General information for g14504.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription factor SPT20-like protein.
Parent gene
- The parent gene g14504 is located on chr_4: 897496..898510 (+ 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 | g14504 | g14504.t2 | TSS | g14504.t2 | 893117 | 893117 |
| chr_4 | g14504 | g14504.t2 | isoform | g14504.t2 | 893692 | 897119 |
| chr_4 | g14504 | g14504.t2 | exon | g14504.t2.exon1 | 893692 | 894255 |
| chr_4 | g14504 | g14504.t2 | cds | g14504.t2.CDS1 | 893692 | 894255 |
| chr_4 | g14504 | g14504.t2 | exon | g14504.t2.exon2 | 895835 | 897119 |
| chr_4 | g14504 | g14504.t2 | cds | g14504.t2.CDS2 | 895835 | 897118 |
| chr_4 | g14504 | g14504.t2 | TTS | g14504.t2 | NA | NA |
Sequences
>g14504.t2 Gene=g14504 Length=1849
ATGAGCAAGCATCACCATTATCATCACTCCCAAGCGGGGAGTTTTCATCATCCAAGCAAA
ACACAGACGACTACGGCTTTCGACATCAGCGAGATGATGGTGCAACAACAGCAGCAACCG
TCAAACGGTCTAATGCGAGTTAATGGTCAAATCAATGGTGACATTGATTCAAATGACACC
AATAATAATTATAATAAACACAATCATCACAATCATCATCATAGTCATGGACATCACAAG
CGTAGTGCGTCGTCATGTGGCGAACCAAGTAGTTCCAAAAGAACGAAACTAAACAGTGGT
GGAAGTAGTAGTAGTAGTAGCCAAAGTGTGCCAAATTATCATGCAAAATATGGAAATTCG
TCAATCAACAGTCATGGCTCACATCTCGATCATTCATCACTGTCAACTACGACAAATAAT
GGCAGCGGTGGAAGCAATAATCATAGTTATGTTAGTAATAGTAATACAATTGGTGGTGCT
GGGTTACAAAATGGTCATTATAATATCATGGAGAAGCTAAAGGAATTGTACAGGGAGTTG
AAAGGAGACAAATCGCTTAAAAATCCTTATCTTTCATCATCATCATTTCTACTTGATAAA
CTCGTCACTCGAGAACGTCTAAATACGCTAATTGTAAATCTCTATCCAGGCAATAAGGGT
TATTCATTAGCCTTTCGTTCACCTAATTCACAAACATCTGCAACTATTACAAAACAATCG
GCACAAAGTCATCAACCAGCAAGTAATCAAACTGATCGAGAAATTATTCATGAGACACCA
ACATGGCTTTATGATAATGCACATCTATTAGATGCTCTCGATGCTGAAGAGTTGCCACCA
TTATTAATTGACTTTTGCAATAAACACTGCCCGCATCTCTATTATAATGGCACAGTCATT
GCTCAAGTACGCGATTACCGACAGAGTTATCCTCTTTTGGACATCTGTGATATTCACTAT
GTGTTATTAAAACCCACTTCGGTGGCATTATGGGATGAAGTAAGTGCAGCTGCCAGTGAT
GCTAGTTGGAGTATGAAAGAGCGTATACTGCTCGAATCACAACTGGTACTTGCTACTGCA
CCACCAATATGCCTCGATCCTTCGCCTGCTATTGGTATTGCAGCTATCAATGCCACGACT
GAGCGATCACCAATTGCATCTGGCGATGGAGTCCTAAAAGCGGCCAAAAAGTTCCTGCAA
GTCACAAAAAATCGCAACAATAAACTCGAAAAGAAAACACATCATCCGCAATTATCATTA
GCAAATCATGTCGCAAATGAAAGACGACAGCGGCGTGATGCGAATGGAATGAGAAGCGCA
AATGCACCAAAGAAACTATCAATGGTCAGTAGCGATGAAGTAAATGCCGTGAGTCTCCAT
AAAGCACTGCCAAATGTGCCACCATCACAACGATATGATTGGCAGGCGCGCAATACAGAA
CGACTGACATTCGAGACAGATAGAGATAATTGTCAATATCGTGTTCGAGTGGAGCTTTTT
GAAAGAGCAACAACATGTGAAGTTAGTGGGCAGCTGACATTAGAAAGACAAAAAGGTGGA
AATAGCAATAAAATTAATGGCAGAACATGTCCATTTAAACTTGCATCACCGCTCGCTGCA
AGACGATATGTTAAGGAATTTATGGGAATTTTTACGGAAGAAGGAAGAAAATTTGTAAAA
ATTACACATGAAAGGGAAACGAGAGCGGGACGTGAAATTATGGAAATGCAAACGGGAGAA
AAATTACAACAGCCAAGTGCCACCAAAGTAGTGCAGACAATTCCAGTCATAACACAACAA
ACTCAGCCTCAAAGTCTACCACATATACAGCAACAGCAGCAGCAGCAAT
>g14504.t2 Gene=g14504 Length=616
MSKHHHYHHSQAGSFHHPSKTQTTTAFDISEMMVQQQQQPSNGLMRVNGQINGDIDSNDT
NNNYNKHNHHNHHHSHGHHKRSASSCGEPSSSKRTKLNSGGSSSSSSQSVPNYHAKYGNS
SINSHGSHLDHSSLSTTTNNGSGGSNNHSYVSNSNTIGGAGLQNGHYNIMEKLKELYREL
KGDKSLKNPYLSSSSFLLDKLVTRERLNTLIVNLYPGNKGYSLAFRSPNSQTSATITKQS
AQSHQPASNQTDREIIHETPTWLYDNAHLLDALDAEELPPLLIDFCNKHCPHLYYNGTVI
AQVRDYRQSYPLLDICDIHYVLLKPTSVALWDEVSAAASDASWSMKERILLESQLVLATA
PPICLDPSPAIGIAAINATTERSPIASGDGVLKAAKKFLQVTKNRNNKLEKKTHHPQLSL
ANHVANERRQRRDANGMRSANAPKKLSMVSSDEVNAVSLHKALPNVPPSQRYDWQARNTE
RLTFETDRDNCQYRVRVELFERATTCEVSGQLTLERQKGGNSNKINGRTCPFKLASPLAA
RRYVKEFMGIFTEEGRKFVKITHERETRAGREIMEMQTGEKLQQPSATKVVQTIPVITQQ
TQPQSLPHIQQQQQQQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g14504.t2 | Coils | Coil | Coil | 392 | 412 | - |
| 8 | g14504.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 6 | g14504.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 110 | - |
| 5 | g14504.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 84 | 110 | - |
| 9 | g14504.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 125 | 144 | - |
| 7 | g14504.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 232 | 251 | - |
| 3 | g14504.t2 | PANTHER | PTHR13526:SF8 | TRANSCRIPTION FACTOR SPT20 HOMOLOG | 19 | 616 | 6.0E-51 |
| 4 | g14504.t2 | PANTHER | PTHR13526 | TRANSCRIPTION FACTOR SPT20 HOMOLOG | 19 | 616 | 6.0E-51 |
| 2 | g14504.t2 | Pfam | PF12090 | Spt20 family | 198 | 310 | 1.3E-15 |
| 1 | g14504.t2 | Pfam | PF12090 | Spt20 family | 314 | 372 | 6.7E-10 |
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:0000124 | SAGA complex | CC |
| GO:0003712 | transcription coregulator activity | MF |
KEGG
Orthology
- This transcript has been annotated with K21245 (transcription factor SPT20 homolog)
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.
