General information for g13728.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13728 is located on chr_1: 32092918..32095357 (+ 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 | g13728 | g13728.t2 | isoform | g13728.t2 | 32087842 | 32089303 |
| chr_1 | g13728 | g13728.t2 | exon | g13728.t2.exon1 | 32087842 | 32088540 |
| chr_1 | g13728 | g13728.t2 | cds | g13728.t2.CDS1 | 32088506 | 32088540 |
| chr_1 | g13728 | g13728.t2 | exon | g13728.t2.exon2 | 32088693 | 32088904 |
| chr_1 | g13728 | g13728.t2 | cds | g13728.t2.CDS2 | 32088693 | 32088904 |
| chr_1 | g13728 | g13728.t2 | exon | g13728.t2.exon3 | 32089020 | 32089303 |
| chr_1 | g13728 | g13728.t2 | cds | g13728.t2.CDS3 | 32089020 | 32089111 |
| chr_1 | g13728 | g13728.t2 | TSS | g13728.t2 | NA | NA |
| chr_1 | g13728 | g13728.t2 | TTS | g13728.t2 | NA | NA |
Sequences
>g13728.t2 Gene=g13728 Length=1195
AAAGCTAAAATTTTATTTTGGTGTTCATTTTGCAACTGTTTTTACTTTTTTGAAAATAGA
CTTCAGCACTTCAATCAGATGTAAGGAAAGTTTGCGAACTTCAAAAACTTATATTCACAC
CCTGTTTCTTTGTCTAATGCTCAGCATAATCTACTATTTTTATCAACTTTATGCTGAACT
ATAAGAAGTTTTTAGTGAAAAACATATCATTCAATTAGTACACGTGGTTAAAAATTATTA
TACACAGATTAAAAAATTATTTTAACATTACTCAACATCAACGATTAAATTATTGGTGTG
AATATCAAAATAAAAAAAGAAACAAAGAATTTTGAACTGCATATAAGAAAATAAAATTTT
ACAGTCTCTAGACTATTTAACTATTTATTTAATTCTATTTCTTATCAATAAGAGAGTTAA
AGTGAACCTACAACATTTAAAAACTAATCTGTGATGTTTTGATAAAAAGCAAAAGGCAAA
AAATCACTTTAAAAAACCCTATAGTGAGAGAAGAACGAAAGAAAGAAAAAAATAAAAAAT
TTACTTATCATCAAAATCGTCATTTCGTAAATTCTCTATTTGACTGATTTCCAATTCATT
GAAAGTGTTGTAATAAATAAAATAAATCAAAATGTTGTACATTTTTAATATGGACCAGGG
AAAAATGATAACGTTTGATGTTAGCTTAGCTCTAGATTCCGTTCAATCATTGAAACTGAC
AATTGAGAGACAACATGCGATTCCAGCTTGCAATCAAGTGTTATTAGTAAGTGGTGGAGA
AACTTTAGATGCGTCTAATCGAGTATGCAGCTATTCTGCGGGAACAGACACAAACCCTAT
TTTTATGTTTAGCAATAGTCTAGAACCTCGTAATCAACCTCAACCATGGCCGAGTATAGA
TGATAGTAATGAAAGAAGTCGATCAATGTTTAGAAGTTCCACAAAATCAACTTTCTGTAA
ATCTAGTAGCACGCCGTGTCCAGATAGCACAGCAAATTTATGAAGCATGCAAGGAAGAGT
TAAAAAATTGTGATAAACTTGTGCATGAACAGCACTTACAACATCAAGGATGGATGGCCG
TAATGGCGAATCTAGAGGATATAACAGATGCCTTTGAGGATCGTTGCAATGAATTTGACA
AAGTATTTAAAGAACACATTGAACGTCGAAAAGAATATAAAGACTATCTCGAAAG
>g13728.t2 Gene=g13728 Length=112
MITFDVSLALDSVQSLKLTIERQHAIPACNQVLLVSGGETLDASNRVCSYSAGTDTNPIF
MFSNSLEPRNQPQPWPSIDDSNERSRSMFRSSTKSTFCKSSSTPCPDSTANL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13728.t2 | CDD | cd17060 | Ubl_RB1CC1 | 1 | 63 | 4.45457E-33 |
| 4 | g13728.t2 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 71 | 4.7E-9 |
| 3 | g13728.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 65 | 112 | - |
| 1 | g13728.t2 | PANTHER | PTHR13222:SF1 | RB1-INDUCIBLE COILED-COIL PROTEIN 1 | 1 | 88 | 2.2E-18 |
| 2 | g13728.t2 | PANTHER | PTHR13222 | RB1-INDUCIBLE COILED-COIL | 1 | 88 | 2.2E-18 |
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:0000045 | autophagosome assembly | BP |
| GO:0000422 | autophagy of mitochondrion | BP |
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.
