General information for g8634.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lamin Dm0.
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.t4 | TSS | g8634.t4 | 31947643 | 31947643 |
| chr_2 | g8634 | g8634.t4 | isoform | g8634.t4 | 31947794 | 31950926 |
| chr_2 | g8634 | g8634.t4 | exon | g8634.t4.exon1 | 31947794 | 31948158 |
| chr_2 | g8634 | g8634.t4 | cds | g8634.t4.CDS1 | 31947794 | 31948158 |
| chr_2 | g8634 | g8634.t4 | exon | g8634.t4.exon2 | 31949056 | 31950094 |
| chr_2 | g8634 | g8634.t4 | cds | g8634.t4.CDS2 | 31949056 | 31950094 |
| chr_2 | g8634 | g8634.t4 | exon | g8634.t4.exon3 | 31950153 | 31950374 |
| chr_2 | g8634 | g8634.t4 | cds | g8634.t4.CDS3 | 31950153 | 31950374 |
| chr_2 | g8634 | g8634.t4 | exon | g8634.t4.exon4 | 31950434 | 31950519 |
| chr_2 | g8634 | g8634.t4 | cds | g8634.t4.CDS4 | 31950434 | 31950519 |
| chr_2 | g8634 | g8634.t4 | exon | g8634.t4.exon5 | 31950578 | 31950926 |
| chr_2 | g8634 | g8634.t4 | cds | g8634.t4.CDS5 | 31950578 | 31950689 |
| chr_2 | g8634 | g8634.t4 | TTS | g8634.t4 | 31950921 | 31950921 |
Sequences
>g8634.t4 Gene=g8634 Length=2061
ATGGCGAGCAGAAACGTAAGAAAAACTACACCCATTTCAACAACTTCGAGTGCAAGACCA
AGTTCACCACTATCACCGATCAGACACTCAAGATTACATGAAAAGAATGAATTACAAAAC
CTTAATGATCGTCTTGCTGCCTATATTGATCGAGTAAGGAATCTTGAGAATGAAAATCAA
AGATTAACAACAGAAATCACTTGCTATCGTGATACTACAACGCGGGAGGTATCAAACATT
AAATCTATGTATGAACATGAGCTGGCAGATGCTCGAAAATTACTCGATGAGACCTCTAAA
GAAAAGGCAAAGCTCGAAATTGACATTAAACGATTCTTTGAAGAGAATGATGATCTAAAG
AAGCGATTGGATAAAAAAACGAAAGAATGTAGTGCTGCTGAGAACAATTATCGACTTTAT
GAACAAAAGTTCCACGATTTAAGTGCAAAATACAATGCTGCATTATCTGATCGTAAAAAA
GCTCAGGATGATCTTAAAGAATTGGAGAAAGAAAACGATAAGTTGAAGAAAATGCTTGAA
GCACTTCGCAAAAATCTTGAAGAAGAAACTTTGGCTCGAGTTGATCTTGAAAATAATATT
CAAAGTCTTAAAGAGGAATTGACTTTCAAAGATCAAGTCTTTCAACAAGAACTTTCCGAA
TCGAGAACACGTCGTCAGGTCGAAATCAGTGAGATCGACGGGCGCTTGAATGAACAATAT
GAAGCAAAATTACAACAAACGCTTCAAGAATTGCGCGATCAATATGAGAGTCAAATGCGC
GCAAATCGCGAAGAAATCGAAGGATTGTATGAGAACAAAATCAAGAGTCTTCAAGCACAA
ATTTCTCGTAGCAATAATGCTTCTACTGCTATTCATGATGAACTTCTTCAAGTTCGTTCA
CGCGCTGATACGCTTAACAGCAAGATTGCCGATTTGGAGGCCATTAATGCAGGTTTATCT
GCTCGTATTCGCGATTTAGAAAGCATTCTCGATGGAGAGCGTGCAAAATCGCAACGAGAA
TTAAAACTCGTAGAAGCAGAATTGGAACGTCTTCGTGAAGAAATGCGTCAACAATTACTT
GAATATCAGGATCTTATGGATATCAAAGTTTCGCTCGATTTGGAACTTGCTGCTTATCGC
AAGCTTTTAGAGTCGGAAGAGACTCGTTTGAACATCACACCCACTCAATCACAAACGTCG
TCTTTTTCTCAATCACTAAGAGCTGGTAGATCAACTCCAGTTCAGTTTCGTACGCCCTCG
AGAGCAGGGAAGCGCAAACGTGCAGTCTTTGAAGACGAAGATCAAACAAACTTCAGTGTA
ACTTCATCAGCAAAGGGTGAAATTGAAATTACAGAAGTCGATCCAGAAGGAAAATTTGTT
AAACTGCTAAATCGTGGAGCTAAAGAGGTACAAATTGGTGGGTGGCAGTTAGTTCGTAAA
AGTGGTGACAACGAAACTTTGTTCAAATTCCATCGAACAGTCAAAGTCGATGCTGGACAA
ATCATAACAATCTGGTCTTCTGATAGCGGTGTCACGCATGAACCGCCAACAAATATTGTC
ATGAAAGGGCAAAGATTCTTTGTTAGTGACAATATGTCAACAAGCTTGCTTAATGGAGAA
GGAGAGTGGCAACTCATGAAAGAAAACTCGTCCAACGTTCAATTCATCGTGAATTCGGTT
ATCGAGGAATCGAAGATTTTCATCATCAACAAGGAGACCCAGCATCAGGAGAAGAAAAAT
GCCGTATTATGTAAATCAGTTTTCCTTTATTTCACTGCCTTATCAAAATTAAGAAATGGA
AGAAGAATCTTCAGTGTCATTTAAAATTTATTCTTATAATCACCCAACTAACAATTCTAT
