Gene loci information

Transcript annotation

  • This transcript has been annotated as TBC1 domain family member 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11880 g11880.t1 TTS g11880.t1 18946801 18946801
chr_1 g11880 g11880.t1 isoform g11880.t1 18946870 18952488
chr_1 g11880 g11880.t1 exon g11880.t1.exon1 18946870 18948081
chr_1 g11880 g11880.t1 cds g11880.t1.CDS1 18946870 18948081
chr_1 g11880 g11880.t1 exon g11880.t1.exon2 18948143 18948732
chr_1 g11880 g11880.t1 cds g11880.t1.CDS2 18948143 18948732
chr_1 g11880 g11880.t1 exon g11880.t1.exon3 18948839 18949002
chr_1 g11880 g11880.t1 cds g11880.t1.CDS3 18948839 18949002
chr_1 g11880 g11880.t1 exon g11880.t1.exon4 18949062 18950137
chr_1 g11880 g11880.t1 cds g11880.t1.CDS4 18949062 18950137
chr_1 g11880 g11880.t1 exon g11880.t1.exon5 18950333 18950665
chr_1 g11880 g11880.t1 cds g11880.t1.CDS5 18950333 18950665
chr_1 g11880 g11880.t1 exon g11880.t1.exon6 18952417 18952488
chr_1 g11880 g11880.t1 cds g11880.t1.CDS6 18952417 18952488
chr_1 g11880 g11880.t1 TSS g11880.t1 18952762 18952762

