General information for g6662.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transducin beta-like protein 3.
Parent gene
- The parent gene g6662 is located on chr_2: 17984900..17987249 (+ 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 | g6662 | g6662.t1 | TSS | g6662.t1 | 17984720 | 17984720 |
| chr_2 | g6662 | g6662.t1 | isoform | g6662.t1 | 17984819 | 17987249 |
| chr_2 | g6662 | g6662.t1 | exon | g6662.t1.exon1 | 17984819 | 17984847 |
| chr_2 | g6662 | g6662.t1 | cds | g6662.t1.CDS1 | 17984819 | 17984847 |
| chr_2 | g6662 | g6662.t1 | exon | g6662.t1.exon2 | 17984900 | 17987249 |
| chr_2 | g6662 | g6662.t1 | cds | g6662.t1.CDS2 | 17984900 | 17987249 |
| chr_2 | g6662 | g6662.t1 | TTS | g6662.t1 | 17987309 | 17987309 |
Sequences
>g6662.t1 Gene=g6662 Length=2379
ATGGAAGAATCTGTAAAGTTAAAAGAAATAATTGAAGTCGAAAAGCAGTATGGTGCATTT
TATACAGGAGGTACTGTTCTTTGGACAAATGATGGCAATTTCTTTTTATGCCGTGATGAA
GAAAAAATAAATATTATTTCAATTAAGTCATTAGAAGTGGAACGAATTATTGGCACTTCA
CAAGAAGGAAGCGAAGATGTTATTTATACTTTTGTTCTAACGATGGATGATGAATATTTA
ATATCTGCACATCGTAGTGGCTTACTAAAATTATGGGACTTTAATTCAGGTGAATTGAAG
AAAATGTGGAAGAACCTTCATTCTGGTCCAATTGCTTGTCTCCAATATTCCCAAGAACAA
CAGCTTGTGGCATCTGGTGGTGCTGATTCTATGGTACGAATATGGGATTTTAAAAATCAA
TTATGCAAGGGAACACTTAAAGGACTTCAGGGAGTTGTAAGCGTAATAATTTTTCATCCA
ATACAAAATTCTGTTCTTGCTGTTGCTGATGATTATAAAATATTAGCATGGTGTTTAGAG
ACACGTGAAATTTTGAAAAAATTCGTTGGACACATATCTCGTGTTACATCAATATCATTT
TCTAAAGATACAAAGACTTTTATTTCATCAGGCCGTGATAAAGTATTGATACTTTGGAAT
TATAATACAGAACAACAACTTAGAACAATTCCAGTTTATGAAGGTATTGAAAGTGCTTTG
GTTTTGAATCACAACTTGATATTACCTAATGGTATTCGACTTGATGACGAAACAAAAGTT
TACGTTGCATCGGCTGGTGAAGAAGGAATTGTTAAAATATGGCAAATGAATGATTCAAAA
ATATTGTACAAACAAGAGTCAAGCGTAATTTCAAGAGCAACAGAAGAAGGTGGTTTAGCA
ATTACTCAAATGCTTTTTAATCAAAAACTTCAACAAATTGCACTTGTTAGTGTTGACCAT
AACATCATCATATATGATTTTCACAATTTTTCATGCTCAAAGCAGCTTATAGGATTTACA
GATGAAATTCTCGATTTGTGTCTCATGGGTAAACGTGATCAATATCTAGCAATGGCAACA
AACAGCAACGATATAAAAATTTATGATACCGTCACAATGAATTCAAAAATTTTAAAGGGT
CACACTGATATTGTTCTTTCTTTATCAGCGTATAAAAATTATTTGCTTTCTGGTAGTAAA
GATAATACGGTTCGATTATGGATTGCTGATTTTGATAAATTTGAATTCGAATGCATTGGA
ATTGGTGCTAAACATACGAACACAGTCGGAAGTGTCGATATTAGTAAAACACACGCTGAT
TTCTTTGTATCAGTCAGTCAAGATCAATGTCTCAAATTATGGAAATTTCCCAAAGAATCA
TACAAAATAGATACCGATATGCTTTGTATAAACACTCAATTGGCTCACGAAAAAGATATT
AATTGTGTAACAATTTCACCTAATGATAAGTATATTGCAACTTCATCTCAGGACAAAACA
GCAAAGTTATGGGATTCTAGTAATCTTAAACTTCTTGGTGTATTTAGAGGACATCGACGA
GGAATTTGGACGGTTCGATTTTCACCAATTGATCAAGTTCTGCTTACTAGTGCAGCAGAT
TGTACAATGCGATTATGGAATTTAAGTGATATGACTTGTCTCAAAAGTCTTGAAGGACAT
GAAAGTTCTGTTTTAAGATGTGAATTTATTTCTAATGGTATGCAGATAATTTCATCTGGT
GCTGATGGTCTTATTAAATTGTGGACTTTAAAATCATCAGAATGTGTTCAAACACTTGAA
