfur_1465, retro_mputfur_1555, retro_mputfur_583,
Mus musculus ENSMUSG000000300571 retrocopy
retro_mmus_230,
Nomascus leucogenys ENSNLEG000000144821 retrocopy
retro_nleu_1986,
Otolemur garnettii ENSOGAG000000138981 retrocopy
retro_ogar_144,
Ochotona princeps ENSOPRG000000054875 retrocopies
retro_opri_139, retro_opri_49, retro_opri_496, retro_opri_566, retro_opri_965,
Pongo abelii ENSPPYG000000134231 retrocopy
retro_pabe_3658,
Pan troglodytes ENSPTRG000000153691 retrocopy
retro_ptro_3131,
Rattus norvegicus ENSRNOG000000102392 retrocopies
retro_rnor_207, retro_rnor_727,
Ictidomys tridecemlineatus ENSSTOG000000001731 retrocopy
retro_itri_113,
Tarsius syrichta ENSTSYG000000043441 retrocopy
retro_tsyr_1889,
Vicugna pacos ENSVPAG000000071381 retrocopy
retro_vpac_548,

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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