Sequences

>g11880.t1 Gene=g11880 Length=3447
ATGTTTTATCTAACGAATCGACGTGATGCATTTCGTGGAGCCTACAGTGATGCTTCTACG
TTAAATAAAAATATTTCAAATTTGTCGGATCGTATAAAGCAGTCTCAAATGGGACGCTCA
ATTGAAAACATGACTTCGACACATTCAACCATGGAAGAGTCAGTACAAGTTAAAAAAGAT
CGAATGGCCAATTTCAAAAAATCACATATTAGTCACTCAACTGGTGATTTGTATTTAAAT
AATCGCTCAAATTTATCACTTTTTGGAGACTTTCAATTAAATGACTCACAATTTTTTGAA
GTCATGTATGTTGGAAAAATTCGTGTTTCACATAAGAAACTACCGAAAACATTTATTGAT
GATGCTCTTCCAAAGTTTATTGCTCACGATAAGATGAAAATAAAGAGTATTGAGGTGAAT
GGGAAACAAAATACAGACAGTCAACAGACGCCAGAAAATTCTCAAAACGGATATGATAAA
AAAATTGACGAGGAAAGCGATTCATCAAGCGTTAAGAGCAGTGATAGCAAAAGTCAGAGT
GATGAAACAAACAAACAACAACCAAATTTTCATCGACTTGATTCAATAAAAGCTGAAGAA
ATACCAAAAAGAAATCGATCAGCTTCATTTAGTTCAATTGAACAAAATCGTACAATGGTA
TACATTTTAGGAAGATCAGATTTGAGATTGATAAGTCCCGATCGAAAACAAATTTTGCTT
CATAAAAATTTTAATGATGTCGTTAATGCTGTTCAAGGAATTAATAGTGCTGAACATTTT
GGAATTATTTGCAATGAAGTGAAAGATAATAAACAAGAATTTATTGGTTATGTCTTTAAA
TGTCAATCTGCTGTCATTGCACATGATGTTGTCTCATCTATGTTGAAATCTTTAGAGACA
CTTGAGCAAGATAAAAAATATTCAGATGAAAATTTTGAAGACTCAAAAAAGATGTCAGGT
TCTTTACAATGCGATCATTGTCCTTTAGTATGGTTCAATAAGCTTCAAAATTCAGTTCAA
GGTCTCAGCGAAAAAAAAATTTATAGTGTCATAATGAAACATATTGAAGAATTGAATGCT
GACGACTATGAAATATTAATGGAAAAATTCTTTGCTTCTGATAAAGTCAATGATTATTCC
CTCACAGAACGTAATAAATTTCTCATGGCACTAATTGAAGCACATTGTCAAATGCGTCAA
CAGCGACATGTGCACGATACAATTGAAAATCGATCAGAATTCTTAAATTACTATCTAGGT
GGCAGTACAATTTTAATGAAGGCAAAACGTTCTTTGTCAAGCTCGTTTGATCAACTATTA
AAAAGAAGAGGAAGTAAGGATTCAAATGAAAATAACCACATTACAATTCATGAAGAAGAG
CAAAGAAAGTTCAAACCAATTAGATCAATATCGTTGACATCTCCTTTAATATCACCTTGT
GATAATAAACAACAATTATTGAATACATCTAAAATGGACATGTTTATGAAAGTGGGAAAT
ACTTCAAAAGACAAAAATATGCACACAATTTCATGGCGTCAAAAAATCCTTAAAAACGTA
ATTTTAACAGAAAAAGAAGAACCAACTTCAAAAGCTTGCCTAAATGACGACTCTATAAAA
TTTCTTTCAAAAAGATCAAACAAGCGACAAAAATCACACAAGAAGAGAAGTACGGAAGAA
TTGCGTGCATTATGGAAATTTGCTATCAAGCAAATAATTGTACTACTTCGAATGGAAAAG
GAAAATGCCCGTCTTCAAGAGCAACAGAATGAACATGAAATCCGTCGAATGAAGCTAAAC
TATGACGAAATTGTGACGTGCGAACAAAAATTAGTTGATGTGTGGGAGAAATTCATTTAT
CAAGCTACAAAATCAGAATTTGACATACGACTTTGTCTGCAAGCGATGAAACAAGGAGTA
CCAAAAATTATTAGAGGTAACGTATGGATCATGCTTGCACAACAGTATCAGAAAACACAT
CCAATAAATATAAACCATGATGAATTTATTAACTACAATGTGCCATATGAGCAACTGCTT
AAAAATTTAACAGATCAACAACACGCGATTTTTCTTGATATTGGAAGAACATTTCCAAAT
AATGAATTTTATAAAGCACCATTTGGTATTGGACAACTTTCACTATTCAACGTACTCAAG
GCATATTCAATTCTCGATAGTGAACTCGGTTATTGTCAAGGACTTGCTTTTATATGTGGT
ATACTTCTGCTTCATATGAATGAAAATGAAGCATTTTGGTTATTAAAATTTTTAATGTTT
GACCGACAATTACGATTAAATTATTTGCCAGATATGAAGCATTTTCAACTGCAATTGTAT
CAAATGTCACGACTTATAAAAGATATGCTGCCTGAAATACATGAGCTTTTTGAGAAAAAT
GAAGTTGCCACAACTCTATTTGCATCTTCATGGATGCTAACAATATTTTCGTCATCATTT
GAACTTGGTTTTGTCACACGTTTATTTGATTTGCTGCTATTTGCATCAAATGAAGTCATT
TTTCGTGTTATCATTGCCCTTCTTGATGTTCATAAATCAGAGTTGCTTAAATTAGATTCA
TTTGAGGACATTATGAACTATTTAAAAAATGTCATTCCTAAAGTTAATGAAATGCAAATG
CAACAAATTTTAAAAAGTGTGTATGAAATGAATATATCACGGCAGCTTCTAGATTATAAA
GTCGAATACAATGTTTTGAAAGAAGAATTACAAAATACTACACAACATATTGAAAATTTA
AAATTAGCACGTGAAGATTTGAAAAATTTACATAAACAAATTCAAGGTGCAGAAATTAAT
ATTCAACGTTTAGAAGCCATTCGACATTCTCAGCAGCAAGAAATTATTACAATGCAATTG
CATATTCAAAGTTTGGAATCTACAATACAAACATTTGGTGACTTTCTCCAATCATTGTCA
ATCAATCGAACAGACATCGACATTCCATCAGACATACGACGACTTTTGCAGCAAATGGAT
CAACAGCAAAACAAGCAGCAAGTTAAACGACGACCAGTGTTTTTAGACAGAAAAATTGGC
AAATCTGTGTCAGTTAATAGTAGCTTAGGAATGAGCTTAAAAGTGTTAATTGAGCAGAAT
GAAAATGACAATCAAACACCGCCATGCGCTGTAACTCCAATATCAGATAGTGCCATCACA
TCAATTTTATGTGAAAGGAAAAGAAATTTTGAAAAGGCATTAGATCAAGTTAAACAACAC
TCTAAACTTATGGAAAATCATGATGAATCTCTTGAAATAACTAATCAAATTGATGAGGCT
GCAATTGAGACAATAGAGAAAGAAACGATTGAAAAAACTTTATCACATCCATTAGTTTGC
GATGATGTGAATTTTCAATTTAATACAATGCAGTTAAAAACGATAAGATCAACAAATACT
TTTAAAAGACCCGAAAAACGAGAATAG