CAGCACGATAACAAAGTATGGGCTTTAGCTTTAACTAATGATGGAAAAAAAATGTTCACT
GGTGGTGCTGATTCTAAATTAATTCGTTGGCGTGATGCAACAGAAGAGAAGAAACGTGAA
GAATTAAGAATAAGGCAGGAAGAATGTCTACAAGAACAAGAGCTAAACAATTTATTGAGT
CAAAAGAAATTACTTAAAGCATTAAAACTTGCATTAAGACTCAATAAACCAAAACTTTCA
CTGAAAATTATCAATACAATAATCAGAAATAAAGATGAAGGACTTGAAGAGACTATTGAA
GGCTTATCTGATTTTCATAAACAAGCACTTCTTCAGCATGCGGTCAATTGGAATACAAAC
AGTAAAAATTGTAGACCGGCACAACTTGTTTTCAATATCATGTTGAATGAAATTTTGAAT
GGTAAATACAGAGTTGAAGGACTTGGAAAAATCATTGAGGACGCACTTCCGTATAGTGAA
CGACACTTTAAGCGAATGACTGAATATTTAAAGGACCTCAAATTCTTAGAATACACAATG
CGATGTATGAAGCCGTATGGTGATGTTACAATGAAGTAA
>g6662.t1 Gene=g6662 Length=792
MEESVKLKEIIEVEKQYGAFYTGGTVLWTNDGNFFLCRDEEKINIISIKSLEVERIIGTS
QEGSEDVIYTFVLTMDDEYLISAHRSGLLKLWDFNSGELKKMWKNLHSGPIACLQYSQEQ
QLVASGGADSMVRIWDFKNQLCKGTLKGLQGVVSVIIFHPIQNSVLAVADDYKILAWCLE
TREILKKFVGHISRVTSISFSKDTKTFISSGRDKVLILWNYNTEQQLRTIPVYEGIESAL
VLNHNLILPNGIRLDDETKVYVASAGEEGIVKIWQMNDSKILYKQESSVISRATEEGGLA
ITQMLFNQKLQQIALVSVDHNIIIYDFHNFSCSKQLIGFTDEILDLCLMGKRDQYLAMAT
NSNDIKIYDTVTMNSKILKGHTDIVLSLSAYKNYLLSGSKDNTVRLWIADFDKFEFECIG
IGAKHTNTVGSVDISKTHADFFVSVSQDQCLKLWKFPKESYKIDTDMLCINTQLAHEKDI
NCVTISPNDKYIATSSQDKTAKLWDSSNLKLLGVFRGHRRGIWTVRFSPIDQVLLTSAAD
CTMRLWNLSDMTCLKSLEGHESSVLRCEFISNGMQIISSGADGLIKLWTLKSSECVQTLE
QHDNKVWALALTNDGKKMFTGGADSKLIRWRDATEEKKREELRIRQEECLQEQELNNLLS
QKKLLKALKLALRLNKPKLSLKIINTIIRNKDEGLEETIEGLSDFHKQALLQHAVNWNTN
SKNCRPAQLVFNIMLNEILNGKYRVEGLGKIIEDALPYSERHFKRMTEYLKDLKFLEYTM
RCMKPYGDVTMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g6662.t1 | CDD | cd00200 | WD40 | 332 | 631 | 1.35153E-69 |
| 18 | g6662.t1 | Gene3D | G3DSA:2.130.10.10 | - | 31 | 249 | 3.4E-37 |
| 17 | g6662.t1 | Gene3D | G3DSA:2.130.10.10 | - | 250 | 346 | 1.6E-8 |
| 19 | g6662.t1 | Gene3D | G3DSA:2.130.10.10 | - | 347 | 548 | 2.6E-46 |
| 16 | g6662.t1 | Gene3D | G3DSA:2.130.10.10 | - | 549 | 721 | 3.9E-22 |
| 9 | g6662.t1 | PANTHER | PTHR19854 | TRANSDUCIN BETA-LIKE 3 | 1 | 784 | 2.9E-216 |
| 10 | g6662.t1 | PANTHER | PTHR19854:SF15 | TRANSDUCIN BETA-LIKE PROTEIN 3 | 1 | 784 | 2.9E-216 |
| 13 | g6662.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 395 | 409 | 4.1E-6 |
| 11 | g6662.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 492 | 506 | 4.1E-6 |
| 12 | g6662.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 576 | 590 | 4.1E-6 |
| 8 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 107 | 136 | 2.7E-4 |
| 4 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 183 | 220 | 3.4E-5 |
| 7 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 375 | 407 | 2.4E-5 |
| 5 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 474 | 505 | 2.1E-6 |
