General information for g4998.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Stress-activated map kinase-interacting protein 1.
Parent gene
- The parent gene g4998 is located on chr_2: 6378623..6380047 (+ 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 | g4998 | g4998.t1 | TSS | g4998.t1 | 6378365 | 6378365 |
| chr_2 | g4998 | g4998.t1 | isoform | g4998.t1 | 6378458 | 6380047 |
| chr_2 | g4998 | g4998.t1 | exon | g4998.t1.exon1 | 6378458 | 6378530 |
| chr_2 | g4998 | g4998.t1 | cds | g4998.t1.CDS1 | 6378458 | 6378530 |
| chr_2 | g4998 | g4998.t1 | exon | g4998.t1.exon2 | 6378621 | 6380047 |
| chr_2 | g4998 | g4998.t1 | cds | g4998.t1.CDS2 | 6378621 | 6380047 |
| chr_2 | g4998 | g4998.t1 | TTS | g4998.t1 | 6380496 | 6380496 |
Sequences
>g4998.t1 Gene=g4998 Length=1500
ATGGCGACTTTTAATAACAAGCACTGGCTTCTCTGTCACATTAGGAACTCCTTTATTTCA
ACCGATGACACCGGAATAAGTGAGCTAGTGATGAGTTCTGATAATTTAGCGAAAAATTTA
GCCAATTCTTATGCGAATGCATCGACATCCGGAAGTAGTTCGATGCCGACAAATGATGAA
ATTTCATTTTATGTCTATCCAGATTTGATAAACAATAATGATGAAGATGAAGAAGACCTC
TTGAGTAATTCATTTGATATAAACTTCACTCAAGAGTTTGCATTTCGATTTAGAACAAAT
ACAGCAGCAAAATTGGAAAAAATTAGTGAAATGAAAAAAAAACAGAGTCAAATTAAAGTT
GTAAAAATTGACGATACAGTGATCAAGTTAAATCAAGAAGCTGGGGATGATAGTGAATTG
TTTGTGAGAAAAGATTTAAGTAAAATATCGCTGCAATCAGATACAGTAAAATCGAAGCTA
ACGCAACAACTTGAAACTTTGCCTAAAATTAAACTGAATAAATATCGTGAATATTCAGTT
TTTGATGGCTCCTCATACCCAAACAACGAATCTAAGACAATTAAAGTGTTTATTACACCC
ATAAAAGATTTAAGAGACTATCCCCTTAAATGTTGCGTCCATTCAACAGCTAAAATAGAA
GAATTTATCGGTTATATTTTATTTAAATGTACAAATTTAAATCCCGAATATGCAGATCAG
CTTGAGGAAGTTAAAAATTATGGCCTCTTCATAAGTGATGAAACAGGTGAGCCGGATTTA
GATTTTCCGGCGTTAGATTTAAAAGAACAAGTCTCAAAGTATCAGTTTAATATTTTGGCG
CTATCGAAAAGAATCATACCACCATATTTTCAAAATCGTACACTTTCAGTTAATTCAGAT
ACAACCACAACAATCATCAATAATCTGCCAGTAAATCGTCAAGCGTCTATCGAGACAAAT
CGCTCAATTGCATCAGCGCACATTCGTCAAAACGAACTAGCAATGAATGTACACGATTCA
ATGGTTGATGCTCCTATTTATCGCGCCTTTCGTGTTCTTCTAGTTACCAAAAAGCATTTC
AAAACAGAAGTTCAGTTGGGCATATCGGCAGAAAAAATTGAAATTGATCCGCTCCAGCAA
AAGAGCTCAAACTATTTCTTTAAATCAAAGTCTTCTCATTATAGTATGGATGCAATTGCA
TTCTGTGAAATAACAAAAAGAAAATCTAGTCGTTTCGAATTTAGAATTGCATACAATCCC
TTATATTACGATCCTCTATCGTTTGCTCCATCTACCTCATTTGCGGAATCAACTACGAGC
TATTCAAGTTATACATTAAAAATCAATACATTTGAAAGTGATCCATCAACAGCCGAGGAA
ATTGTTTTAAAAATAAATAATATATTACTCTTAAGATCTGGTTCTGTGCGAAAAGAATAT
TTAAGTCGTCATGAAAAAATCAAAAAAAGTTTTATACAAAAAAAGAAATTTCCAATTTAA
>g4998.t1 Gene=g4998 Length=499
MATFNNKHWLLCHIRNSFISTDDTGISELVMSSDNLAKNLANSYANASTSGSSSMPTNDE
ISFYVYPDLINNNDEDEEDLLSNSFDINFTQEFAFRFRTNTAAKLEKISEMKKKQSQIKV
VKIDDTVIKLNQEAGDDSELFVRKDLSKISLQSDTVKSKLTQQLETLPKIKLNKYREYSV
FDGSSYPNNESKTIKVFITPIKDLRDYPLKCCVHSTAKIEEFIGYILFKCTNLNPEYADQ
LEEVKNYGLFISDETGEPDLDFPALDLKEQVSKYQFNILALSKRIIPPYFQNRTLSVNSD
TTTTIINNLPVNRQASIETNRSIASAHIRQNELAMNVHDSMVDAPIYRAFRVLLVTKKHF
KTEVQLGISAEKIEIDPLQQKSSNYFFKSKSSHYSMDAIAFCEITKRKSSRFEFRIAYNP
LYYDPLSFAPSTSFAESTTSYSSYTLKINTFESDPSTAEEIVLKINNILLLRSGSVRKEY
LSRHEKIKKSFIQKKKFPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4998.t1 | Gene3D | G3DSA:2.30.29.30 | - | 333 | 475 | 0 |
| 4 | g4998.t1 | PANTHER | PTHR13335 | TARGET OF RAPAMYCIN COMPLEX 2 SUBUNIT MAPKAP1 | 1 | 319 | 0 |
| 5 | g4998.t1 | PANTHER | PTHR13335 | TARGET OF RAPAMYCIN COMPLEX 2 SUBUNIT MAPKAP1 | 335 | 475 | 0 |
| 2 | g4998.t1 | Pfam | PF05422 | Stress-activated map kinase interacting protein 1 (SIN1) | 18 | 146 | 0 |
| 1 | g4998.t1 | Pfam | PF16978 | SAPK-interacting protein 1 (Sin1), middle CRIM domain | 157 | 283 | 0 |
| 3 | g4998.t1 | Pfam | PF16979 | SAPK-interacting protein 1 (Sin1), Pleckstrin-homology | 345 | 469 | 0 |
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:0031932 | TORC2 complex | CC |
KEGG
Orthology
- This transcript has been annotated with K20410 (target of rapamycin complex 2 subunit MAPKAP1)
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.
