General information for g17448.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Huntingtin.
Parent gene
- The parent gene g17448 is located on chr_4: 13557767..13566979 (+ 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_4 | g17448 | g17448.t3 | TSS | g17448.t3 | 13557257 | 13557257 |
| chr_4 | g17448 | g17448.t3 | isoform | g17448.t3 | 13557321 | 13559187 |
| chr_4 | g17448 | g17448.t3 | exon | g17448.t3.exon1 | 13557321 | 13557376 |
| chr_4 | g17448 | g17448.t3 | cds | g17448.t3.CDS1 | 13557321 | 13557376 |
| chr_4 | g17448 | g17448.t3 | exon | g17448.t3.exon2 | 13557436 | 13557690 |
| chr_4 | g17448 | g17448.t3 | cds | g17448.t3.CDS2 | 13557436 | 13557690 |
| chr_4 | g17448 | g17448.t3 | exon | g17448.t3.exon3 | 13557762 | 13559187 |
| chr_4 | g17448 | g17448.t3 | cds | g17448.t3.CDS3 | 13557762 | 13559187 |
| chr_4 | g17448 | g17448.t3 | TTS | g17448.t3 | 13559182 | 13559182 |
Sequences
>g17448.t3 Gene=g17448 Length=1737
ATGGATAAATTAGCATTTCAAAAAGCAATTGATACTCTTAAGAGTACAGATTGCAACTCA
AAAGAAAAAATACAAAAATTTGATCAAATTTATTCAACTCTTTCATTGCTGACTAATCAC
AGCAATTATAAAAATTATCTTCAAAAAGCTGTGCAAATTTTGATATTATTTTGTGAAGAT
AACGACTCGAATGTTCGAATTAGTGCAGAAGAAAATTTAAATCGAATAATAAGAAATTGT
GAGCGGCAGCATCAATTGATTTTGATACAAATTGAGCTTTACCATGAAATTAAGAAAAAT
GGAAATGAAAGATCACTTCGAATTTGCCTCAATCTTTTTTCGCATTACTGTCACTTGATA
AAACATCGAAGAAAGAAAATTTATGCACAAAACCTAATTCCATGTCTTTTATCAATTGCA
AAGCGTAGAGAGCCACTTGTGATTGAAACATTTGCAGAATTTATGAAAACTTTCTCACGA
AATCTTCTGAACTGCTTAAATGACTATGAAGTAATGAAATTGATTGACCTTCTGATCGAT
AATTTATCACAAGAATGTGCAATAAAGAAAAGATGTTCAGCACAAATTATCATAACAATT
TTAGAACATTCAACAAGAAATAAATCTATAATGAGATCAATAATTGTGAGAATTCAAGAA
AATTTATCAAAAAGTCAAGAAGTGAACACAATTTTAGGAACACTTGGTCTGCTTCGATTG
ATAATTCCACATTTGATGATGTCACAAGAATTTCATCAAAAAATAATTGAAATGCTTGAA
AATTGTCTAAATTATCTTAAAAATGATTCACACAATCATACGATAATTAATGCAAATTTA
GAATTTATCAATTCATTGCTAAATGCAAGTAATGAAAACCATAAAATGTCAAAACTAATC
TGCGATAATGAAGCACATAAAGAAATACTTCTATCACGACATTCAGCATTATTGAATAAT
TCAAGAAAGTCCAGCATTGAAACAATAAAAAATCAAGATTTATTGCAAGTTCCAACATCA
AATAAATCATCAATTAGTCCTGGCAGTGGCGATTTTAGTGATGTTGAAGGTGATTCTTTC
AAATCAACAGATTTTTCATCATCATCACCTGGTGCTTTAAAAAATGTTATTGGTGCAGCT
GAAACAATGTCAATAAAATCAACAGATTCAATAAATTCGTTTTTTACATCAATTCTTGGC
AATTCGAGTACTGACAGTGTTACAAAATTCTTTAGAAAATCATCAACTGATTCGCCAGCA
CATCAATCAAAATTAAGTGAATCAGCAGATGAAAAATCAATTGATCTTTCCTTAGGTCAT
TTAAAAGATGAAAATGTTGAATATCGTGATTCACAAATGTTGCCTGAAACTGCAGAAATG
GCTTTAGATGATAATTTAGAAATGGATGAAACTCTTGAGATTGTTGAGGCATCAAATAAT
GAACAAAAAATTTATATTGGTTCAATTTATGATCAAAGTATTGTCGAATATATTGTACGA
CTTGTGTCATCAAAATTTCTACTTGATGGAAAACCAAAAATTCTCATTAATGATCAAATT
GTAAGAGTTTCAATTAAAAATTTGGCATTATTGACAATTGCAGCTTGTGTTGAGCTAAAA
AGTGAAATTTTATTGCTTAAACTTTCAAAAGATTACACGGATGAATCAATGATGGTTGAA
AGTCTTTTAAGTTATTTAGTTGATGAAGATATTCGACTTGAAGAAGAAGAAGAAAAA
>g17448.t3 Gene=g17448 Length=579
MDKLAFQKAIDTLKSTDCNSKEKIQKFDQIYSTLSLLTNHSNYKNYLQKAVQILILFCED
NDSNVRISAEENLNRIIRNCERQHQLILIQIELYHEIKKNGNERSLRICLNLFSHYCHLI
KHRRKKIYAQNLIPCLLSIAKRREPLVIETFAEFMKTFSRNLLNCLNDYEVMKLIDLLID
NLSQECAIKKRCSAQIIITILEHSTRNKSIMRSIIVRIQENLSKSQEVNTILGTLGLLRL
IIPHLMMSQEFHQKIIEMLENCLNYLKNDSHNHTIINANLEFINSLLNASNENHKMSKLI
CDNEAHKEILLSRHSALLNNSRKSSIETIKNQDLLQVPTSNKSSISPGSGDFSDVEGDSF
KSTDFSSSSPGALKNVIGAAETMSIKSTDSINSFFTSILGNSSTDSVTKFFRKSSTDSPA
HQSKLSESADEKSIDLSLGHLKDENVEYRDSQMLPETAEMALDDNLEMDETLEIVEASNN
EQKIYIGSIYDQSIVEYIVRLVSSKFLLDGKPKILINDQIVRVSIKNLALLTIAACVELK
SEILLLKLSKDYTDESMMVESLLSYLVDEDIRLEEEEEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g17448.t3 | Coils | Coil | Coil | 573 | 579 | - |
| 3 | g17448.t3 | Gene3D | G3DSA:1.25.10.10 | - | 21 | 301 | 1.3E-6 |
| 1 | g17448.t3 | PANTHER | PTHR10170 | HUNTINGTON DISEASE PROTEIN | 3 | 570 | 9.6E-95 |
| 2 | g17448.t3 | SUPERFAMILY | SSF48371 | ARM repeat | 33 | 293 | 4.11E-16 |
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 K04533 (huntingtin)
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