RetrogeneDB ID:

retro_mmus_230

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:103630672..103631185(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000031330
Aliases:Zcchc13, 4930513O09Rik, Cnbp2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Cnbp
Ensembl ID:ENSMUSG00000030057
Aliases:Cnbp, AA408710, Cnbp1, Znf9
Description:cellular nucleic acid binding protein [Source:MGI Symbol;Acc:MGI:88431]


Retrocopy-Parental alignment summary:






>retro_mmus_230
ATGAGCAGTAAAAGTTGCTTCAAGTGTGGACACTCTGGCCACTGGGCCCGGGAGTGTCCTAAGGGAGGAACCCGAGGGCG
AACAGCAAGAGGTCGTACCAGAGGTCCCCAGTGCAGCACCGCCAACCAGTCCGATGTTTGTTATCGCTGTGGTGAAACTG
GTCACTACGCCAAGGACTGTGATCTTCTCCAGGATACCTGCTACAACTGCGGGAGAAGAGGACACATAGCTAAGGACTGT
ACCCAGGCTAAACGAGAGAGGGAGCAGTGCTGTTACATCTGCAGTCAGCCTGGTCATCTGGCTCGGGACTGCAACCGGCA
AGAAGAACAGAAATGCTACACTTGTGGTGAATTTGGGCACATCCAGAAAGATTGTACCCAAATTAAGTGCTACAGATGTG
GTGAGAATGGCCACATGGCGGTGAACTGCAGCAAGACGAGCGAAGTCAGCTGCTACCGCTGTGGAGAGTCTGGACATCTG
GCTCGGGAATGCCCCATTGAGGCTACCGCTTAG

ORF - retro_mmus_230 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.79 %
Parental protein coverage: 83.05 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYN
.RGR......RG.Q.......D.CYRCGE.GH.AKDCDL..D.CYNCGR.GHIAKDC...KREREQCCY.
RetrocopyTRGRTARGRTRGPQCSTANQSDVCYRCGETGHYAKDCDLLQDTCYNCGRRGHIAKDCTQAKREREQCCYI
ParentalCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARE
C..PGHLARDC....EQKCY.CGEFGHIQKDCT..KCYRCGE.GH.A.NCSKTSEV.CYRCGESGHLARE
RetrocopyCSQPGHLARDCNRQEEQKCYTCGEFGHIQKDCTQIKCYRCGENGHMAVNCSKTSEVSCYRCGESGHLARE
ParentalCTIEATA
C.IEATA
RetrocopyCPIEATA

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
SRP007412_brain 0 .05 RPM 174 .75 RPM
SRP007412_cerebellum 0 .00 RPM 178 .81 RPM
SRP007412_heart 0 .00 RPM 183 .05 RPM
SRP007412_kidney 0 .02 RPM 163 .14 RPM
SRP007412_liver 0 .03 RPM 166 .50 RPM
SRP007412_testis 26 .30 RPM 96 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_230 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001YIJ POLR2A X:103630393..103631584

EST - click to see more details

No EST(s) were mapped for retro_mmus_230 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_1546951049 libraries18 libraries2 libraries0 libraries3 libraries
TSS #2 TSS_1546961064 libraries4 libraries1 library1 library2 libraries

The graphical summary, for retro_mmus_230 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 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_mmus_230 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_230 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_207
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 ENSG000001697141 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 ENSMUSG00000030057 1 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,


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