>g11880.t1 Gene=g11880 Length=1148
MFYLTNRRDAFRGAYSDASTLNKNISNLSDRIKQSQMGRSIENMTSTHSTMEESVQVKKD
RMANFKKSHISHSTGDLYLNNRSNLSLFGDFQLNDSQFFEVMYVGKIRVSHKKLPKTFID
DALPKFIAHDKMKIKSIEVNGKQNTDSQQTPENSQNGYDKKIDEESDSSSVKSSDSKSQS
DETNKQQPNFHRLDSIKAEEIPKRNRSASFSSIEQNRTMVYILGRSDLRLISPDRKQILL
HKNFNDVVNAVQGINSAEHFGIICNEVKDNKQEFIGYVFKCQSAVIAHDVVSSMLKSLET
LEQDKKYSDENFEDSKKMSGSLQCDHCPLVWFNKLQNSVQGLSEKKIYSVIMKHIEELNA
DDYEILMEKFFASDKVNDYSLTERNKFLMALIEAHCQMRQQRHVHDTIENRSEFLNYYLG
GSTILMKAKRSLSSSFDQLLKRRGSKDSNENNHITIHEEEQRKFKPIRSISLTSPLISPC
DNKQQLLNTSKMDMFMKVGNTSKDKNMHTISWRQKILKNVILTEKEEPTSKACLNDDSIK
FLSKRSNKRQKSHKKRSTEELRALWKFAIKQIIVLLRMEKENARLQEQQNEHEIRRMKLN
YDEIVTCEQKLVDVWEKFIYQATKSEFDIRLCLQAMKQGVPKIIRGNVWIMLAQQYQKTH
PININHDEFINYNVPYEQLLKNLTDQQHAIFLDIGRTFPNNEFYKAPFGIGQLSLFNVLK
AYSILDSELGYCQGLAFICGILLLHMNENEAFWLLKFLMFDRQLRLNYLPDMKHFQLQLY
QMSRLIKDMLPEIHELFEKNEVATTLFASSWMLTIFSSSFELGFVTRLFDLLLFASNEVI
FRVIIALLDVHKSELLKLDSFEDIMNYLKNVIPKVNEMQMQQILKSVYEMNISRQLLDYK
VEYNVLKEELQNTTQHIENLKLAREDLKNLHKQIQGAEINIQRLEAIRHSQQQEIITMQL
HIQSLESTIQTFGDFLQSLSINRTDIDIPSDIRRLLQQMDQQQNKQQVKRRPVFLDRKIG
KSVSVNSSLGMSLKVLIEQNENDNQTPPCAVTPISDSAITSILCERKRNFEKALDQVKQH
SKLMENHDESLEITNQIDEAAIETIEKETIEKTLSHPLVCDDVNFQFNTMQLKTIRSTNT
FKRPEKRE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11880.t1 CDD cd01269 PTB_TBC1D1_like 90 294 2.29538E-48
13 g11880.t1 Coils Coil Coil 575 600 -
12 g11880.t1 Coils Coil Coil 896 954 -
9 g11880.t1 Gene3D G3DSA:2.30.29.30 - 95 307 2.8E-5
11 g11880.t1 Gene3D G3DSA:1.10.10.2750 - 583 662 1.2E-20
8 g11880.t1 Gene3D G3DSA:1.10.8.270 putative rabgap domain of human tbc1 domain family member 14 like domains 668 760 1.6E-32
10 g11880.t1 Gene3D G3DSA:1.10.472.80 - 761 914 2.4E-44
17 g11880.t1 MobiDBLite mobidb-lite consensus disorder prediction 139 209 -
18 g11880.t1 MobiDBLite mobidb-lite consensus disorder prediction 139 156 -
20 g11880.t1 MobiDBLite mobidb-lite consensus disorder prediction 157 171 -
19 g11880.t1 MobiDBLite mobidb-lite consensus disorder prediction 172 191 -
3 g11880.t1 PANTHER PTHR22957 TBC1 DOMAIN FAMILY MEMBER GTPASE-ACTIVATING PROTEIN 523 905 2.8E-72
4 g11880.t1 PANTHER PTHR22957:SF195 TBC1 DOMAIN FAMILY MEMBER 4 523 905 2.8E-72
2 g11880.t1 Pfam PF11830 Domain of unknown function (DUF3350) 533 586 3.1E-16
1 g11880.t1 Pfam PF00566 Rab-GTPase-TBC domain 644 856 7.3E-48
21 g11880.t1 ProSiteProfiles PS50086 TBC/rab GAP domain profile. 639 836 30.799
15 g11880.t1 SMART SM00462 PTB_9 94 310 2.5E-10
16 g11880.t1 SMART SM00164 tbc_4 636 859 5.5E-68
5 g11880.t1 SUPERFAMILY SSF50729 PH domain-like 87 293 5.33E-12
6 g11880.t1 SUPERFAMILY SSF47923 Ypt/Rab-GAP domain of gyp1p 614 794 1.44E-39
7 g11880.t1 SUPERFAMILY SSF47923 Ypt/Rab-GAP domain of gyp1p 772 890 1.6E-26

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values