General information for g11718.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Lamin-B receptor.
Parent gene
- The parent gene g11718 is located on chr_1: 18069343..18070673 (+ 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_1 | g11718 | g11718.t1 | isoform | g11718.t1 | 18067855 | 18069687 |
| chr_1 | g11718 | g11718.t1 | exon | g11718.t1.exon1 | 18067855 | 18069343 |
| chr_1 | g11718 | g11718.t1 | cds | g11718.t1.CDS1 | 18067855 | 18069343 |
| chr_1 | g11718 | g11718.t1 | exon | g11718.t1.exon2 | 18069401 | 18069687 |
| chr_1 | g11718 | g11718.t1 | cds | g11718.t1.CDS2 | 18069401 | 18069687 |
| chr_1 | g11718 | g11718.t1 | TSS | g11718.t1 | NA | NA |
| chr_1 | g11718 | g11718.t1 | TTS | g11718.t1 | NA | NA |
Sequences
>g11718.t1 Gene=g11718 Length=1776
ATGGAAAAGAAACGTGGTAGACCTCGAAATGTGAGGGAAGCTAGTCCACCACCATCAAGC
CGAACTCGTAGTAAATCGCCAGCACGAGTTGAGACATCGGGAAGAGATTCTGCACCAATT
ATTAAAAAGCGTGCAAGTCGTTCAAAGAAAAATGAGACACCTTCTGAAGAAATATCATCA
TCGAGTCAATCAAGTACACCGAAAAAGACGAAAGTAGTGAAAAATGAAAAGCAAGCAACT
ATTATTTTAGATGATTCCGGTGATAATGAAGAAGTAGCAAATATCAATTCGAGACTAGCA
ACACTCAGAAAACGGCTCACTCCAGCAAACTACAAAAATACTCCAACGCCAACAGAAGAT
AAGAATCGTTCAGTTAGTAGAACAGCAAGTTCACTAACCAAAGAAGACAGCGATGAAAAT
GACGATGATGAGGAAGTGAAAGTTGTACCTAAGGAACAAAAACATTTTCAAGATTTGGGA
ATTTTTTCAAAACCTATCATAAACTGTCTATTGTTGATTTTGCTATCTGTAACTCCTATT
ATCTTGTCGGTATGTTTTCAAACTAATTGGAAATGGTCAAAATTTCTCATCCATTTTAAA
CATGTAGAGAACTTTTTCAATGTGCAGGCAATTTCATTTATTCTCGCGATTCATAGCGGA
GTAGCATTACTCTCGTTATTGCCTGTTGGAAGATATATCAAACTTCCTGATTCAGAAACG
GAATTGAAATTTAACGGAATTTTAACAACTCTGATTATAATTGGATTTTTGTTTGCACTC
GAATTAAAAGGTCTGAATGCATTTATTGCAATTTATAATAATCTCGATCAATTGCTTTTC
TTAAGCATTCTCCGAAGTTTTCTAGGATCAATTGAAGTTTTTCTTTTGTCCAAATATAGA
CCCTCAAGTGAATCAAATGCATATGGAAGAAGCGGTAAATTCATTATTGATTTCACAGTG
GGCCGTGAACTAAACCCAAAACTTTTGAATTTTGACCTTAAACAAGTCCATTATAATGAA
TCAATTATCTATCTTCTCATCATAAATATTTCTTTACTCTTTAAAAATGTATCAATTCCA
ATTGTGGAAACTATTCCAAACGAAGGAAATTCAATTATTGAACTTTTAAAACAGACTTAT
AGCAACACGCTTTTCATCCTTAATAATTCTGAATACAATTCTGCAGCATTCATTATTTCA
AGTTTACTCATTCTCTATGCTCTTGATCTTTTGATTCATGAGCATCATCTTTCATCATCA
TTTCAATTAAATTATGAAGGTATGGGTGCTGAAATTTTATGTCGTTTCGCGTCATTCCCA
TTTTTAATTTCGTTGCTTCCGCGCTATCTATTTGTACAAAATATTACAGTAAACTTTTAT
CTACTTGCCATTATTGTAATATTATTTATAATTGGACTTTTAATTAAGCGATGCAGCAAT
TCTCTAAAATATGAATATAGAATTCATCCATCAGATCCTAAATTTAAAGAACTTTCAACA
ATACCGACTTTTCAGAATCGACGATTAATTATATCAAAATGGTTTAGAAAAATTCGTCAA
CCAAATCTTTTGGGTGAAATATTAATGCATCTGGCATTAGCTATTACACTTGTATCAAGT
TTTAATTTGGCTACATTCTTGGGAATTTTTATAATTATATTTTATCTCATCTATCGATCA
ATCAGCATTAATAGAAAAAATGCCATAAGGTATGAGTCGTCATGGCAACGATATATATCT
GCTGTACCCAATAATTTATTGCCAAGAGTCTACTAA
>g11718.t1 Gene=g11718 Length=591
MEKKRGRPRNVREASPPPSSRTRSKSPARVETSGRDSAPIIKKRASRSKKNETPSEEISS
SSQSSTPKKTKVVKNEKQATIILDDSGDNEEVANINSRLATLRKRLTPANYKNTPTPTED
KNRSVSRTASSLTKEDSDENDDDEEVKVVPKEQKHFQDLGIFSKPIINCLLLILLSVTPI
ILSVCFQTNWKWSKFLIHFKHVENFFNVQAISFILAIHSGVALLSLLPVGRYIKLPDSET
ELKFNGILTTLIIIGFLFALELKGLNAFIAIYNNLDQLLFLSILRSFLGSIEVFLLSKYR
PSSESNAYGRSGKFIIDFTVGRELNPKLLNFDLKQVHYNESIIYLLIINISLLFKNVSIP
IVETIPNEGNSIIELLKQTYSNTLFILNNSEYNSAAFIISSLLILYALDLLIHEHHLSSS
FQLNYEGMGAEILCRFASFPFLISLLPRYLFVQNITVNFYLLAIIVILFIIGLLIKRCSN
SLKYEYRIHPSDPKFKELSTIPTFQNRRLIISKWFRKIRQPNLLGEILMHLALAITLVSS
FNLATFLGIFIIIFYLIYRSISINRKNAIRYESSWQRYISAVPNNLLPRVY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g11718.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 74 | - |
