General information for g11264.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinoblastoma-binding protein 5-like protein.
Parent gene
- The parent gene g11264 is located on chr_1: 15159937..15160435 (- 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 | g11264 | g11264.t1 | TTS | g11264.t1 | 15158245 | 15158245 |
| chr_1 | g11264 | g11264.t1 | isoform | g11264.t1 | 15158406 | 15159937 |
| chr_1 | g11264 | g11264.t1 | exon | g11264.t1.exon1 | 15158406 | 15159853 |
| chr_1 | g11264 | g11264.t1 | cds | g11264.t1.CDS1 | 15158406 | 15159853 |
| chr_1 | g11264 | g11264.t1 | exon | g11264.t1.exon2 | 15159919 | 15159937 |
| chr_1 | g11264 | g11264.t1 | cds | g11264.t1.CDS2 | 15159919 | 15159937 |
| chr_1 | g11264 | g11264.t1 | TSS | g11264.t1 | 15160029 | 15160029 |
Sequences
>g11264.t1 Gene=g11264 Length=1467
ATGAATTTGGAATTGTTGGAGTCATTTTGCCAAAACTTTCCTGAAGAATATGATGGTGCA
CTCGATTGTATTTCGTTAGCAGTAACTTGCTGCTTTAATAAGTATGGTACGCTTTTAGCT
GTAGGCTGTAATGATGGAAGAATTGTTATTTGGGATTTCTTAACTAGAGGAATTGCAAAA
ATTATATCAGCCCACGTTCATCCAATTTGTTCACTTAGTTGGTCAAGAAATGGACATAAA
TTGTTATCGGCGTCAACAGATAATAACGCTTGTATATGGGACGTTTTAACTGGTGACTGT
GAAAATAAATATCGGTTTCCATCGCCAATTCTAAAAGTGCAATTTCATCCGCGCAATGAT
TCAAAATTTCTTGTTTGCCCAATGAGATATGCAGCTATTTTAGTTGAAGTAGGAGGAAAA
CATCAAGTGCTTCCAATTGACAGTGATGGAGATCTTAATATTGTCGCTACATTCGATCGA
AGAGGACAACATATTTTTACAGGAAATGCAAAAGGAAAAATTCTAGTTCTTGACACTGAA
ACTCTGAAAATTGTTGCAAGTTTTAAAATTACTGTGGGAACATCAAGTGCGACTGCAGTT
AAGAGTATTGAATTTGCTCGTCGTGGTGATTCATTTCTTGTAAATACAGCTGATCGTGTT
ATTCGAGTTTATGATTCAAAAGAAGTGCTGACATGTAAAGGTGATCCAGAGCCAATTCAG
AAATTACAAGATCTTGTGAATAAAACGACATGGAAAAAGTGTTGTTTCTCAGGTGATGGT
GAATATATATGTGCTGGTTCAGCAAGACAACATGCACTTTATATTTGGGAAAAATCTGTT
GGAAATCTTGTAAAAATTCTTCATGGAACAAAAGGTGAATTGCTTTTAGACGTTATATGG
CATCCTGTAAGACCAATTATTGCAAGTATAAGTTCTGGATTGGTCTCAATATGGGCCCAA
AATCAAGTTGAAAATTGGTCAGCTTTTGCTCCTGATTTCAAAGAATTGGATGAAAATGTT
GAATATGAAGAAAGAGAGTCTGAATTTGATATTGCAGATGAAGACAAATCGGTTGACCTT
GCAGCAGAAAATAAAACAGAAGAGGATCTTGAAGTTGACATTGTAACAACAGAGCCAATT
GCTGCATTTTGTAGTTCAGATGAAGAAACAGAAGACAATAATGCACTACAATTTCTTCCA
ATCGCTCCTGAGGTGGAGGATCCTGAAGACGGATGGGCTAATCAAGAAGCAGATGCCTTA
GCTGAACAAGAACAATTGTCAAATTCACGAGATTTTAATGATTCTTTGGATGGAGGTGGA
AGTGCAAAGAAAAGAAAAATTTCCTCATACGACATTGAACTTGAAAATGCACCACCAGCT
GATGAAACACATCCATTACTTCAAAATAAAACAATGAAAGAGAAACAAAACACAAATAAC
AAATCAAAAGGACGACCGAGAAAATAG
>g11264.t1 Gene=g11264 Length=488
MNLELLESFCQNFPEEYDGALDCISLAVTCCFNKYGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHVHPICSLSWSRNGHKLLSASTDNNACIWDVLTGDCENKYRFPSPILKVQFHPRND
SKFLVCPMRYAAILVEVGGKHQVLPIDSDGDLNIVATFDRRGQHIFTGNAKGKILVLDTE
TLKIVASFKITVGTSSATAVKSIEFARRGDSFLVNTADRVIRVYDSKEVLTCKGDPEPIQ
KLQDLVNKTTWKKCCFSGDGEYICAGSARQHALYIWEKSVGNLVKILHGTKGELLLDVIW
HPVRPIIASISSGLVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIADEDKSVDL
AAENKTEEDLEVDIVTTEPIAAFCSSDEETEDNNALQFLPIAPEVEDPEDGWANQEADAL
AEQEQLSNSRDFNDSLDGGGSAKKRKISSYDIELENAPPADETHPLLQNKTMKEKQNTNN
KSKGRPRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11264.t1 | Gene3D | G3DSA:2.130.10.10 | - | 25 | 322 | 2.0E-45 |
| 12 | g11264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 419 | 488 | - |
| 13 | g11264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 420 | 435 | - |
| 14 | g11264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 437 | 451 | - |
| 3 | g11264.t1 | PANTHER | PTHR44040 | RETINOBLASTOMA-BINDING PROTEIN 5 | 1 | 477 | 1.3E-159 |
| 1 | g11264.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 28 | 52 | 0.0037 |
| 2 | g11264.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 61 | 94 | 6.6E-4 |
| 6 | g11264.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 81 | 95 | - |
| 15 | g11264.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 32 | 103 | 15.926 |
| 16 | g11264.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 62 | 103 | 12.881 |
| 7 | g11264.t1 | SMART | SM00320 | WD40_4 | 14 | 52 | 0.022 |
| 10 | g11264.t1 | SMART | SM00320 | WD40_4 | 55 | 94 | 5.6E-7 |
| 8 | g11264.t1 | SMART | SM00320 | WD40_4 | 181 | 225 | 4.0 |
| 11 | g11264.t1 | SMART | SM00320 | WD40_4 | 235 | 277 | 30.0 |
| 9 | g11264.t1 | SMART | SM00320 | WD40_4 | 280 | 319 | 14.0 |
| 4 | g11264.t1 | SUPERFAMILY | SSF117289 | Nucleoporin domain | 28 | 354 | 1.31E-46 |
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:0048188 | Set1C/COMPASS complex | CC |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14961 (COMPASS component SWD1)
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.