| 2 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 510 | 547 | 9.7E-5 |
| 3 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 552 | 588 | 3.5E-4 |
| 6 | g6662.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 594 | 628 | 0.13 |
| 1 | g6662.t1 | Pfam | PF08625 | Utp13 specific WD40 associated domain | 652 | 783 | 2.6E-31 |
| 22 | g6662.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 123 | 137 | - |
| 21 | g6662.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 492 | 506 | - |
| 23 | g6662.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 534 | 548 | - |
| 37 | g6662.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 61 | 640 | 74.823 |
| 43 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 61 | 102 | 9.205 |
| 41 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 104 | 139 | 13.048 |
| 45 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 188 | 229 | 14.251 |
| 40 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 378 | 407 | 12.046 |
| 39 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 473 | 514 | 13.382 |
| 42 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 515 | 556 | 14.051 |
| 44 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 557 | 598 | 14.285 |
| 38 | g6662.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 599 | 640 | 9.94 |
| 25 | g6662.t1 | SMART | SM00320 | WD40_4 | 50 | 93 | 2.1 |
| 28 | g6662.t1 | SMART | SM00320 | WD40_4 | 96 | 136 | 2.4E-6 |
| 34 | g6662.t1 | SMART | SM00320 | WD40_4 | 139 | 178 | 10.0 |
| 30 | g6662.t1 | SMART | SM00320 | WD40_4 | 181 | 220 | 7.8E-7 |
| 32 | g6662.t1 | SMART | SM00320 | WD40_4 | 235 | 275 | 260.0 |
| 31 | g6662.t1 | SMART | SM00320 | WD40_4 | 287 | 326 | 61.0 |
| 27 | g6662.t1 | SMART | SM00320 | WD40_4 | 329 | 369 | 0.67 |
| 35 | g6662.t1 | SMART | SM00320 | WD40_4 | 371 | 408 | 0.025 |
| 36 | g6662.t1 | SMART | SM00320 | WD40_4 | 415 | 455 | 0.0036 |
| 33 | g6662.t1 | SMART | SM00320 | WD40_4 | 466 | 505 | 4.0E-9 |
| 24 | g6662.t1 | SMART | SM00320 | WD40_4 | 508 | 547 | 1.6E-7 |
| 26 | g6662.t1 | SMART | SM00320 | WD40_4 | 550 | 589 | 3.7E-7 |
| 29 | g6662.t1 | SMART | SM00320 | WD40_4 | 592 | 631 | 1.3E-5 |
| 14 | g6662.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 62 | 369 | 2.09E-50 |
| 15 | g6662.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 300 | 634 | 7.1E-72 |
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:0032040 | small-subunit processome | CC |
| GO:0005515 | protein binding | MF |
| GO:0006364 | rRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K14555 (U3 small nucleolar RNA-associated protein 13)
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.
