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.t3 TTS g11880.t3 18946801 18946801
chr_1 g11880 g11880.t3 isoform g11880.t3 18946870 18950665
chr_1 g11880 g11880.t3 exon g11880.t3.exon1 18946870 18948081
chr_1 g11880 g11880.t3 cds g11880.t3.CDS1 18946870 18948081
chr_1 g11880 g11880.t3 exon g11880.t3.exon2 18948143 18948732
chr_1 g11880 g11880.t3 cds g11880.t3.CDS2 18948143 18948732
chr_1 g11880 g11880.t3 exon g11880.t3.exon3 18948839 18949002
chr_1 g11880 g11880.t3 cds g11880.t3.CDS3 18948839 18949002
chr_1 g11880 g11880.t3 exon g11880.t3.exon4 18949062 18950137
chr_1 g11880 g11880.t3 cds g11880.t3.CDS4 18949062 18950137
chr_1 g11880 g11880.t3 exon g11880.t3.exon5 18950333 18950665
chr_1 g11880 g11880.t3 cds g11880.t3.CDS5 18950333 18950629
chr_1 g11880 g11880.t3 TSS g11880.t3 18950637 18950637

Sequences

>g11880.t3 Gene=g11880 Length=3375
ATTTCAAATTTGTCGGATCGTATAAAGCAGTCTCAAATGGGACGCTCAATTGAAAACATG
ACTTCGACACATTCAACCATGGAAGAGTCAGTACAAGTTAAAAAAGATCGAATGGCCAAT
TTCAAAAAATCACATATTAGTCACTCAACTGGTGATTTGTATTTAAATAATCGCTCAAAT
TTATCACTTTTTGGAGACTTTCAATTAAATGACTCACAATTTTTTGAAGTCATGTATGTT
GGAAAAATTCGTGTTTCACATAAGAAACTACCGAAAACATTTATTGATGATGCTCTTCCA
AAGTTTATTGCTCACGATAAGATGAAAATAAAGAGTATTGAGGTGAATGGGAAACAAAAT
ACAGACAGTCAACAGACGCCAGAAAATTCTCAAAACGGATATGATAAAAAAATTGACGAG
GAAAGCGATTCATCAAGCGTTAAGAGCAGTGATAGCAAAAGTCAGAGTGATGAAACAAAC
AAACAACAACCAAATTTTCATCGACTTGATTCAATAAAAGCTGAAGAAATACCAAAAAGA
AATCGATCAGCTTCATTTAGTTCAATTGAACAAAATCGTACAATGGTATACATTTTAGGA
AGATCAGATTTGAGATTGATAAGTCCCGATCGAAAACAAATTTTGCTTCATAAAAATTTT
AATGATGTCGTTAATGCTGTTCAAGGAATTAATAGTGCTGAACATTTTGGAATTATTTGC
AATGAAGTGAAAGATAATAAACAAGAATTTATTGGTTATGTCTTTAAATGTCAATCTGCT
GTCATTGCACATGATGTTGTCTCATCTATGTTGAAATCTTTAGAGACACTTGAGCAAGAT
AAAAAATATTCAGATGAAAATTTTGAAGACTCAAAAAAGATGTCAGGTTCTTTACAATGC
GATCATTGTCCTTTAGTATGGTTCAATAAGCTTCAAAATTCAGTTCAAGGTCTCAGCGAA
AAAAAAATTTATAGTGTCATAATGAAACATATTGAAGAATTGAATGCTGACGACTATGAA
ATATTAATGGAAAAATTCTTTGCTTCTGATAAAGTCAATGATTATTCCCTCACAGAACGT
AATAAATTTCTCATGGCACTAATTGAAGCACATTGTCAAATGCGTCAACAGCGACATGTG
CACGATACAATTGAAAATCGATCAGAATTCTTAAATTACTATCTAGGTGGCAGTACAATT
TTAATGAAGGCAAAACGTTCTTTGTCAAGCTCGTTTGATCAACTATTAAAAAGAAGAGGA
AGTAAGGATTCAAATGAAAATAACCACATTACAATTCATGAAGAAGAGCAAAGAAAGTTC
AAACCAATTAGATCAATATCGTTGACATCTCCTTTAATATCACCTTGTGATAATAAACAA
CAATTATTGAATACATCTAAAATGGACATGTTTATGAAAGTGGGAAATACTTCAAAAGAC