TTCTTTTTTCGCGAATATGCATTTTCAAAATTTAATACTTTATAAATAGAAATGTCACTT
TATGAAGAGAAATTATAAGAAAGAAAAATCCTAACTTTGTTTACAAGAAAGAAAATTTTT
TGTTACTAAACAATAAATTTAATAAATTAAGTTTAAGACGATTAAAAAATTAATGTCTTT
GAGGTAGTAGCCAATAAATAA
>g8634.t4 Gene=g8634 Length=607
MASRNVRKTTPISTTSSARPSSPLSPIRHSRLHEKNELQNLNDRLAAYIDRVRNLENENQ
RLTTEITCYRDTTTREVSNIKSMYEHELADARKLLDETSKEKAKLEIDIKRFFEENDDLK
KRLDKKTKECSAAENNYRLYEQKFHDLSAKYNAALSDRKKAQDDLKELEKENDKLKKMLE
ALRKNLEEETLARVDLENNIQSLKEELTFKDQVFQQELSESRTRRQVEISEIDGRLNEQY
EAKLQQTLQELRDQYESQMRANREEIEGLYENKIKSLQAQISRSNNASTAIHDELLQVRS
RADTLNSKIADLEAINAGLSARIRDLESILDGERAKSQRELKLVEAELERLREEMRQQLL
EYQDLMDIKVSLDLELAAYRKLLESEETRLNITPTQSQTSSFSQSLRAGRSTPVQFRTPS
RAGKRKRAVFEDEDQTNFSVTSSAKGEIEITEVDPEGKFVKLLNRGAKEVQIGGWQLVRK
SGDNETLFKFHRTVKVDAGQIITIWSSDSGVTHEPPTNIVMKGQRFFVSDNMSTSLLNGE
GEWQLMKENSSNVQFIVNSVIEESKIFIINKETQHQEKKNAVLCKSVFLYFTALSKLRNG
RRIFSVI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g8634.t4 | Coils | Coil | Coil | 31 | 72 | - |
| 14 | g8634.t4 | Coils | Coil | Coil | 81 | 213 | - |
| 13 | g8634.t4 | Coils | Coil | Coil | 237 | 272 | - |
| 17 | g8634.t4 | Coils | Coil | Coil | 302 | 329 | - |
| 16 | g8634.t4 | Coils | Coil | Coil | 334 | 368 | - |
| 9 | g8634.t4 | Gene3D | G3DSA:1.20.5.1160 | - | 29 | 123 | 2.0E-23 |
| 8 | g8634.t4 | Gene3D | G3DSA:1.20.5.1160 | - | 138 | 219 | 2.6E-6 |
| 10 | g8634.t4 | Gene3D | G3DSA:1.20.5.500 | Single helix bin | 243 | 310 | 4.7E-8 |
| 11 | g8634.t4 | Gene3D | G3DSA:1.20.5.170 | - | 311 | 390 | 1.1E-20 |
| 12 | g8634.t4 | Gene3D | G3DSA:2.60.40.1260 | Lamin A/C globular tail domain | 411 | 553 | 1.3E-43 |
| 21 | g8634.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 22 | g8634.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 19 | g8634.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 393 | 418 | - |
| 20 | g8634.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 393 | 429 | - |
| 3 | g8634.t4 | PANTHER | PTHR45721:SF11 | LAMIN DM0-RELATED | 9 | 543 | 1.9E-188 |
| 4 | g8634.t4 | PANTHER | PTHR45721 | LAMIN DM0-RELATED | 9 | 543 | 1.9E-188 |
| 2 | g8634.t4 | Pfam | PF00038 | Intermediate filament protein | 34 | 389 | 3.1E-72 |
| 1 | g8634.t4 | Pfam | PF00932 | Lamin Tail Domain | 442 | 541 | 7.7E-15 |
| 23 | g8634.t4 | ProSiteProfiles | PS51842 | Intermediate filament (IF) rod domain profile. | 34 | 390 | 51.856 |
| 24 | g8634.t4 | ProSiteProfiles | PS51841 | Lamin-tail (LTD) domain profile. | 436 | 559 | 20.554 |
| 18 | g8634.t4 | SMART | SM01391 | Filament_2 | 33 | 389 | 2.6E-54 |
| 6 | g8634.t4 | SUPERFAMILY | SSF64593 | Intermediate filament protein, coiled coil region | 33 | 66 | 2.14E-9 |
| 7 | g8634.t4 | SUPERFAMILY | SSF64593 | Intermediate filament protein, coiled coil region | 318 | 389 | 1.74E-17 |
| 5 | g8634.t4 | SUPERFAMILY | SSF74853 | Lamin A/C globular tail domain | 422 | 542 | 9.94E-36 |
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 transcript has been annotated with K07611 (lamin B)
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. There were no conditions that were differentially expressed