General information for g13342.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Non-structural maintenance of chromosomes element 3-like protein.
Parent gene
- The parent gene g13342 is located on chr_1: 29379337..29380257 (+ 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 | g13342 | g13342.t1 | isoform | g13342.t1 | 29379337 | 29380257 |
| chr_1 | g13342 | g13342.t1 | exon | g13342.t1.exon1 | 29379337 | 29379577 |
| chr_1 | g13342 | g13342.t1 | cds | g13342.t1.CDS1 | 29379337 | 29379577 |
| chr_1 | g13342 | g13342.t1 | exon | g13342.t1.exon2 | 29379633 | 29379887 |
| chr_1 | g13342 | g13342.t1 | cds | g13342.t1.CDS2 | 29379633 | 29379887 |
| chr_1 | g13342 | g13342.t1 | exon | g13342.t1.exon3 | 29379944 | 29380257 |
| chr_1 | g13342 | g13342.t1 | cds | g13342.t1.CDS3 | 29379944 | 29380257 |
| chr_1 | g13342 | g13342.t1 | TTS | g13342.t1 | 29381175 | 29381175 |
| chr_1 | g13342 | g13342.t1 | TSS | g13342.t1 | NA | NA |
Sequences
>g13342.t1 Gene=g13342 Length=810
ATGCCGCGACCATCCCGTAAATCAACAAATTCACAGTTTTCGCAACCATCAACCAGTCAT
GCAACACAAAGAGTATCGGAAAGTGAGTCCAGTGATGAAGAAAATAATAAAAGCCGGCGT
AAAAAAAGTCAACTTTCACAATCTCAAATTCATTCCACTGTAAATATTGAACTTCTAACT
ACAAATCTCGTAAAGTATGTGATTAATCATTCCTGTAATAAAATTCCTATGAAACGAGCA
GATTTAACAAAACAGTTAACCATACCACGAAAAGAATTTGATGAAATCTTCGAAGGAGCT
CAAGAAATTTTGAAAAATGTATATGGATTAGAATTAACTGAAATACCTGAAACAAAATCA
TCAAAATTACTCATCACGTACTCGTCGATTCCATTAGTTACACCTTTACAAATGAATGAT
GAAGAAACAAAAGATATGCAACTTCTTTTTATTATACTTTCTTACTTATTCATGAAAAAT
GCAGATATTCCTGAAGACAATGTCATTAATTTTATGAATCAATTGGGAATTGAGGCAGAA
GATTTTACGAAATCACGAGAAATATTCATCAAACAGCTCTATTTAAAACGTAACAAAGTT
GAAATTGAAGGAAAAAATGATGCATATTTCACTCTCTCATGGGGTGAACGAGCCAAACTC
GAATTTGATAAGAAACAAATTCTTGAAGCTGTTGCAAAAATCATGGAAAAGTCACCACAA
GCATTTATTAATCAGTATCACGCTGCTCATGGTCATGATCCAAATCAAAGTCAAAATTTA
ACTCAAGTGTCAATGATTATTGATGATTAA
>g13342.t1 Gene=g13342 Length=269
MPRPSRKSTNSQFSQPSTSHATQRVSESESSDEENNKSRRKKSQLSQSQIHSTVNIELLT
TNLVKYVINHSCNKIPMKRADLTKQLTIPRKEFDEIFEGAQEILKNVYGLELTEIPETKS
SKLLITYSSIPLVTPLQMNDEETKDMQLLFIILSYLFMKNADIPEDNVINFMNQLGIEAE
DFTKSREIFIKQLYLKRNKVEIEGKNDAYFTLSWGERAKLEFDKKQILEAVAKIMEKSPQ
AFINQYHAAHGHDPNQSQNLTQVSMIIDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13342.t1 | Gene3D | G3DSA:1.10.10.1200 | - | 49 | 129 | 6.2E-11 |
| 9 | g13342.t1 | Gene3D | G3DSA:1.10.10.1210 | - | 135 | 257 | 2.8E-24 |
| 6 | g13342.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 47 | - |
| 8 | g13342.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 7 | g13342.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 26 | 41 | - |
| 3 | g13342.t1 | PANTHER | PTHR11736:SF14 | MAGE PROTEIN | 10 | 252 | 1.3E-34 |
| 4 | g13342.t1 | PANTHER | PTHR11736 | MELANOMA-ASSOCIATED ANTIGEN MAGE ANTIGEN | 10 | 252 | 1.3E-34 |
| 2 | g13342.t1 | Pfam | PF01454 | MAGE family | 63 | 122 | 1.6E-10 |
| 1 | g13342.t1 | Pfam | PF01454 | MAGE family | 139 | 224 | 1.2E-7 |
| 11 | g13342.t1 | ProSiteProfiles | PS50838 | MAGE conserved domain profile. | 56 | 249 | 19.486 |
| 5 | g13342.t1 | SMART | SM01373 | MAGE_2 | 63 | 227 | 3.7E-20 |
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.
