General information for g12724.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12724 is located on chr_1: 25467038..25468035 (- 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 | g12724 | g12724.t1 | TTS | g12724.t1 | 25465791 | 25465791 |
| chr_1 | g12724 | g12724.t1 | isoform | g12724.t1 | 25465894 | 25468035 |
| chr_1 | g12724 | g12724.t1 | exon | g12724.t1.exon1 | 25465894 | 25466084 |
| chr_1 | g12724 | g12724.t1 | cds | g12724.t1.CDS1 | 25465894 | 25466084 |
| chr_1 | g12724 | g12724.t1 | exon | g12724.t1.exon2 | 25466141 | 25467341 |
| chr_1 | g12724 | g12724.t1 | cds | g12724.t1.CDS2 | 25466141 | 25467341 |
| chr_1 | g12724 | g12724.t1 | exon | g12724.t1.exon3 | 25467405 | 25467554 |
| chr_1 | g12724 | g12724.t1 | cds | g12724.t1.CDS3 | 25467405 | 25467554 |
| chr_1 | g12724 | g12724.t1 | exon | g12724.t1.exon4 | 25467610 | 25467956 |
| chr_1 | g12724 | g12724.t1 | cds | g12724.t1.CDS4 | 25467610 | 25467956 |
| chr_1 | g12724 | g12724.t1 | exon | g12724.t1.exon5 | 25468026 | 25468035 |
| chr_1 | g12724 | g12724.t1 | cds | g12724.t1.CDS5 | 25468026 | 25468035 |
| chr_1 | g12724 | g12724.t1 | TSS | g12724.t1 | 25468311 | 25468311 |
Sequences
>g12724.t1 Gene=g12724 Length=1899
ATGGAACAAGAAAATTCACAGAAAAAGACTCAAGAAGAGGAATTCAATTCCCAGCGTGCA
AAAATGAAAGAGATTTATTTAGCAAAAGAGAAGGAATGTGTACAGTTGAAACAAAAAATT
ATAAGTTTAAAGAAAGACCTTGATGAGGCTTCATCACAAATAGTCATTGCTGAGTACAAC
CGAGAAAAAGATTTAGAACGTTTTGAACAAGAGACATTGACTCTTAATCAAATAATTCAA
GAAACTTGTGACGAATCGACTATAGCTCAAACCGAAATAAAACGACTTCAAGAGGAAAAT
GAGAAAATTAAACAAGAAATGGCGCTATTAAGAGAAACATTGATACAACAGCAACAAGAA
TCAAATAAGAGTTTAGAATCTATTCTTGGACTAAAAACTTTAGCTAGAAATGTTAAGAAA
ATAACTGGAACACATAGTAATAGTCAAGAGAATTTAGATGAATCAATGCGAAAAGTAGCA
GCGACATCAGCTAGTGCAGCGAAATATGCTCAAGAAGATGCTGATACGTTAAGGTCATTA
GTTGTTCCTCTGGAAAGTGAAATTATACAATTAAAAGAAAAATTAAGAGCTGCATATGAC
GAAATTGAACTATTGAAAACTGCCAAAGGTGAAAGTATTCAAGTAAAATCAGCATTAGTT
GGTTTACTAGGTGAGACTCAAAAAGAAAATGAAGGTGATGTCAAAGAAGAACCAATGGAG
CAGGAAGAAACAGCAAAATCTCAAGAGTCATGTAATATGTGCAAAAATTATGAACTCCAG
TTAGTTCAAGCTCAAGAATCCATCGAGAATGAAAAGATGAAAATAGTAAAAGTAGAAAAA
ATAGTTGATCGTTTAAAGCAAGATTTACTGAAAGAGTCGGCACTTCGACTCGATTTAGAG
AAGACGTGGCAAGAAAAACGTGAAGAGCATCGAGATGCTGTTCAAAAATTATGTGACAAA
TTAAATGAAAGTGAAAGGCAGATGATTCAGCTACAAACTGAATTTGGCAATTTCAAAGAT
GAAATAAGTAATGAGTTAAAAAAGAATTTTGGTGAACGGCAAGACATCTTTGATCATTTA
GAAACTCTTCAAAATGATAATGAATACTTAAGTGGACGATATTTAGAACATTCAAATGAA
ATGAAAGATAAAGAAATAAATCTGCCACAAAGTATAGAAGAGCTACACGAATTTATTTTA
GATCTTAATGAAAAGTTGATTGTATCAAAAGTTGGGCAAGAATTTAATGAAGCAAAATGT
GTTACATTTAGAGATGAGTCAAATATATTACGCGAACAATTACATCAAAAAGAAAAGGAA
AAACAGTTTCTTGAGCAAAAATTAAACCATAGAATTCACAGTCTTGAGGATAAATTGAAA
CAAAATCATCAAAGTCATTTGAAGCTCATTAGCGAGAAAGAGGAACTGCTGAAAGTGGAA
AATGATAATAAAAAAGAAATTAGTGATTTGCGAATGCAAAATATTGAACTGAGTGAGAAT
GTAGATAGACTGGAGAAAGCAAATATTGATATTAAATCTAAACTTTCCATGCTTCAACAA
GAATTGTCCACAAGTGAACAAGTTCAAAAAGATTTTGTCAAGTTATCACAATCATTACAA
ATGCAATTAGAGAAAATTCGTTCTGCTGACTCTCAAGTTCGTTGGCAAGATTTCGATGAT
GTTGATAATTGTCCAAATTGCAAGCAAGAATTCACTGTGACAAGAAGAAAAAGAAATTGC
CGTCATTGTGGAACAATATTTTGTGAAAAATGTTGTGATCGTTCTGTCAAGAGTGGACCT
