General information for g5735.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rabenosyn-5.
Parent gene
- The parent gene g5735 is located on chr_2: 11453276..11463782 (- 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_2 | g5735 | g5735.t1 | TTS | g5735.t1 | 11453221 | 11453221 |
| chr_2 | g5735 | g5735.t1 | isoform | g5735.t1 | 11453276 | 11454768 |
| chr_2 | g5735 | g5735.t1 | exon | g5735.t1.exon1 | 11453276 | 11454093 |
| chr_2 | g5735 | g5735.t1 | cds | g5735.t1.CDS1 | 11453276 | 11454093 |
| chr_2 | g5735 | g5735.t1 | exon | g5735.t1.exon2 | 11454147 | 11454294 |
| chr_2 | g5735 | g5735.t1 | cds | g5735.t1.CDS2 | 11454147 | 11454294 |
| chr_2 | g5735 | g5735.t1 | exon | g5735.t1.exon3 | 11454349 | 11454768 |
| chr_2 | g5735 | g5735.t1 | cds | g5735.t1.CDS3 | 11454349 | 11454768 |
| chr_2 | g5735 | g5735.t1 | TSS | g5735.t1 | 11454959 | 11454959 |
Sequences
>g5735.t1 Gene=g5735 Length=1386
ATGTTTGATGAAAGTGAAATAAAGGAAGGATTCATTTGTCCTATTTGTAAAAGTGATGAG
AAGAATATAGAAGTGTTGTTGAAACACTTTGATGAACAGCATTCAGAAGAGAAAGATTTA
ATTACAACATTTCGTGATGTTTTCAAAATTGCTAAAAAGAAGATTTTGAATTTTGATGAA
AAAACTTTTGAAAACACTCTCAAAATAAGCAAACCAACTAATCCATTCCAAGAATATGAT
TTTATAGATGAAGTTCAAGAAATTGGTTTATTTACAAATCATTTCGAATATTTTAAAGCA
ATAAGAGATCCAAGAATCGAAAGGTATGCGACTGAAACAAATAAACTGATCATCAGACTC
AATAAACTGCTCACTAATCGGCCAAATGATCCTCAACAAATTAAGCAACATGAACAAAAT
TTGGTTCCATGGATAGATGGAAAACTTGTCAAATTATGTCCTTCATGTGCTAAAAGCTTC
TTCCTAACTCGAAGACAACATCATTGTCGTTTATGCGGATCAATTATGTGCAATGATTGC
TCTCAATTCTTATCAATTGATGAATCCAAATCAATAATAAGTCCATCTAATGAGAGCAAA
CAAGATGATAGTGTTGATATTATTTTAAAACAACCAGAAGATTCAATTCGAATGTGTGAG
CATTGTCTTCATCTTCTCATAACACGCAAAGAAATGCAAGATAGTAAATTATCTAAACCT
ATTATAACGAAAATTTATGAGCAAATAGAAACATTGAAAAAAGAAATCATGCCACACATC
ACAATGTATGAAAAGATGATTGACAGTTTATACAAAGGTGATTCTGTTTACACACTAGCC
GATGCAGGAGTGTTGAGAGGAAAAATTGGATCAACAGCTGAAACACTTGATGATCTCAGT
AAGAAAGTTCTAACATTAAAATGCATGAAAGGCAGTCGACAGGAAGCTATCCAAAAAAGC
CTTCGAATGGCAGCAATTAAATTCATCAAAGAAAATATGCTAACGTTACCACAAATACCT
GTTGAGGAAGAAATCAAAAAGATTCAACAAAAAAGAATAATGGAATTAAATCAAAAAATT
GAAAGAGATAGGCGACTTGCACAAGAAGCATTTGAAAAATATGACTTGAGTGAAAATTAT
CCAGCAACATCTTCTAAAACGGGATCATCAATAAAAATGGTAGACAATTGGTCAGGATTT
CAACAAAACATTCAAGTTAATGCAAACGATCCACTAGTCGAACAAATGAACATAATTAAA
GGATACATAAAGCAAGCGAGAGAAGCATTACGCTTTGAAGAAATTGAAACATTGGAGGCA
AATTTAAAAGAACTTCAACATGAGTACTGGCTTAGAGCGCAACAAAAAGAAAATTCTGAA
AATTGA
>g5735.t1 Gene=g5735 Length=461
MFDESEIKEGFICPICKSDEKNIEVLLKHFDEQHSEEKDLITTFRDVFKIAKKKILNFDE
KTFENTLKISKPTNPFQEYDFIDEVQEIGLFTNHFEYFKAIRDPRIERYATETNKLIIRL
NKLLTNRPNDPQQIKQHEQNLVPWIDGKLVKLCPSCAKSFFLTRRQHHCRLCGSIMCNDC
SQFLSIDESKSIISPSNESKQDDSVDIILKQPEDSIRMCEHCLHLLITRKEMQDSKLSKP
IITKIYEQIETLKKEIMPHITMYEKMIDSLYKGDSVYTLADAGVLRGKIGSTAETLDDLS
KKVLTLKCMKGSRQEAIQKSLRMAAIKFIKENMLTLPQIPVEEEIKKIQQKRIMELNQKI
ERDRRLAQEAFEKYDLSENYPATSSKTGSSIKMVDNWSGFQQNIQVNANDPLVEQMNIIK
GYIKQAREALRFEEIETLEANLKELQHEYWLRAQQKENSEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5735.t1 | CDD | cd15716 | FYVE_RBNS5 | 141 | 229 | 4.31697E-28 |
| 9 | g5735.t1 | Coils | Coil | Coil | 346 | 373 | - |
| 8 | g5735.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 132 | 235 | 6.1E-14 |
| 7 | g5735.t1 | Gene3D | G3DSA:4.10.860.20 | - | 407 | 458 | 4.4E-19 |
| 3 | g5735.t1 | PANTHER | PTHR13510:SF44 | RABENOSYN-5 | 120 | 449 | 2.1E-23 |
| 4 | g5735.t1 | PANTHER | PTHR13510 | FYVE-FINGER-CONTAINING RAB5 EFFECTOR PROTEIN RABENOSYN-5-RELATED | 120 | 449 | 2.1E-23 |
| 1 | g5735.t1 | Pfam | PF01363 | FYVE zinc finger | 143 | 224 | 3.6E-17 |
| 2 | g5735.t1 | Pfam | PF11464 | Rabenosyn Rab binding domain | 411 | 450 | 4.4E-17 |
| 12 | g5735.t1 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 147 | 227 | 10.387 |
| 11 | g5735.t1 | SMART | SM00064 | fyve_4 | 139 | 228 | 6.3E-13 |
| 6 | g5735.t1 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 144 | 246 | 6.24E-18 |
| 5 | g5735.t1 | SUPERFAMILY | SSF140125 | Rabenosyn-5 Rab-binding domain-like | 399 | 450 | 5.49E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5735/g5735.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5735.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046872 | metal ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12481 (rabenosyn-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.
