Gene loci information

Transcript annotation

  • This transcript has been annotated as Transducin beta-like protein 3.

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_2 g6662 g6662.t2 TSS g6662.t2 17984720 17984720
chr_2 g6662 g6662.t2 isoform g6662.t2 17984900 17987249
chr_2 g6662 g6662.t2 exon g6662.t2.exon1 17984900 17987249
chr_2 g6662 g6662.t2 cds g6662.t2.CDS1 17985093 17987249
chr_2 g6662 g6662.t2 TTS g6662.t2 17987309 17987309

Sequences

>g6662.t2 Gene=g6662 Length=2350
AATTGAAGTCGAAAAGCAGTATGGTGCATTTTATACAGGAGGTACTGTTCTTTGGACAAA
TGATGGCAATTTCTTTTTATGCCGTGATGAAGAAAAAATAAATATTATTTCAATTAAGTC
ATTAGAAGTGGAACGAATTATTGGCACTTCACAAGAAGGAAGCGAAGATGTTATTTATAC
TTTTGTTCTAACGATGGATGATGAATATTTAATATCTGCACATCGTAGTGGCTTACTAAA
ATTATGGGACTTTAATTCAGGTGAATTGAAGAAAATGTGGAAGAACCTTCATTCTGGTCC
AATTGCTTGTCTCCAATATTCCCAAGAACAACAGCTTGTGGCATCTGGTGGTGCTGATTC
TATGGTACGAATATGGGATTTTAAAAATCAATTATGCAAGGGAACACTTAAAGGACTTCA
GGGAGTTGTAAGCGTAATAATTTTTCATCCAATACAAAATTCTGTTCTTGCTGTTGCTGA
TGATTATAAAATATTAGCATGGTGTTTAGAGACACGTGAAATTTTGAAAAAATTCGTTGG
ACACATATCTCGTGTTACATCAATATCATTTTCTAAAGATACAAAGACTTTTATTTCATC
AGGCCGTGATAAAGTATTGATACTTTGGAATTATAATACAGAACAACAACTTAGAACAAT
TCCAGTTTATGAAGGTATTGAAAGTGCTTTGGTTTTGAATCACAACTTGATATTACCTAA
TGGTATTCGACTTGATGACGAAACAAAAGTTTACGTTGCATCGGCTGGTGAAGAAGGAAT
TGTTAAAATATGGCAAATGAATGATTCAAAAATATTGTACAAACAAGAGTCAAGCGTAAT
TTCAAGAGCAACAGAAGAAGGTGGTTTAGCAATTACTCAAATGCTTTTTAATCAAAAACT
TCAACAAATTGCACTTGTTAGTGTTGACCATAACATCATCATATATGATTTTCACAATTT
TTCATGCTCAAAGCAGCTTATAGGATTTACAGATGAAATTCTCGATTTGTGTCTCATGGG
TAAACGTGATCAATATCTAGCAATGGCAACAAACAGCAACGATATAAAAATTTATGATAC
CGTCACAATGAATTCAAAAATTTTAAAGGGTCACACTGATATTGTTCTTTCTTTATCAGC
GTATAAAAATTATTTGCTTTCTGGTAGTAAAGATAATACGGTTCGATTATGGATTGCTGA
TTTTGATAAATTTGAATTCGAATGCATTGGAATTGGTGCTAAACATACGAACACAGTCGG
AAGTGTCGATATTAGTAAAACACACGCTGATTTCTTTGTATCAGTCAGTCAAGATCAATG
TCTCAAATTATGGAAATTTCCCAAAGAATCATACAAAATAGATACCGATATGCTTTGTAT
AAACACTCAATTGGCTCACGAAAAAGATATTAATTGTGTAACAATTTCACCTAATGATAA
GTATATTGCAACTTCATCTCAGGACAAAACAGCAAAGTTATGGGATTCTAGTAATCTTAA
ACTTCTTGGTGTATTTAGAGGACATCGACGAGGAATTTGGACGGTTCGATTTTCACCAAT
TGATCAAGTTCTGCTTACTAGTGCAGCAGATTGTACAATGCGATTATGGAATTTAAGTGA
TATGACTTGTCTCAAAAGTCTTGAAGGACATGAAAGTTCTGTTTTAAGATGTGAATTTAT
TTCTAATGGTATGCAGATAATTTCATCTGGTGCTGATGGTCTTATTAAATTGTGGACTTT
AAAATCATCAGAATGTGTTCAAACACTTGAACAGCACGATAACAAAGTATGGGCTTTAGC
TTTAACTAATGATGGAAAAAAAATGTTCACTGGTGGTGCTGATTCTAAATTAATTCGTTG
GCGTGATGCAACAGAAGAGAAGAAACGTGAAGAATTAAGAATAAGGCAGGAAGAATGTCT
ACAAGAACAAGAGCTAAACAATTTATTGAGTCAAAAGAAATTACTTAAAGCATTAAAACT
TGCATTAAGACTCAATAAACCAAAACTTTCACTGAAAATTATCAATACAATAATCAGAAA
TAAAGATGAAGGACTTGAAGAGACTATTGAAGGCTTATCTGATTTTCATAAACAAGCACT
TCTTCAGCATGCGGTCAATTGGAATACAAACAGTAAAAATTGTAGACCGGCACAACTTGT
TTTCAATATCATGTTGAATGAAATTTTGAATGGTAAATACAGAGTTGAAGGACTTGGAAA
AATCATTGAGGACGCACTTCCGTATAGTGAACGACACTTTAAGCGAATGACTGAATATTT
AAAGGACCTCAAATTCTTAGAATACACAATGCGATGTATGAAGCCGTATGGTGATGTTAC
AATGAAGTAA