| 13 | g11718.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 36 | 54 | - |
| 17 | g11718.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 55 | 69 | - |
| 14 | g11718.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 106 | 145 | - |
| 16 | g11718.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 106 | 131 | - |
| 3 | g11718.t1 | PANTHER | PTHR21257:SF37 | DELTA(14)-STEROL REDUCTASE | 165 | 591 | 2.1E-68 |
| 4 | g11718.t1 | PANTHER | PTHR21257 | DELTA(14)-STEROL REDUCTASE | 165 | 591 | 2.1E-68 |
| 2 | g11718.t1 | Pfam | PF01222 | Ergosterol biosynthesis ERG4/ERG24 family | 223 | 358 | 7.4E-12 |
| 1 | g11718.t1 | Pfam | PF01222 | Ergosterol biosynthesis ERG4/ERG24 family | 397 | 591 | 2.2E-23 |
| 20 | g11718.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 168 | - |
| 31 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 169 | 190 | - |
| 23 | g11718.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 191 | 209 | - |
| 30 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 233 | - |
| 18 | g11718.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 234 | 244 | - |
| 29 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 245 | 272 | - |
| 25 | g11718.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 273 | 277 | - |
| 35 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 278 | 296 | - |
| 19 | g11718.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 297 | 341 | - |
| 32 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 342 | 362 | - |
| 27 | g11718.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 363 | 391 | - |
| 34 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 392 | 412 | - |
| 22 | g11718.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 413 | 431 | - |
| 36 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 432 | 451 | - |
| 24 | g11718.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 452 | 456 | - |
| 28 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 457 | 475 | - |
| 21 | g11718.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 476 | 526 | - |
| 33 | g11718.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 527 | 558 | - |
| 26 | g11718.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 559 | 591 | - |
| 10 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 188 | - |
| 7 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 208 | 230 | - |
| 6 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 242 | 260 | - |
| 5 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 275 | 297 | - |
| 11 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 390 | 412 | - |
| 12 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 432 | 451 | - |
| 8 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 458 | 475 | - |
| 9 | g11718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 535 | 557 | - |
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:0016020 | membrane | CC |
| GO:0016126 | sterol biosynthetic process | BP |
| GO:0016628 | oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor | MF |
KEGG
Orthology
- This transcript has been annotated with K19532 (Delta14-sterol reductase (lamin-B receptor))
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.
