General information for g5515.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5515 is located on chr_2: 10028251..10029373 (- 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_2 | g5515 | g5515.t12 | TTS | g5515.t12 | 10027731 | 10027731 |
| chr_2 | g5515 | g5515.t12 | isoform | g5515.t12 | 10028251 | 10029139 |
| chr_2 | g5515 | g5515.t12 | exon | g5515.t12.exon1 | 10028251 | 10028364 |
| chr_2 | g5515 | g5515.t12 | cds | g5515.t12.CDS1 | 10028252 | 10028364 |
| chr_2 | g5515 | g5515.t12 | exon | g5515.t12.exon2 | 10028429 | 10028579 |
| chr_2 | g5515 | g5515.t12 | cds | g5515.t12.CDS2 | 10028429 | 10028579 |
| chr_2 | g5515 | g5515.t12 | exon | g5515.t12.exon3 | 10028655 | 10028792 |
| chr_2 | g5515 | g5515.t12 | cds | g5515.t12.CDS3 | 10028655 | 10028792 |
| chr_2 | g5515 | g5515.t12 | exon | g5515.t12.exon4 | 10028902 | 10029139 |
| chr_2 | g5515 | g5515.t12 | cds | g5515.t12.CDS4 | 10028902 | 10029024 |
| chr_2 | g5515 | g5515.t12 | TSS | g5515.t12 | 10029368 | 10029368 |
Sequences
>g5515.t12 Gene=g5515 Length=641
CACGAATAATTGTCAACATACCAATAGAAAGAGAGAGCAAACTGTATCGTAGTGAGGAAA
CAGCCGCATAAAAGCTTAGAATCAAATAAGGATCATTTGATTTGATTTTATAGTGATGGA
TCCTATTGAAGAAAACTCTTCAAATATTGAAACTTCTGTTTCATCTGCAACATCAGGAAC
CACAAATATTGTCCATCATCTAATTCCGCCATCACAAGTGAATCCTTCAGCACATCAAGC
CCACGTTCAATCTTCATCTGTAATACAACCAAATCAACAATCAGTTATAACCGCTACTGG
AGTGCAACTTGTAAAAAGTGTTTTGCTGGTGAATAGTAAACCAAATTCTGTCATTCATAC
GACTCAAGCTATTCAAATAAAACCTGAACCAAATATTGGTCATATGATAACTTCAGATGA
TTCTGACGACTATTCTGATGATGATTCTCCAAAAAAGCGTAGAGATTTATTGACGAGACG
TCCTTCATATCGAAAAATTTTAAATGACCTCGGAGGAGGTGAAATGGGGGGAACAATATT
GACACAAGCTGGAAATCCAAATGATCATGCGATTCATGGTGGAAGTACGATTGTACAATA
TAATAATCAGGATGGATCAGGTTTGGTGTCATATGTCCCTG
>g5515.t12 Gene=g5515 Length=175
MDPIEENSSNIETSVSSATSGTTNIVHHLIPPSQVNPSAHQAHVQSSSVIQPNQQSVITA
TGVQLVKSVLLVNSKPNSVIHTTQAIQIKPEPNIGHMITSDDSDDYSDDDSPKKRRDLLT
RRPSYRKILNDLGGGEMGGTILTQAGNPNDHAIHGGSTIVQYNNQDGSGLVSYVP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5515.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 2 | g5515.t12 | PANTHER | PTHR45879:SF3 | CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B | 12 | 140 | 2.4E-15 |
| 3 | g5515.t12 | PANTHER | PTHR45879 | CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B | 12 | 140 | 2.4E-15 |
| 1 | g5515.t12 | Pfam | PF02173 | pKID domain | 108 | 136 | 3.2E-15 |
| 5 | g5515.t12 | ProSiteProfiles | PS50953 | KID domain profile. | 92 | 151 | 12.714 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5515/g5515.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5515.t12.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0003700 | DNA-binding transcription factor activity | MF |
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.