>g6662.t2 Gene=g6662 Length=718
MDDEYLISAHRSGLLKLWDFNSGELKKMWKNLHSGPIACLQYSQEQQLVASGGADSMVRI
WDFKNQLCKGTLKGLQGVVSVIIFHPIQNSVLAVADDYKILAWCLETREILKKFVGHISR
VTSISFSKDTKTFISSGRDKVLILWNYNTEQQLRTIPVYEGIESALVLNHNLILPNGIRL
DDETKVYVASAGEEGIVKIWQMNDSKILYKQESSVISRATEEGGLAITQMLFNQKLQQIA
LVSVDHNIIIYDFHNFSCSKQLIGFTDEILDLCLMGKRDQYLAMATNSNDIKIYDTVTMN
SKILKGHTDIVLSLSAYKNYLLSGSKDNTVRLWIADFDKFEFECIGIGAKHTNTVGSVDI
SKTHADFFVSVSQDQCLKLWKFPKESYKIDTDMLCINTQLAHEKDINCVTISPNDKYIAT
SSQDKTAKLWDSSNLKLLGVFRGHRRGIWTVRFSPIDQVLLTSAADCTMRLWNLSDMTCL
KSLEGHESSVLRCEFISNGMQIISSGADGLIKLWTLKSSECVQTLEQHDNKVWALALTND
GKKMFTGGADSKLIRWRDATEEKKREELRIRQEECLQEQELNNLLSQKKLLKALKLALRL
NKPKLSLKIINTIIRNKDEGLEETIEGLSDFHKQALLQHAVNWNTNSKNCRPAQLVFNIM
LNEILNGKYRVEGLGKIIEDALPYSERHFKRMTEYLKDLKFLEYTMRCMKPYGDVTMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g6662.t2 CDD cd00200 WD40 258 557 9.51902E-70
19 g6662.t2 Gene3D G3DSA:2.130.10.10 - 1 178 4.8E-35
18 g6662.t2 Gene3D G3DSA:2.130.10.10 - 179 275 1.4E-8
17 g6662.t2 Gene3D G3DSA:2.130.10.10 - 276 473 1.0E-45
16 g6662.t2 Gene3D G3DSA:2.130.10.10 - 474 649 2.2E-22
9 g6662.t2 PANTHER PTHR19854 TRANSDUCIN BETA-LIKE 3 3 710 4.7E-205
10 g6662.t2 PANTHER PTHR19854:SF15 TRANSDUCIN BETA-LIKE PROTEIN 3 3 710 4.7E-205
13 g6662.t2 PRINTS PR00320 G protein beta WD-40 repeat signature 321 335 3.1E-6
12 g6662.t2 PRINTS PR00320 G protein beta WD-40 repeat signature 418 432 3.1E-6
11 g6662.t2 PRINTS PR00320 G protein beta WD-40 repeat signature 502 516 3.1E-6
2 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 33 62 2.4E-4
6 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 109 146 3.0E-5
7 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 301 333 2.2E-5
4 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 400 431 1.9E-6
8 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 436 473 8.6E-5
3 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 478 514 3.1E-4
5 g6662.t2 Pfam PF00400 WD domain, G-beta repeat 520 554 0.12
1 g6662.t2 Pfam PF08625 Utp13 specific WD40 associated domain 578 709 2.2E-31
21 g6662.t2 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 49 63 -
22 g6662.t2 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 418 432 -
23 g6662.t2 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 460 474 -
36 g6662.t2 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 1 566 74.585
44 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 1 28 8.904
42 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 30 65 13.048
43 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 114 155 14.251
38 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 304 333 12.046
40 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 399 440 13.382
37 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 441 482 14.051
41 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 483 524 14.285
39 g6662.t2 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 525 566 9.94
28 g6662.t2 SMART SM00320 WD40_4 22 62 2.4E-6
30 g6662.t2 SMART SM00320 WD40_4 65 104 10.0
27 g6662.t2 SMART SM00320 WD40_4 107 146 7.8E-7
33 g6662.t2 SMART SM00320 WD40_4 161 201 260.0
34 g6662.t2 SMART SM00320 WD40_4 213 252 61.0
29 g6662.t2 SMART SM00320 WD40_4 255 295 0.67
35 g6662.t2 SMART SM00320 WD40_4 297 334 0.025
24 g6662.t2 SMART SM00320 WD40_4 341 381 0.0036
25 g6662.t2 SMART SM00320 WD40_4 392 431 4.0E-9
26 g6662.t2 SMART SM00320 WD40_4 434 473 1.6E-7
32 g6662.t2 SMART SM00320 WD40_4 476 515 3.7E-7
31 g6662.t2 SMART SM00320 WD40_4 518 557 1.3E-5
15 g6662.t2 SUPERFAMILY SSF50978 WD40 repeat-like 32 298 2.01E-45
14 g6662.t2 SUPERFAMILY SSF50978 WD40 repeat-like 226 560 8.55E-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

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