AAAAATATGCACACAATTTCATGGCGTCAAAAAATCCTTAAAAACGTAATTTTAACAGAA
AAAGAAGAACCAACTTCAAAAGCTTGCCTAAATGACGACTCTATAAAATTTCTTTCAAAA
AGATCAAACAAGCGACAAAAATCACACAAGAAGAGAAGTACGGAAGAATTGCGTGCATTA
TGGAAATTTGCTATCAAGCAAATAATTGTACTACTTCGAATGGAAAAGGAAAATGCCCGT
CTTCAAGAGCAACAGAATGAACATGAAATCCGTCGAATGAAGCTAAACTATGACGAAATT
GTGACGTGCGAACAAAAATTAGTTGATGTGTGGGAGAAATTCATTTATCAAGCTACAAAA
TCAGAATTTGACATACGACTTTGTCTGCAAGCGATGAAACAAGGAGTACCAAAAATTATT
AGAGGTAACGTATGGATCATGCTTGCACAACAGTATCAGAAAACACATCCAATAAATATA
AACCATGATGAATTTATTAACTACAATGTGCCATATGAGCAACTGCTTAAAAATTTAACA
GATCAACAACACGCGATTTTTCTTGATATTGGAAGAACATTTCCAAATAATGAATTTTAT
AAAGCACCATTTGGTATTGGACAACTTTCACTATTCAACGTACTCAAGGCATATTCAATT
CTCGATAGTGAACTCGGTTATTGTCAAGGACTTGCTTTTATATGTGGTATACTTCTGCTT
CATATGAATGAAAATGAAGCATTTTGGTTATTAAAATTTTTAATGTTTGACCGACAATTA
CGATTAAATTATTTGCCAGATATGAAGCATTTTCAACTGCAATTGTATCAAATGTCACGA
CTTATAAAAGATATGCTGCCTGAAATACATGAGCTTTTTGAGAAAAATGAAGTTGCCACA
ACTCTATTTGCATCTTCATGGATGCTAACAATATTTTCGTCATCATTTGAACTTGGTTTT
GTCACACGTTTATTTGATTTGCTGCTATTTGCATCAAATGAAGTCATTTTTCGTGTTATC
ATTGCCCTTCTTGATGTTCATAAATCAGAGTTGCTTAAATTAGATTCATTTGAGGACATT
ATGAACTATTTAAAAAATGTCATTCCTAAAGTTAATGAAATGCAAATGCAACAAATTTTA
AAAAGTGTGTATGAAATGAATATATCACGGCAGCTTCTAGATTATAAAGTCGAATACAAT
GTTTTGAAAGAAGAATTACAAAATACTACACAACATATTGAAAATTTAAAATTAGCACGT
GAAGATTTGAAAAATTTACATAAACAAATTCAAGGTGCAGAAATTAATATTCAACGTTTA
GAAGCCATTCGACATTCTCAGCAGCAAGAAATTATTACAATGCAATTGCATATTCAAAGT
TTGGAATCTACAATACAAACATTTGGTGACTTTCTCCAATCATTGTCAATCAATCGAACA
GACATCGACATTCCATCAGACATACGACGACTTTTGCAGCAAATGGATCAACAGCAAAAC
AAGCAGCAAGTTAAACGACGACCAGTGTTTTTAGACAGAAAAATTGGCAAATCTGTGTCA
GTTAATAGTAGCTTAGGAATGAGCTTAAAAGTGTTAATTGAGCAGAATGAAAATGACAAT
CAAACACCGCCATGCGCTGTAACTCCAATATCAGATAGTGCCATCACATCAATTTTATGT
GAAAGGAAAAGAAATTTTGAAAAGGCATTAGATCAAGTTAAACAACACTCTAAACTTATG
GAAAATCATGATGAATCTCTTGAAATAACTAATCAAATTGATGAGGCTGCAATTGAGACA
ATAGAGAAAGAAACGATTGAAAAAACTTTATCACATCCATTAGTTTGCGATGATGTGAAT
TTTCAATTTAATACAATGCAGTTAAAAACGATAAGATCAACAAATACTTTTAAAAGACCC
GAAAAACGAGAATAG

>g11880.t3 Gene=g11880 Length=1112
MGRSIENMTSTHSTMEESVQVKKDRMANFKKSHISHSTGDLYLNNRSNLSLFGDFQLNDS
QFFEVMYVGKIRVSHKKLPKTFIDDALPKFIAHDKMKIKSIEVNGKQNTDSQQTPENSQN
GYDKKIDEESDSSSVKSSDSKSQSDETNKQQPNFHRLDSIKAEEIPKRNRSASFSSIEQN
RTMVYILGRSDLRLISPDRKQILLHKNFNDVVNAVQGINSAEHFGIICNEVKDNKQEFIG
YVFKCQSAVIAHDVVSSMLKSLETLEQDKKYSDENFEDSKKMSGSLQCDHCPLVWFNKLQ
NSVQGLSEKKIYSVIMKHIEELNADDYEILMEKFFASDKVNDYSLTERNKFLMALIEAHC
