RetrogeneDB ID:

retro_trub_23

Retrocopy
location
Organism:Fugu rubripes (Takifugu rubripes)
Coordinates:scaffold_1215:34243..34594(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TKT (1 of 3)
Ensembl ID:ENSTRUG00000003009
Aliases:None
Description:transketolase [Source:HGNC Symbol;Acc:11834]


Retrocopy-Parental alignment summary:






>retro_trub_23
CAAGAGCAACTACACCAATGGCATGAATTAGCGCAACAATTGCGAATAGATAGTATTCGCGCCACAACCGTCGCTGGTTC
AGGCCACCCCACTTCTTCCATGTCCTCTGCCGATTTAATGGCGGTGTTATTAACTAATTATCTTCACTACGATTTTGACA
ATCCACATCACCCTAATAACGATCGCTTTATTCTCTCTAAAGGACACGCTGCACCCTTACTTTACGCCATGTATAAAGCG
GCTGGGGTCATCACCGATGAGGAATTAATGTCATTGCGGCAAATGGGTAGCCGTCTGGAAGGTCATCCCACCCCAGTATT
ACCTTGGGTGGATGTGGCGACTGGTTCCTTA

ORF - retro_trub_23 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.99 %
Parental protein coverage: 71.78 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalQQTLQALKNIATRLRINSIKATTAAGSGHPTSCCSVAEIMSVLFFHTMKYRPEDPRHSSNDRFVLSKGHA
Q..L......A..LRI.SI.ATT.AGSGHPTS..S.A..M.VL......Y....P.H..NDRF.LSKGHA
RetrocopyQEQLHQWHELAQQLRIDSIRATTVAGSGHPTSSMSSADLMAVLLTNYLHYDFDNPHHPNNDRFILSKGHA
ParentalAPVLYAVWAETGYLKENELLNLRKVDSILEGHPVPKQQFVDVATGSL
AP.LYA.....G.....EL..LR...S.LEGHP.P....VDVATGSL
RetrocopyAPLLYAMYKAAGVITDEELMSLRQMGSRLEGHPTPVLPWVDVATGSL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Takifugu rubripes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_trub_23 retrocopy.

TSS - click to see more details

Takifugu rubripes was not studied using FANTOM5 data.

Lab - click to see more details

retro_trub_23 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_trub_23 has 0 orthologous retrocopies within teleost group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000037581 retrocopy
retro_btau_176,
Callithrix jacchus ENSCJAG000000072531 retrocopy
retro_cjac_2128,
Cavia porcellus ENSCPOG000000000721 retrocopy
retro_cpor_45,
Dipodomys ordii ENSDORG000000013921 retrocopy
retro_dord_329,
Homo sapiens ENSG000001639311 retrocopy
retro_hsap_47,
Macropus eugenii ENSMEUG000000053123 retrocopies
retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus ENSMLUG000000009431 retrocopy
retro_mluc_67,
Macaca mulatta ENSMMUG000000144331 retrocopy
retro_mmul_74,
Mus musculus ENSMUSG000000219571 retrocopy
retro_mmus_220,
Oryctolagus cuniculus ENSOCUG000000159042 retrocopies
retro_ocun_319, retro_ocun_62,
Otolemur garnettii ENSOGAG000000169111 retrocopy
retro_ogar_5,
Ochotona princeps ENSOPRG000000098911 retrocopy
retro_opri_10,
Pan troglodytes ENSPTRG000000150241 retrocopy
retro_ptro_126,
Pteropus vampyrus ENSPVAG000000162831 retrocopy
retro_pvam_352,
Rattus norvegicus ENSRNOG000000160641 retrocopy
retro_rnor_146,
Sarcophilus harrisii ENSSHAG000000173491 retrocopy
retro_shar_827,
Sus scrofa ENSSSCG000000214081 retrocopy
retro_sscr_996,
Tupaia belangeri ENSTBEG000000121141 retrocopy
retro_tbel_3510,
Takifugu rubripes ENSTRUG00000003009 1 retrocopy
retro_trub_23 ,


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