Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Rab11 family-interacting protein 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 g13346 g13346.t4 TSS g13346.t4 29387879 29387879
chr_1 g13346 g13346.t4 isoform g13346.t4 29387994 29390027
chr_1 g13346 g13346.t4 exon g13346.t4.exon1 29387994 29388024
chr_1 g13346 g13346.t4 cds g13346.t4.CDS1 29387994 29388024
chr_1 g13346 g13346.t4 exon g13346.t4.exon2 29389109 29389253
chr_1 g13346 g13346.t4 cds g13346.t4.CDS2 29389109 29389253
chr_1 g13346 g13346.t4 exon g13346.t4.exon3 29389318 29389854
chr_1 g13346 g13346.t4 cds g13346.t4.CDS3 29389318 29389854
chr_1 g13346 g13346.t4 exon g13346.t4.exon4 29389914 29390027
chr_1 g13346 g13346.t4 cds g13346.t4.CDS4 29389914 29390025
chr_1 g13346 g13346.t4 TTS g13346.t4 29391017 29391017

Sequences

>g13346.t4 Gene=g13346 Length=827
ATGTATACACCGACTCATATTCAAGTTACAGTTCAACGTGCCAAAGGTCTCTTGACAAAA
GGCAAGAATGGAACGAACAATTGCTTTACCACAATTGCACTAGGCAAGGAAAAATATCAG
ACGTCTCTGAAGGAAAATGCCACAACAAATGTAGACTGGCACGAAGAATGTGAATTAGCT
ATTCCGTCGCAAGGAAATCGTGCTGAATTAATTTTGACGGTTCTGCATAGAAATGGTTTG
GGACTAGATGAATTCCTTGGTCAAATTACGCTTCCACTTAATGAAATGGATCACTTTGAT
CGACCAAGAAGTCGATGGTATAAGTTACAGAGTAAACCAGGTCAAGAGAAAAAAGACAAA
GATCGTGGTGAATTAGAGGTTCGAACAGCATTCACTGTCAAGGCAGGATCTTTGAGTGAC
TTGAGTAAAAAAGATAAAACAAAATCATCTCTTAGTAATATTGCTAATAATGTTGGCGGA
AGTCTCTTATCACTTGGACAAATAGAAAAACATAAGAGTCTGAAAAAGTTTGCTAAATCA
CTTGGCAATAAGATGCACGTAACTGGAAAGAAGAAAAAAGACAAAGGTGAAGATTCAGAT
TCATATACTGGTAGCTTTTCGAGTCTTGGTACACCTAGCTTGGGAACAAGAAATAGTTTT
CATTTACGCAACGAAGGAAATGCTGATCCAGGTGTTATCAGTGAGGATGAAGATGAATTT
GCTTTCGAGAATTTGTCTCATAAAAGTTCATCAAATTCTCTCAACGTTCGACAAAAGAAT
AATAACTTAATTTTGACAAAACAAGAAGATTTATCGACTCCAGTTGC

>g13346.t4 Gene=g13346 Length=275
MYTPTHIQVTVQRAKGLLTKGKNGTNNCFTTIALGKEKYQTSLKENATTNVDWHEECELA
IPSQGNRAELILTVLHRNGLGLDEFLGQITLPLNEMDHFDRPRSRWYKLQSKPGQEKKDK
DRGELEVRTAFTVKAGSLSDLSKKDKTKSSLSNIANNVGGSLLSLGQIEKHKSLKKFAKS
LGNKMHVTGKKKKDKGEDSDSYTGSFSSLGTPSLGTRNSFHLRNEGNADPGVISEDEDEF
AFENLSHKSSSNSLNVRQKNNNLILTKQEDLSTPV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13346.t4 Gene3D G3DSA:2.60.40.150 - 4 160 5.3E-24
6 g13346.t4 MobiDBLite mobidb-lite consensus disorder prediction 185 207 -
2 g13346.t4 PANTHER PTHR15746:SF23 RAB11 INTERACTING PROTEIN, ISOFORM A 3 260 2.3E-81
3 g13346.t4 PANTHER PTHR15746 RAB11-RELATED 3 260 2.3E-81
1 g13346.t4 Pfam PF00168 C2 domain 6 109 4.3E-14
5 g13346.t4 SMART SM00239 C2_3c 6 105 6.7E-7
4 g13346.t4 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 6 131 2.96E-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

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