TCCCAGAAAATAGCAAAAGTATGCGATCTTTGCAATACAATTCTGCAATCGCACTGTGCT
CCATATTTTAGTGAAAATGCTCCTCAAAGTCCAATTTAG
>g12724.t1 Gene=g12724 Length=632
MEQENSQKKTQEEEFNSQRAKMKEIYLAKEKECVQLKQKIISLKKDLDEASSQIVIAEYN
REKDLERFEQETLTLNQIIQETCDESTIAQTEIKRLQEENEKIKQEMALLRETLIQQQQE
SNKSLESILGLKTLARNVKKITGTHSNSQENLDESMRKVAATSASAAKYAQEDADTLRSL
VVPLESEIIQLKEKLRAAYDEIELLKTAKGESIQVKSALVGLLGETQKENEGDVKEEPME
QEETAKSQESCNMCKNYELQLVQAQESIENEKMKIVKVEKIVDRLKQDLLKESALRLDLE
KTWQEKREEHRDAVQKLCDKLNESERQMIQLQTEFGNFKDEISNELKKNFGERQDIFDHL
ETLQNDNEYLSGRYLEHSNEMKDKEINLPQSIEELHEFILDLNEKLIVSKVGQEFNEAKC
VTFRDESNILREQLHQKEKEKQFLEQKLNHRIHSLEDKLKQNHQSHLKLISEKEELLKVE
NDNKKEISDLRMQNIELSENVDRLEKANIDIKSKLSMLQQELSTSEQVQKDFVKLSQSLQ
MQLEKIRSADSQVRWQDFDDVDNCPNCKQEFTVTRRKRNCRHCGTIFCEKCCDRSVKSGP
SQKIAKVCDLCNTILQSHCAPYFSENAPQSPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g12724.t1 | CDD | cd15739 | FYVE_RABE_unchar | 552 | 624 | 5.73348E-38 |
| 18 | g12724.t1 | Coils | Coil | Coil | 1 | 21 | - |
| 19 | g12724.t1 | Coils | Coil | Coil | 26 | 53 | - |
| 12 | g12724.t1 | Coils | Coil | Coil | 79 | 120 | - |
| 14 | g12724.t1 | Coils | Coil | Coil | 188 | 208 | - |
| 13 | g12724.t1 | Coils | Coil | Coil | 254 | 288 | - |
| 15 | g12724.t1 | Coils | Coil | Coil | 307 | 341 | - |
| 17 | g12724.t1 | Coils | Coil | Coil | 427 | 447 | - |
| 16 | g12724.t1 | Coils | Coil | Coil | 487 | 521 | - |
| 10 | g12724.t1 | Gene3D | G3DSA:1.20.5.730 | Single helix bin | 513 | 564 | 3.2E-19 |
| 11 | g12724.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 565 | 617 | 1.4E-13 |
| 22 | g12724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 247 | - |
| 23 | g12724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 244 | - |
| 4 | g12724.t1 | PANTHER | PTHR31179:SF7 | RABAPTIN (RAB EFFECTOR) | 5 | 207 | 1.2E-93 |
| 6 | g12724.t1 | PANTHER | PTHR31179 | RAB GTPASE-BINDING EFFECTOR PROTEIN | 5 | 207 | 1.2E-93 |
| 5 | g12724.t1 | PANTHER | PTHR31179:SF7 | RABAPTIN (RAB EFFECTOR) | 223 | 625 | 1.2E-93 |
| 7 | g12724.t1 | PANTHER | PTHR31179 | RAB GTPASE-BINDING EFFECTOR PROTEIN | 223 | 625 | 1.2E-93 |
| 3 | g12724.t1 | Pfam | PF03528 | Rabaptin | 8 | 209 | 3.3E-8 |
| 2 | g12724.t1 | Pfam | PF09311 | Rabaptin-like protein | 251 | 550 | 1.9E-38 |
| 1 | g12724.t1 | Pfam | PF01363 | FYVE zinc finger | 554 | 616 | 1.3E-13 |
| 24 | g12724.t1 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 558 | 616 | 11.673 |
| 21 | g12724.t1 | SMART | SM00064 | fyve_4 | 550 | 617 | 4.1E-19 |
| 8 | g12724.t1 | SUPERFAMILY | SSF103652 | G protein-binding domain | 514 | 562 | 3.19E-18 |
| 9 | g12724.t1 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 554 | 622 | 2.3E-15 |
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:0046872 | metal ion binding | MF |
| GO:0008083 | growth factor activity | MF |
| GO:0006897 | endocytosis | BP |
| GO:0005096 | GTPase activator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12480 (Rab GTPase-binding effector protein 1)
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.
