RetrogeneDB ID:

retro_tbel_3323

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:scaffold_137290:97472..98423(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP0
Ensembl ID:ENSTBEG00000005498
Aliases:None
Description:ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]


Retrocopy-Parental alignment summary:






>retro_tbel_3323
ATGCCCAGGGAAGACAGGGCGACCTGGAAGTCCAACTACTTCCTTAAGATCATCCAACTTCTGGATGATTATCCAAAATG
CTTCGTTGTGGGTGCAGACAATGTGGGCTCCAGGCAGATGCAGCAGATCCGCATGTCCCTCCGCAGGAAGGCCGTGGTGC
TGATGGGCAAGATCACCATGATGCGCAAGGCCATCCAGGGGCATCTGGAAAACAACCCAGCTCTGGAGAAGCTGTTGCCT
CACATCCAGGGGAATGTGGGCTTCATGTTCACCAAGGAGGACCTCACTGAGATCAGGGACATGTTGCTGGCCAACACGGT
TCCAGCTGCTGCCCATGCTGGTGCCATTGCCCCTTGCGAAGTCAATGTGCCAGCCCAGACCACTGGTCTGGGGCCCGAGA
AGACCTCCTTCTTCCAGGCTTTGGGCATCACCGCTAAGATTTCCAGGGGCACCATTGAAATCCTGAGCAATGTGCAGCTG
ATAAAGACTGGAGACAAGGTGGGAGCCAGAGAAGCCACACTGCTGAACATGCTGAACATCTCCCCCTTCTCCTTCGGGCT
GATCATCCAGCAGGTGTTTGACAACGGCAGCATCTACAACCCCGAAGTGCTTGACATCACAGAGGAGGCTCTGCATTCTC
GCTTCCTGGAGGGTGTCCGCAATGTTGCCAGTGTGTGCCTGCAAATTGGCTATCCCACTGTCGCTTCAGTGCCACATTCT
ATCATCAATGGGTACAAGCAGGTCCTGGCTTTGTCTGTGGAGACTGACTACACCTTCCCACTTGCCGAGAAAGTCAAGGC
CTTCTTGGCTGATCCATCTGCATTTATGGCTGCCGCCCCCGTGGCTGCTGCCACCACTGCTGCTCCTGCTGCTGCTGCAG
CCCCAGCCAAGGTTGAAGCCAAGGAAGAGTCGGAGGAGTCAGACGAAGATATGGGATTTGGTCTCTTTGAC

ORF - retro_tbel_3323 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.17 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
MPREDRATWKSNYFLKIIQLLDDYPKCF.VGADNVGS.QMQQIRMSLR.KAVVLMGK.TMMRKAI.GHLE
RetrocopyMPREDRATWKSNYFLKIIQLLDDYPKCFVVGADNVGSRQMQQIRMSLRRKAVVLMGKITMMRKAIQGHLE
ParentalNNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
NNPALEKLLPHI.GNVGF.FTKEDLTEIRDMLLAN.VPAAA.AGAIAPCEV.VPAQ.TGLGPEKTSFFQA
RetrocopyNNPALEKLLPHIQGNVGFMFTKEDLTEIRDMLLANTVPAAAHAGAIAPCEVNVPAQTTGLGPEKTSFFQA
ParentalLGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEEA
LGIT.KISRGTIEILS.VQLIKTGDKVGA.EATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEEA
RetrocopyLGITAKISRGTIEILSNVQLIKTGDKVGAREATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEEA
ParentalLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAP
LHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYK.VLALSVETDYTFPLAEKVKAFLADPSAF.AAAP
RetrocopyLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKQVLALSVETDYTFPLAEKVKAFLADPSAFMAAAP
ParentalVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD
V............APAKVEAKEESEESDEDMGFGLFD
RetrocopyVXXXXXXXXXXXXAPAKVEAKEESEESDEDMGFGLFD

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






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_3323 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_3323 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000027452 retrocopies
retro_chof_1115, retro_chof_2341,
Callithrix jacchus ENSCJAG000000086773 retrocopies
retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus ENSCPOG000000218125 retrocopies
retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Erinaceus europaeus ENSEEUG000000075531 retrocopy
retro_eeur_612,
Gorilla gorilla ENSGGOG000000265825 retrocopies
retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macaca mulatta ENSMMUG000000091572 retrocopies
retro_mmul_2245, retro_mmul_939,
Mus musculus ENSMUSG000000672742 retrocopies
retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus ENSOCUG000000057492 retrocopies
retro_ocun_293, retro_ocun_376,
Otolemur garnettii ENSOGAG000000038434 retrocopies
retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus ENSPMAG000000013391 retrocopy
retro_pmar_6,
Pongo abelii ENSPPYG000000050225 retrocopies
retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus ENSRNOG000000011483 retrocopies
retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii ENSSHAG000000016232 retrocopies
retro_shar_286, retro_shar_413,
Tupaia belangeri ENSTBEG00000005498 1 retrocopy
retro_tbel_3323 ,


Copyright © RetrogeneDB 2014-2017