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.t1 TSS g13346.t1 29387879 29387879
chr_1 g13346 g13346.t1 isoform g13346.t1 29387994 29391020
chr_1 g13346 g13346.t1 exon g13346.t1.exon1 29387994 29388024
chr_1 g13346 g13346.t1 cds g13346.t1.CDS1 29387994 29388024
chr_1 g13346 g13346.t1 exon g13346.t1.exon2 29389109 29389253
chr_1 g13346 g13346.t1 cds g13346.t1.CDS2 29389109 29389253
chr_1 g13346 g13346.t1 exon g13346.t1.exon3 29389318 29389854
chr_1 g13346 g13346.t1 cds g13346.t1.CDS3 29389318 29389854
chr_1 g13346 g13346.t1 exon g13346.t1.exon4 29389914 29390727
chr_1 g13346 g13346.t1 cds g13346.t1.CDS4 29389914 29390727
chr_1 g13346 g13346.t1 exon g13346.t1.exon5 29390789 29390940
chr_1 g13346 g13346.t1 cds g13346.t1.CDS5 29390789 29390940
chr_1 g13346 g13346.t1 exon g13346.t1.exon6 29391014 29391020
chr_1 g13346 g13346.t1 cds g13346.t1.CDS6 29391014 29391020
chr_1 g13346 g13346.t1 TTS g13346.t1 29391109 29391109

Sequences

>g13346.t1 Gene=g13346 Length=1686
ATGTATACACCGACTCATATTCAAGTTACAGTTCAACGTGCCAAAGGTCTCTTGACAAAA
GGCAAGAATGGAACGAACAATTGCTTTACCACAATTGCACTAGGCAAGGAAAAATATCAG
ACGTCTCTGAAGGAAAATGCCACAACAAATGTAGACTGGCACGAAGAATGTGAATTAGCT
ATTCCGTCGCAAGGAAATCGTGCTGAATTAATTTTGACGGTTCTGCATAGAAATGGTTTG
GGACTAGATGAATTCCTTGGTCAAATTACGCTTCCACTTAATGAAATGGATCACTTTGAT
CGACCAAGAAGTCGATGGTATAAGTTACAGAGTAAACCAGGTCAAGAGAAAAAAGACAAA
GATCGTGGTGAATTAGAGGTTCGAACAGCATTCACTGTCAAGGCAGGATCTTTGAGTGAC
TTGAGTAAAAAAGATAAAACAAAATCATCTCTTAGTAATATTGCTAATAATGTTGGCGGA
AGTCTCTTATCACTTGGACAAATAGAAAAACATAAGAGTCTGAAAAAGTTTGCTAAATCA
CTTGGCAATAAGATGCACGTAACTGGAAAGAAGAAAAAAGACAAAGGTGAAGATTCAGAT
TCATATACTGGTAGCTTTTCGAGTCTTGGTACACCTAGCTTGGGAACAAGAAATAGTTTT
CATTTACGCAACGAAGGAAATGCTGATCCAGGTGTTATCAGTGAGGATGAAGATGAATTT
GCTTTCGAGAATTTGTCTCATAAAAGTTCATCAAATTCTCTCAACGTTCGACAAAAGAAT
AATAACTTAATTTTGACAAAACAAGAAGATTTATCGACTCCAGTTGCTACACTGCGTGAA
AGTGCCACACTTCCGCAGTTGAGTAAGCCATCAACGAAAAATGTTCACGAGACGCCAACA
AAAGAATCATCTAAAGTGGATGAGTGGGAAGCGAAATTGTATGGGAAAAATGTAGAAATT
GGACATAGTACTGACTCACTTAAACGACGATCGTGGGAAAATTCTCGCGTTCCATTCAAT
AATTCAGAACATGAGTTAAAAGAGAAAGAACGTGAACCAACAATTCAAGAACAATCATTA
GAACGTGTATCTTTGGACTTTGCTTCAACTGCACCAGCTTCGCCTGAGCTTAATACTAAA
AAAATTAATAATGCTTTGGATTCAAAGCCATTACCGTTGCCACGTGCAGCAACAGCAGCA
GAACCAATTGTCTCACTCAATATTGACGATGAGTTACGTTCAAACAATAAAAACAACATG
TCACCAACATCACTCAAGGGCGAGAAAGCAGAAAAAGAAAACATTTTCTCAAAGAAATGG
AAAAACTTTAGAAAAGAGCACACGCCAAATAAAAATGAAAGTGAATCGATAAAAAATCAA
TATAATAAATCATCAACAGGCAGTGGTAATGGAGGTGAAAGAATTATAATTGGAGGTGAT
AATGCTTTCAATTCACAGTCATATGTTGAGAAAAAAATTGATTTGCCAAAAGAAGTGCTC
GCAAAATATGATGGAAAATCAAAAGAGGAAATAATGAAGATTGCTCATAATCTTGAAGGC
GATTTGATTCAACAGAGACAAAAGAACAAGGAACTGGAAGAATATCTCGATATATTGTTA
TTGAAGGTCATGGAAACTCATCCAAAAATATTGCAAAATCCTTATATCAATTCGCAGAGC
GGCTAA