QMRQQRHVHDTIENRSEFLNYYLGGSTILMKAKRSLSSSFDQLLKRRGSKDSNENNHITI
HEEEQRKFKPIRSISLTSPLISPCDNKQQLLNTSKMDMFMKVGNTSKDKNMHTISWRQKI
LKNVILTEKEEPTSKACLNDDSIKFLSKRSNKRQKSHKKRSTEELRALWKFAIKQIIVLL
RMEKENARLQEQQNEHEIRRMKLNYDEIVTCEQKLVDVWEKFIYQATKSEFDIRLCLQAM
KQGVPKIIRGNVWIMLAQQYQKTHPININHDEFINYNVPYEQLLKNLTDQQHAIFLDIGR
TFPNNEFYKAPFGIGQLSLFNVLKAYSILDSELGYCQGLAFICGILLLHMNENEAFWLLK
FLMFDRQLRLNYLPDMKHFQLQLYQMSRLIKDMLPEIHELFEKNEVATTLFASSWMLTIF
SSSFELGFVTRLFDLLLFASNEVIFRVIIALLDVHKSELLKLDSFEDIMNYLKNVIPKVN
EMQMQQILKSVYEMNISRQLLDYKVEYNVLKEELQNTTQHIENLKLAREDLKNLHKQIQG
AEINIQRLEAIRHSQQQEIITMQLHIQSLESTIQTFGDFLQSLSINRTDIDIPSDIRRLL
QQMDQQQNKQQVKRRPVFLDRKIGKSVSVNSSLGMSLKVLIEQNENDNQTPPCAVTPISD
SAITSILCERKRNFEKALDQVKQHSKLMENHDESLEITNQIDEAAIETIEKETIEKTLSH
PLVCDDVNFQFNTMQLKTIRSTNTFKRPEKRE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11880.t3 CDD cd01269 PTB_TBC1D1_like 54 258 2.53567E-48
12 g11880.t3 Coils Coil Coil 539 564 -
13 g11880.t3 Coils Coil Coil 860 918 -
9 g11880.t3 Gene3D G3DSA:2.30.29.30 - 59 271 2.6E-5
11 g11880.t3 Gene3D G3DSA:1.10.10.2750 - 547 626 1.2E-20
8 g11880.t3 Gene3D G3DSA:1.10.8.270 putative rabgap domain of human tbc1 domain family member 14 like domains 632 724 1.6E-32
10 g11880.t3 Gene3D G3DSA:1.10.472.80 - 725 878 2.3E-44
17 g11880.t3 MobiDBLite mobidb-lite consensus disorder prediction 103 173 -
19 g11880.t3 MobiDBLite mobidb-lite consensus disorder prediction 103 120 -
18 g11880.t3 MobiDBLite mobidb-lite consensus disorder prediction 121 135 -
20 g11880.t3 MobiDBLite mobidb-lite consensus disorder prediction 136 155 -
3 g11880.t3 PANTHER PTHR22957 TBC1 DOMAIN FAMILY MEMBER GTPASE-ACTIVATING PROTEIN 487 869 2.6E-72
4 g11880.t3 PANTHER PTHR22957:SF195 TBC1 DOMAIN FAMILY MEMBER 4 487 869 2.6E-72
2 g11880.t3 Pfam PF11830 Domain of unknown function (DUF3350) 497 550 3.0E-16
1 g11880.t3 Pfam PF00566 Rab-GTPase-TBC domain 608 820 7.0E-48
21 g11880.t3 ProSiteProfiles PS50086 TBC/rab GAP domain profile. 603 800 30.799
15 g11880.t3 SMART SM00462 PTB_9 58 274 2.5E-10
16 g11880.t3 SMART SM00164 tbc_4 600 823 5.5E-68
5 g11880.t3 SUPERFAMILY SSF50729 PH domain-like 51 257 5.06E-12
6 g11880.t3 SUPERFAMILY SSF47923 Ypt/Rab-GAP domain of gyp1p 578 758 1.44E-39
7 g11880.t3 SUPERFAMILY SSF47923 Ypt/Rab-GAP domain of gyp1p 736 854 1.54E-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