General information for g12129.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine/threonine-protein kinase Smg1.
Parent gene
- The parent gene g12129 is located on chr_1: 21211425..21217553 (- 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 | g12129 | g12129.t3 | isoform | g12129.t3 | 21211425 | 21212644 |
| chr_1 | g12129 | g12129.t3 | exon | g12129.t3.exon1 | 21211425 | 21212440 |
| chr_1 | g12129 | g12129.t3 | cds | g12129.t3.CDS1 | 21211426 | 21212391 |
| chr_1 | g12129 | g12129.t3 | exon | g12129.t3.exon2 | 21212505 | 21212644 |
| chr_1 | g12129 | g12129.t3 | TSS | g12129.t3 | NA | NA |
| chr_1 | g12129 | g12129.t3 | TTS | g12129.t3 | NA | NA |
Sequences
>g12129.t3 Gene=g12129 Length=1156
TTTACCATTTGAAACTTATAAAAATAAATTTTTGTTTAATAAAATAAAAATTCACAAGTA
TTTCACTTTAAAAGGTACATCTATCGTTACTTTAAAATTTTCTTCATCATAATCACATAA
AGATGATATTGATATGATCGGCTATTTTATTATATCATGATAAGAGCTTAATCATTAATA
ACAAAAACGATGGACAAATATGGTGAAAGTAAATCAAATAGAAATCGATGGAAGGATGAA
CATCGTCATCCAAAATTGTATGATGAACGACTGGACACTCCAGGACAACAACAAAATGGA
AAAATTACTACTGCCAGTTCCTCATCTTCTTCTTCAAAGACACAAAGTAGTAATAGCAGC
AGTAATAAACTTTTGAAAACTGACATAGTCAATCAACTAGCTCAAAATCCAAATCTTCCT
GAGGATGTTCGCATTTCAAAGTTGTTGCGACGTTTAGAGACGGAAACTACTGTAACTGGA
ACAATTGAAATTTGTGGAAAACTTAAAACAGTCGTTCAAGACCAAGCAAATGCCAATTAC
ATCAAGCGATCGTTTGACATGCTCACCAATTCATTAATTTCGGTTATGAAGGAATGTCAC
ACAGGTGAAGCAGTCAATCATGTTGCGGAAGTATATGGAATGATGGGTTTTGTGATGAGA
AATGATTTTCCTCTTTATAAATCATGGATTTGCAAGACTTACAAGAATGTTAAAACACTT
CGTGTCGCAATGATGAAAGCTTTAGAAAAAACTCTCACAATGGACTCAAATGAGCTACGA
TTGAGTGATCAAATAGGAAGATTGATGGAATTATTGAGAGATTTTCTTGAACAGACTGAT
GATTATCGAGTTTTTATGGCTATCACAAATGTTTTAATTGTCATTGCTAATAATTATAAT
ATGAGATATTTTAAGTCACATTTTACAAATGTGGTCGATATTGTAATTGGTTGGATGATG
GAAAATCAATTGACAAAAGTGAAAGTTCATTGTGCAGTTGTTTTACAAAGTTTGGGACAA
TTTTGGAAAAATGATTCACAATTTTCACTTGATCTTATTGGTCAACTTTTAGAAGATATC
GATGGATGCATTGAAAAAATGGAAGACAGCAACGAAGATAAAGTTAAAAATTTTAAAGAT
TTTGGTGCATTTGTTG
>g12129.t3 Gene=g12129 Length=322
MDKYGESKSNRNRWKDEHRHPKLYDERLDTPGQQQNGKITTASSSSSSSKTQSSNSSSNK
LLKTDIVNQLAQNPNLPEDVRISKLLRRLETETTVTGTIEICGKLKTVVQDQANANYIKR
SFDMLTNSLISVMKECHTGEAVNHVAEVYGMMGFVMRNDFPLYKSWICKTYKNVKTLRVA
MMKALEKTLTMDSNELRLSDQIGRLMELLRDFLEQTDDYRVFMAITNVLIVIANNYNMRY
FKSHFTNVVDIVIGWMMENQLTKVKVHCAVVLQSLGQFWKNDSQFSLDLIGQLLEDIDGC
IEKMEDSNEDKVKNFKDFGAFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12129.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 6 | g12129.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 60 | - |
| 4 | g12129.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 29 | 60 | - |
| 1 | g12129.t3 | PANTHER | PTHR11139:SF108 | AGAP000368-PA | 101 | 308 | 2.8E-22 |
| 2 | g12129.t3 | PANTHER | PTHR11139 | ATAXIA TELANGIECTASIA MUTATED ATM -RELATED | 101 | 308 | 2.8E-22 |
| 3 | g12129.t3 | SUPERFAMILY | SSF48371 | ARM repeat | 172 | 304 | 3.94E-7 |
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 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.
