General information for g13455.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13455 is located on chr_1: 30233159..30233779 (- 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 | g13455 | g13455.t1 | TTS | g13455.t1 | 30232654 | 30232654 |
| chr_1 | g13455 | g13455.t1 | isoform | g13455.t1 | 30232752 | 30233779 |
| chr_1 | g13455 | g13455.t1 | exon | g13455.t1.exon1 | 30232752 | 30233099 |
| chr_1 | g13455 | g13455.t1 | cds | g13455.t1.CDS1 | 30232752 | 30233099 |
| chr_1 | g13455 | g13455.t1 | exon | g13455.t1.exon2 | 30233157 | 30233523 |
| chr_1 | g13455 | g13455.t1 | cds | g13455.t1.CDS2 | 30233157 | 30233523 |
| chr_1 | g13455 | g13455.t1 | exon | g13455.t1.exon3 | 30233727 | 30233779 |
| chr_1 | g13455 | g13455.t1 | cds | g13455.t1.CDS3 | 30233727 | 30233779 |
| chr_1 | g13455 | g13455.t1 | TSS | g13455.t1 | 30233862 | 30233862 |
Sequences
>g13455.t1 Gene=g13455 Length=768
ATGTTATCAATCACAAAGATTTTTCAAGCGACAAGATCTATTATAAATCCAAGGATCGCT
TGTCAATTTCATTTCGCAAACACACAATCGGCATCACTGGAAGAAAAATTAGGGCTCCCA
CCGAGACCAAAAAGACCGCTTACCCCATTCTTTCGTTTTCTTGTAGATAATAGACCAAAA
ATTGCAAAAGAAAATCCCAATTTAAAGCCAGTGGATTTGATACAGTTGTGTGCAAAGAAA
TACGCTGACATTGACTCTGAAGTTAGAAACAAATACCATGAAGAATTTTTAAAAGAACAA
GAAGTTTATCTTAAGAAACGTTCTGCATATGAGAATAGTTTATCAGATGAACAAAAGTTT
GAAATCGCCAATGCCAAACAAGAGAAGCAAGACAAGAAATTGAAAAGTGAGCACAAAAAG
AAATTACGAGAAAATGGCAAACCTAAAAAGCCTGCTTCAGCATATTTGAGGTTTTTAAAC
GACACCTCAGCACATCATCGAGAACCAAATCAAAGTTACAGAGACTATATAATTTCTGTG
GCAGAAAAATGGAAAAATTTACCAGAAGATAAAAAGCAGGTCTATATAAAAGCATCTTTG
AAAGACCATGACGCCTATAAACAGGAAATTTCCAAGTGGGAATTAAAAATGATACGCTTA
GGTAACACCGATTTAGTTCGTGAAAAATCTGCGATTAAAGATGTTTCAAAACCAAGAGCT
CGTGGAAGCAAGTTTAAGTCTCGTTCAGTCTCATCTGACTCAGATTAA
>g13455.t1 Gene=g13455 Length=255
MLSITKIFQATRSIINPRIACQFHFANTQSASLEEKLGLPPRPKRPLTPFFRFLVDNRPK
IAKENPNLKPVDLIQLCAKKYADIDSEVRNKYHEEFLKEQEVYLKKRSAYENSLSDEQKF
EIANAKQEKQDKKLKSEHKKKLRENGKPKKPASAYLRFLNDTSAHHREPNQSYRDYIISV
AEKWKNLPEDKKQVYIKASLKDHDAYKQEISKWELKMIRLGNTDLVREKSAIKDVSKPRA
RGSKFKSRSVSSDSD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13455.t1 | CDD | cd01390 | HMGB-UBF_HMG-box | 43 | 108 | 1.3415E-12 |
| 11 | g13455.t1 | CDD | cd01390 | HMGB-UBF_HMG-box | 148 | 211 | 4.57812E-10 |
| 9 | g13455.t1 | Coils | Coil | Coil | 125 | 145 | - |
| 8 | g13455.t1 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 38 | 145 | 2.9E-22 |
| 7 | g13455.t1 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 146 | 228 | 2.0E-18 |
| 14 | g13455.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 122 | 138 | - |
| 16 | g13455.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 122 | 154 | - |
| 15 | g13455.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 233 | 255 | - |
| 3 | g13455.t1 | PANTHER | PTHR48112:SF1 | TRANSCRIPTION FACTOR A, MITOCHONDRIAL | 20 | 239 | 4.7E-37 |
| 4 | g13455.t1 | PANTHER | PTHR48112 | HIGH MOBILITY GROUP PROTEIN DSP1 | 20 | 239 | 4.7E-37 |
| 1 | g13455.t1 | Pfam | PF00505 | HMG (high mobility group) box | 43 | 111 | 7.8E-16 |
| 2 | g13455.t1 | Pfam | PF00505 | HMG (high mobility group) box | 148 | 213 | 1.2E-8 |
| 17 | g13455.t1 | ProSiteProfiles | PS50118 | HMG boxes A and B DNA-binding domains profile. | 43 | 111 | 13.171 |
| 18 | g13455.t1 | ProSiteProfiles | PS50118 | HMG boxes A and B DNA-binding domains profile. | 148 | 214 | 13.094 |
| 12 | g13455.t1 | SMART | SM00398 | hmgende2 | 42 | 112 | 9.3E-15 |
| 13 | g13455.t1 | SMART | SM00398 | hmgende2 | 147 | 215 | 4.0E-7 |
| 6 | g13455.t1 | SUPERFAMILY | SSF47095 | HMG-box | 37 | 118 | 7.33E-19 |
| 5 | g13455.t1 | SUPERFAMILY | SSF47095 | HMG-box | 142 | 229 | 1.57E-17 |
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 K11830 (transcription factor A, mitochondrial)
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.
