RetrogeneDB ID:

retro_tbel_1428

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:GeneScaffold_4684:56791..58096(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSP90AB1
Ensembl ID:ENSTBEG00000014873
Aliases:None
Description:heat shock protein 90kDa alpha (cytosolic), class B member 1 [Source:HGNC Symbol;Acc:5258]


Retrocopy-Parental alignment summary:






>retro_tbel_1428
AAGTACATTGATCAAGAAGAACTCAACAAAACCAAACCTATTTGGACCAGAAATCCTGATGATATTACTAATGAAGAGTA
TGGAGAATTCTACAAGAGCTTGACCAATGACTGGGAAGATCACTTGGCAGTGAAGCACTTTTCAGTCGAAGGACAGCTGG
AATTCAGAGCTCTTTTTTTCGTTCCAAGACGTGCTCCTTTTGACTTGTTTGAAAACAGGAAGAAAAAGAACAACATTAAG
TTGTATGTACGCAGAGTATTCATCATGGACAATTGTGAAGAGCTGATCACTGAATGTCTGAATTTCATTAGAGGAGTAGT
GGACTCTGAGGATCTCCCTCTAAATATTTCCCATGAGATGTTGCAGCAAAGTAAAATTCTGAAAGTTATCAGAAAGAATT
TGGTCAAAAAATGCTTAGAACTTTTCACCGAATTGGCGGAAGATAAAGAGAACTGCAAGAAGTTCTATGAGCAGTTTTCT
AAAAATATAAAGCTTGGAATTCATGAAGACTCTCAAAATCGTAAGAAACTTTCAGAGTTGTTAAGGTATTACACGTCTGC
TTCTGGTGATGAGATGGTATCCCTGAAGGGTTATTGCACCAGAATGAAGGAAAACCAGAAGCATATCTATTATATCACAG
GTGAGCCCAAGGACCAGGTAGCTAATTCGGCCTTCATAGAACGTCTTCGGAAAGCACGGCTTAGAAGTGATCTATATGAT
TGACCTATCGATGAGTACTGTGTCCAACAGCTGAAGGAATTTGAGGGGAAGACTTTAGTGTCAGTCACCAAAGAGGGTCT
AGAACTTCCAGAAGATGAAGAAGAGAAAAAGAAACAGGAAGAGAAAAAAACAAAGTTTGAAAACCTTTGCAAAATCATGA
AAGATATCTTGGAGAAAAGAGTGGAGAAGGTAGTTGTCTCAAACCGGTTGGTAATGTCCCCATGCTGCATCATCACAAGC
ACATACGGCTGGACAGCAAACATGGAGAGAATCATGAAAGCGCAAGCCTTAACAGACAACTCCACAATGGGTTACCGGGC
TGCCAAGAAGCACCTGGAGATCAACCCTGATCATTCCATCATTGAGACCTTAAGGCAAAAGGCAGAGGCTGACAAGAACA
ACAAGTCTGTGAAGGATTTGGTCATCTTGCTTGATGAAACCACACTCCTGTCTTCTGGGTTTAGTCTGGAAGATCCCCAG
ACACATGCTAACAGAATCTACAGGATGATCAAACTTGGTCTGGGTATTGATGAAGATGACCCTACTGCTGATGATACCAG
TGCTGCTGTGACTGAAGAAATGCCA

ORF - retro_tbel_1428 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.32 %
Parental protein coverage: 60.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLF
KYIDQEELNKTKPIWTRNPDDIT.EEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRAL.F.PRRAPFDLF
RetrocopyKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALFFVPRRAPFDLF
ParentalENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLE
EN.KKKNNIKLYVRRVFIMD.C.ELI.E.LNFIRGVVDSEDLPLNIS.EMLQQSKILKVIRKN.VKKCLE
RetrocopyENRKKKNNIKLYVRRVFIMDNCEELITECLNFIRGVVDSEDLPLNISHEMLQQSKILKVIRKNLVKKCLE
ParentalLFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIY
LF.ELAEDKEN.KKFYE.FSKN.KLGIHEDS.NR..LSELLRY.TS.SGDEM.SL..Y..RMKE.QK.IY
RetrocopyLFTELAEDKENCKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKGYCTRMKENQKHIY
ParentalYITGESKEQVANSAFVERVR-KRGFEVVYMTE-PIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKK
YITGE.K.QVANSAF.ER.R.K.G.EV.YM...PIDEYCVQQLKEF.GK.LVSVTKEGLEL.........
RetrocopyYITGEPKDQVANSAFIERLR>KHGLEVIYMID<PIDEYCVQQLKEFEGKTLVSVTKEGLELXXXXXXXXX
ParentalMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMA
...........CK.MK.IL.K.VEKV..SNRLV.SPCCI.TSTYGWTANMERIMKAQAL.DNSTMGY..A
RetrocopyXXXXXXXXXXXCKIMKDILEKRVEKVVVSNRLVMSPCCIITSTYGWTANMERIMKAQALTDNSTMGYRAA
ParentalKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDE
KKHLEINPDH.I.ETLRQKAEADKN.K.VKDLV.LL.ET.LLSSGFSLEDPQTH.NRIYRMIKLGLGIDE
RetrocopyKKHLEINPDHSIIETLRQKAEADKNNKSVKDLVILLDETTLLSSGFSLEDPQTHANRIYRMIKLGLGIDE
ParentalDEVTAEEPSAAVPDEIP
D..TA...SAAV..E.P
RetrocopyDDPTADDTSAAVTEEMP

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_1428 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_1428 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 10 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000019814 retrocopies
retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus ENSFCAG000000097641 retrocopy
retro_fcat_1177,
Gorilla gorilla ENSGGOG000000088892 retrocopies
retro_ggor_1011, retro_ggor_701,
Macropus eugenii ENSMEUG000000137351 retrocopy
retro_meug_1896,
Myotis lucifugus ENSMLUG000000052392 retrocopies
retro_mluc_1604, retro_mluc_865,
Mus musculus ENSMUSG000000239443 retrocopies
retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii ENSOGAG000000119611 retrocopy
retro_ogar_2574,
Pongo abelii ENSPPYG000000166552 retrocopies
retro_pabe_2425, retro_pabe_415,
Pan troglodytes ENSPTRG000000182174 retrocopies
retro_ptro_1850, retro_ptro_1968, retro_ptro_2003, retro_ptro_880,
Tupaia belangeri ENSTBEG00000014873 1 retrocopy
retro_tbel_1428 ,


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