Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin-60S ribosomal protein L40.

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_1 g11385 g11385.t3 TTS g11385.t3 15890382 15890382
chr_1 g11385 g11385.t3 isoform g11385.t3 15890503 15891269
chr_1 g11385 g11385.t3 exon g11385.t3.exon1 15890503 15890898
chr_1 g11385 g11385.t3 cds g11385.t3.CDS1 15890503 15890889
chr_1 g11385 g11385.t3 exon g11385.t3.exon2 15891106 15891269
chr_1 g11385 g11385.t3 TSS g11385.t3 NA NA

Sequences

>g11385.t3 Gene=g11385 Length=560
TTTTCACTAATTTTTATTAAAATATAATTCTTTAGGTGATGTATTTTTTTTCCGAAAAAG
TCGTATTCTTGTCAATAACGTATAAACTTTTTCACGAAGTTTTCGTTAAAATTTTTAGAC
GAGTTTTCTATCTTTTCTCTTGCACACTTATTCGAGTAAAATTTGAATAAAATATGCAGA
TCTTCGTCAAAACACTAACAGGCAAGACCATTACACTTGAGGTCGAGCCATCTGATACAA
TTGAAAATGTTAAGGCAAAGATTCAAGATAAAGAGGGAATTCCTCCAGATCAACAGCGTT
TAATTTTTGCTGGTAAGCAATTGGAAGATGGACGAACATTGAGCGATTACAACATTCAAA
AGGAATCAACATTGCACTTGGTCCTTCGTCTTCGTGGTGGTATCATTGAACCATCATTGC
GTATTTTGGCTCAAAAATACAATTGCGATAAAATGATTTGCCGTAAGTGCTATGCTCGCT
TACATCCTCGTGCAACTAATTGTCGTAAAACAAAGTGCGGACACACAAATAATTTGCGTC
CAAAGAAGAAGCTGAAGTAA

>g11385.t3 Gene=g11385 Length=128
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGIIEPSLRILAQKYNCDKMICRKCYARLHPRATNCRKTKCGHTNN
LRPKKKLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11385.t3 CDD cd01803 Ubl_ubiquitin 1 76 2.1613E-56
9 g11385.t3 Gene3D G3DSA:3.10.20.90 - 1 77 5.6E-45
10 g11385.t3 Gene3D G3DSA:2.20.28.70 - 78 128 3.6E-33
3 g11385.t3 PANTHER PTHR10666 UBIQUITIN 1 125 1.3E-73
4 g11385.t3 PANTHER PTHR10666:SF368 UBIQUITIN-60S RIBOSOMAL PROTEIN L40 1 125 1.3E-73
7 g11385.t3 PRINTS PR00348 Ubiquitin signature 11 31 4.1E-39
6 g11385.t3 PRINTS PR00348 Ubiquitin signature 32 52 4.1E-39
5 g11385.t3 PRINTS PR00348 Ubiquitin signature 53 74 4.1E-39
1 g11385.t3 Pfam PF00240 Ubiquitin family 3 74 1.5E-34
2 g11385.t3 Pfam PF01020 Ribosomal L40e family 78 127 1.0E-31
12 g11385.t3 ProSitePatterns PS00299 Ubiquitin domain signature. 27 52 -
15 g11385.t3 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 76 31.018
14 g11385.t3 SMART SM00213 ubq_7 1 72 2.9E-36
13 g11385.t3 SMART SM01377 Ribosomal_L40e_3 77 128 1.3E-32
8 g11385.t3 SUPERFAMILY SSF54236 Ubiquitin-like 1 96 1.66E-35

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:0005840 ribosome CC
GO:0005515 protein binding MF
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF

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