General information for g614.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable U2 small nuclear ribonucleoprotein A’.
Parent gene
- The parent gene g614 is located on chr_3: 4511155..4512076 (+ 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_3 | g614 | g614.t1 | TSS | g614.t1 | 4511086 | 4511086 |
| chr_3 | g614 | g614.t1 | isoform | g614.t1 | 4511155 | 4512076 |
| chr_3 | g614 | g614.t1 | exon | g614.t1.exon1 | 4511155 | 4511236 |
| chr_3 | g614 | g614.t1 | cds | g614.t1.CDS1 | 4511155 | 4511236 |
| chr_3 | g614 | g614.t1 | exon | g614.t1.exon2 | 4511315 | 4511462 |
| chr_3 | g614 | g614.t1 | cds | g614.t1.CDS2 | 4511315 | 4511462 |
| chr_3 | g614 | g614.t1 | exon | g614.t1.exon3 | 4511518 | 4511700 |
| chr_3 | g614 | g614.t1 | cds | g614.t1.CDS3 | 4511518 | 4511700 |
| chr_3 | g614 | g614.t1 | exon | g614.t1.exon4 | 4511761 | 4512076 |
| chr_3 | g614 | g614.t1 | cds | g614.t1.CDS4 | 4511761 | 4512076 |
| chr_3 | g614 | g614.t1 | TTS | g614.t1 | 4513023 | 4513023 |
Sequences
>g614.t1 Gene=g614 Length=729
ATGGTCAAATTAACTCCAGAGCTTATAAATTCATGTATGCAGTTTATCAATCCATGTCGT
GATCGTGAATTGGATCTGAGAGGATACAAAATTCCAGAAATACAAAACACTGGAGCAACA
TTAGATCAATTTGATACAATCGACTTTTCAGATAATGATTTGAGAAAGCTTGGTGGATTC
GCTTATCTGCCCAGATTAAAACAACTTCTTTTGAATAACAATCGCATCACTCGTATCGCT
GATGATTTGCATGAAACTATTCCAAATTTGGAGAGCATAATACTTACAGGAAATAATCTG
CAAGAACTTGGTGATATTGATCCTCTCTCAAAACTTCAAAAACTCACAGTTCTATCGCTT
CTTACAAATCCAATTGCTAGTAAAAAGTTTTATCGTGAATATGTAATCTACAAATTGCCG
CATCTTCGATTGCTGGATTTCAAGAAGATAAAGGACAAAGAACGTCAAGAAAGTGTTACA
TTCTTTAAAAGCAAGAAAGGAAAAGAAGTCCAGAGAGAGATTCAAAAGAAAGCCCGTTTG
AGCTTAGCTAATGATAACACTAATGCATCAAAACCTAAAATTCAAGCATCATCTGCTGAA
ATTCAAAAGATTCGTGACATGATAACAAATGCTACATCATTACATGAAGTCGAAAGATTG
ACAAAAATGTTGCAGAGTGGTAACATAAGTGAAGTTTTAATACAAGATGAGGATGAACCA
ATGAATTGA
>g614.t1 Gene=g614 Length=242
MVKLTPELINSCMQFINPCRDRELDLRGYKIPEIQNTGATLDQFDTIDFSDNDLRKLGGF
AYLPRLKQLLLNNNRITRIADDLHETIPNLESIILTGNNLQELGDIDPLSKLQKLTVLSL
LTNPIASKKFYREYVIYKLPHLRLLDFKKIKDKERQESVTFFKSKKGKEVQREIQKKARL
SLANDNTNASKPKIQASSAEIQKIRDMITNATSLHEVERLTKMLQSGNISEVLIQDEDEP
MN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g614.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 1 | 176 | 0.000 |
| 2 | g614.t1 | PANTHER | PTHR10552 | U2 SMALL NUCLEAR RIBONUCLEOPROTEIN A | 1 | 235 | 0.000 |
| 3 | g614.t1 | PANTHER | PTHR10552:SF6 | U2 SMALL NUCLEAR RIBONUCLEOPROTEIN A’ | 1 | 235 | 0.000 |
| 1 | g614.t1 | Pfam | PF14580 | Leucine-rich repeat | 1 | 174 | 0.000 |
| 6 | g614.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 43 | 64 | 5.756 |
| 9 | g614.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 65 | 86 | 7.450 |
| 8 | g614.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 89 | 110 | 7.365 |
| 7 | g614.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 114 | 135 | 4.516 |
| 4 | g614.t1 | SUPERFAMILY | SSF52058 | L domain-like | 14 | 153 | 0.000 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K11092 (U2 small nuclear ribonucleoprotein A’)
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.