>g13346.t1 Gene=g13346 Length=561
MYTPTHIQVTVQRAKGLLTKGKNGTNNCFTTIALGKEKYQTSLKENATTNVDWHEECELA
IPSQGNRAELILTVLHRNGLGLDEFLGQITLPLNEMDHFDRPRSRWYKLQSKPGQEKKDK
DRGELEVRTAFTVKAGSLSDLSKKDKTKSSLSNIANNVGGSLLSLGQIEKHKSLKKFAKS
LGNKMHVTGKKKKDKGEDSDSYTGSFSSLGTPSLGTRNSFHLRNEGNADPGVISEDEDEF
AFENLSHKSSSNSLNVRQKNNNLILTKQEDLSTPVATLRESATLPQLSKPSTKNVHETPT
KESSKVDEWEAKLYGKNVEIGHSTDSLKRRSWENSRVPFNNSEHELKEKEREPTIQEQSL
ERVSLDFASTAPASPELNTKKINNALDSKPLPLPRAATAAEPIVSLNIDDELRSNNKNNM
SPTSLKGEKAEKENIFSKKWKNFRKEHTPNKNESESIKNQYNKSSTGSGNGGERIIIGGD
NAFNSQSYVEKKIDLPKEVLAKYDGKSKEEIMKIAHNLEGDLIQQRQKNKELEEYLDILL
LKVMETHPKILQNPYINSQSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13346.t1 Coils Coil Coil 515 535 -
9 g13346.t1 Gene3D G3DSA:2.60.40.150 - 4 158 2.7E-23
15 g13346.t1 MobiDBLite mobidb-lite consensus disorder prediction 185 210 -
14 g13346.t1 MobiDBLite mobidb-lite consensus disorder prediction 281 306 -
13 g13346.t1 MobiDBLite mobidb-lite consensus disorder prediction 445 469 -
12 g13346.t1 MobiDBLite mobidb-lite consensus disorder prediction 454 469 -
4 g13346.t1 PANTHER PTHR15746:SF23 RAB11 INTERACTING PROTEIN, ISOFORM A 3 357 4.1E-96
6 g13346.t1 PANTHER PTHR15746 RAB11-RELATED 3 357 4.1E-96
3 g13346.t1 PANTHER PTHR15746:SF23 RAB11 INTERACTING PROTEIN, ISOFORM A 497 558 4.1E-96
5 g13346.t1 PANTHER PTHR15746 RAB11-RELATED 497 558 4.1E-96
1 g13346.t1 Pfam PF00168 C2 domain 6 109 1.6E-13
2 g13346.t1 Pfam PF09457 FIP domain 507 554 3.0E-11
16 g13346.t1 ProSiteProfiles PS51511 FIP-RBD domain profile. 492 554 12.047
11 g13346.t1 SMART SM00239 C2_3c 6 105 6.7E-7
8 g13346.t1 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 6 131 1.29E-19
7 g13346.t1 SUPERFAMILY SSF144270 Eferin C-derminal domain-like 525 555 2.35E-8

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