General information for g8634.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lamin-C.
Parent gene
- The parent gene g8634 is located on chr_2: 31950619..31951572 (+ 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 | g8634 | g8634.t2 | TSS | g8634.t2 | 31947643 | 31947643 |
| chr_2 | g8634 | g8634.t2 | isoform | g8634.t2 | 31947794 | 31949418 |
| chr_2 | g8634 | g8634.t2 | exon | g8634.t2.exon1 | 31947794 | 31948158 |
| chr_2 | g8634 | g8634.t2 | cds | g8634.t2.CDS1 | 31947794 | 31948158 |
| chr_2 | g8634 | g8634.t2 | exon | g8634.t2.exon2 | 31949056 | 31949418 |
| chr_2 | g8634 | g8634.t2 | cds | g8634.t2.CDS2 | 31949056 | 31949416 |
| chr_2 | g8634 | g8634.t2 | TTS | g8634.t2 | NA | NA |
Sequences
>g8634.t2 Gene=g8634 Length=728
ATGGCGAGCAGAAACGTAAGAAAAACTACACCCATTTCAACAACTTCGAGTGCAAGACCA
AGTTCACCACTATCACCGATCAGACACTCAAGATTACATGAAAAGAATGAATTACAAAAC
CTTAATGATCGTCTTGCTGCCTATATTGATCGAGTAAGGAATCTTGAGAATGAAAATCAA
AGATTAACAACAGAAATCACTTGCTATCGTGATACTACAACGCGGGAGGTATCAAACATT
AAATCTATGTATGAACATGAGCTGGCAGATGCTCGAAAATTACTCGATGAGACCTCTAAA
GAAAAGGCAAAGCTCGAAATTGACATTAAACGATTCTTTGAAGAGAATGATGATCTAAAG
AAGCGATTGGATAAAAAAACGAAAGAATGTAGTGCTGCTGAGAACAATTATCGACTTTAT
GAACAAAAGTTCCACGATTTAAGTGCAAAATACAATGCTGCATTATCTGATCGTAAAAAA
GCTCAGGATGATCTTAAAGAATTGGAGAAAGAAAACGATAAGTTGAAGAAAATGCTTGAA
GCACTTCGCAAAAATCTTGAAGAAGAAACTTTGGCTCGAGTTGATCTTGAAAATAATATT
CAAAGTCTTAAAGAGGAATTGACTTTCAAAGATCAAGTCTTTCAACAAGAACTTTCCGAA
TCGAGAACACGTCGTCAGGTCGAAATCAGTGAGATCGACGGGCGCTTGAATGAACAATAT
GAAGCAAA
>g8634.t2 Gene=g8634 Length=242
MASRNVRKTTPISTTSSARPSSPLSPIRHSRLHEKNELQNLNDRLAAYIDRVRNLENENQ
RLTTEITCYRDTTTREVSNIKSMYEHELADARKLLDETSKEKAKLEIDIKRFFEENDDLK
KRLDKKTKECSAAENNYRLYEQKFHDLSAKYNAALSDRKKAQDDLKELEKENDKLKKMLE
ALRKNLEEETLARVDLENNIQSLKEELTFKDQVFQQELSESRTRRQVEISEIDGRLNEQY
EA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g8634.t2 | Coils | Coil | Coil | 31 | 72 | - |
| 10 | g8634.t2 | Coils | Coil | Coil | 81 | 213 | - |
| 8 | g8634.t2 | Gene3D | G3DSA:1.20.5.1160 | - | 29 | 123 | 3.8E-24 |
| 9 | g8634.t2 | Gene3D | G3DSA:1.20.5.1160 | - | 138 | 226 | 3.3E-7 |
| 6 | g8634.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 7 | g8634.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 2 | g8634.t2 | PANTHER | PTHR45721:SF11 | LAMIN DM0-RELATED | 9 | 241 | 1.0E-81 |
| 3 | g8634.t2 | PANTHER | PTHR45721 | LAMIN DM0-RELATED | 9 | 241 | 1.0E-81 |
| 1 | g8634.t2 | Pfam | PF00038 | Intermediate filament protein | 34 | 228 | 3.0E-35 |
| 12 | g8634.t2 | ProSiteProfiles | PS51842 | Intermediate filament (IF) rod domain profile. | 34 | 242 | 29.879 |
| 5 | g8634.t2 | SUPERFAMILY | SSF64593 | Intermediate filament protein, coiled coil region | 33 | 66 | 5.75E-10 |
| 4 | g8634.t2 | SUPERFAMILY | SSF90257 | Myosin rod fragments | 109 | 208 | 8.63E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
