General information for g13346.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Rab11 family-interacting protein 1.
Parent gene
- The parent gene g13346 is located on chr_1: 29391016..29391553 (+ strand)
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 | g13346 | g13346.t3 | TSS | g13346.t3 | 29387879 | 29387879 |
| chr_1 | g13346 | g13346.t3 | isoform | g13346.t3 | 29387994 | 29389848 |
| chr_1 | g13346 | g13346.t3 | exon | g13346.t3.exon1 | 29387994 | 29388024 |
| chr_1 | g13346 | g13346.t3 | cds | g13346.t3.CDS1 | 29387994 | 29388024 |
| chr_1 | g13346 | g13346.t3 | exon | g13346.t3.exon2 | 29389109 | 29389253 |
| chr_1 | g13346 | g13346.t3 | cds | g13346.t3.CDS2 | 29389109 | 29389253 |
| chr_1 | g13346 | g13346.t3 | exon | g13346.t3.exon3 | 29389318 | 29389848 |
| chr_1 | g13346 | g13346.t3 | cds | g13346.t3.CDS3 | 29389318 | 29389846 |
| chr_1 | g13346 | g13346.t3 | TTS | g13346.t3 | NA | NA |
Sequences
>g13346.t3 Gene=g13346 Length=707
ATGTATACACCGACTCATATTCAAGTTACAGTTCAACGTGCCAAAGGTCTCTTGACAAAA
GGCAAGAATGGAACGAACAATTGCTTTACCACAATTGCACTAGGCAAGGAAAAATATCAG
ACGTCTCTGAAGGAAAATGCCACAACAAATGTAGACTGGCACGAAGAATGTGAATTAGCT
ATTCCGTCGCAAGGAAATCGTGCTGAATTAATTTTGACGGTTCTGCATAGAAATGGTTTG
GGACTAGATGAATTCCTTGGTCAAATTACGCTTCCACTTAATGAAATGGATCACTTTGAT
CGACCAAGAAGTCGATGGTATAAGTTACAGAGTAAACCAGGTCAAGAGAAAAAAGACAAA
GATCGTGGTGAATTAGAGGTTCGAACAGCATTCACTGTCAAGGCAGGATCTTTGAGTGAC
TTGAGTAAAAAAGATAAAACAAAATCATCTCTTAGTAATATTGCTAATAATGTTGGCGGA
AGTCTCTTATCACTTGGACAAATAGAAAAACATAAGAGTCTGAAAAAGTTTGCTAAATCA
CTTGGCAATAAGATGCACGTAACTGGAAAGAAGAAAAAAGACAAAGGTGAAGATTCAGAT
TCATATACTGGTAGCTTTTCGAGTCTTGGTACACCTAGCTTGGGAACAAGAAATAGTTTT
CATTTACGCAACGAAGGAAATGCTGATCCAGGTGTTATCAGTGAGGA
>g13346.t3 Gene=g13346 Length=235
MYTPTHIQVTVQRAKGLLTKGKNGTNNCFTTIALGKEKYQTSLKENATTNVDWHEECELA
IPSQGNRAELILTVLHRNGLGLDEFLGQITLPLNEMDHFDRPRSRWYKLQSKPGQEKKDK
DRGELEVRTAFTVKAGSLSDLSKKDKTKSSLSNIANNVGGSLLSLGQIEKHKSLKKFAKS
LGNKMHVTGKKKKDKGEDSDSYTGSFSSLGTPSLGTRNSFHLRNEGNADPGVISE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13346.t3 | Gene3D | G3DSA:2.60.40.150 | - | 4 | 159 | 3.6E-24 |
| 6 | g13346.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 185 | 235 | - |
| 7 | g13346.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 223 | - |
| 2 | g13346.t3 | PANTHER | PTHR15746:SF23 | RAB11 INTERACTING PROTEIN, ISOFORM A | 3 | 211 | 3.7E-78 |
| 3 | g13346.t3 | PANTHER | PTHR15746 | RAB11-RELATED | 3 | 211 | 3.7E-78 |
| 1 | g13346.t3 | Pfam | PF00168 | C2 domain | 6 | 109 | 3.0E-14 |
| 5 | g13346.t3 | SMART | SM00239 | C2_3c | 6 | 105 | 6.7E-7 |
| 4 | g13346.t3 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 6 | 131 | 2.03E-20 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0031267 | small GTPase binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12484 (Rab11 family-interacting protein 1/2/5)
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.
