General information for g11954.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative MICAL-like protein 2.
Parent gene
- The parent gene g11954 is located on chr_1: 19775063..19776052 (+ 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 | g11954 | g11954.t4 | isoform | g11954.t4 | 19774594 | 19776052 |
| chr_1 | g11954 | g11954.t4 | exon | g11954.t4.exon1 | 19774594 | 19775437 |
| chr_1 | g11954 | g11954.t4 | TSS | g11954.t4 | 19774608 | 19774608 |
| chr_1 | g11954 | g11954.t4 | cds | g11954.t4.CDS1 | 19775173 | 19775437 |
| chr_1 | g11954 | g11954.t4 | exon | g11954.t4.exon2 | 19775498 | 19775697 |
| chr_1 | g11954 | g11954.t4 | cds | g11954.t4.CDS2 | 19775498 | 19775697 |
| chr_1 | g11954 | g11954.t4 | exon | g11954.t4.exon3 | 19775762 | 19776052 |
| chr_1 | g11954 | g11954.t4 | cds | g11954.t4.CDS3 | 19775762 | 19775923 |
| chr_1 | g11954 | g11954.t4 | TTS | g11954.t4 | NA | NA |
Sequences
>g11954.t4 Gene=g11954 Length=1335
TCAACGCAAAGCACACCGAAGAAAAAAAGACAAGCGCCAACGCCTCCTTCTTCTACGTCA
TTCAAAGCACCTGAAAAAGCGTCAACAGAGGTTATAGAAAATACAGAAAATACTCTTAAT
GATGCAGCACTCTACGTGACACCATCAGAAACAATTAATGGAGAAAATCATGAAAATAAT
GTGAATGAAAGCACCGATATCGACATTTCACTCAATGCCAGTAGCTTACAATCTGATGGT
GATCAACGTCGACTTATTCCACTTGAGGAATCGCTCATTGAAGAAGGTGCAAGCAGTAGT
TCTATAAATAGTCGCAATGAAACGCAAGAAGTGACGTACAGGAGAAAAATTGTACCTCTT
TCGCCCACATCACCAGATGATGACAGTTGCGAAAATTTGGAGCAAATAAAAGACCACAAA
GAAGCGGAAAATCGTCAACGTCAAAGTCAAAGCAGTCTTAAAGCGGACTCAACTGATTCG
CTGCCATATCTCAACAAGTCATCACACGGAAAATGGAAAAGAAGAAAAGGCAAAGCACCA
ACTTTACCTTTTGCTCTTCCACAGCGACGTGTTTTACAAATGTTGCCATTGCAAGAAATT
CGTCATGAACTAGAAATCATCGAAGTGCAGCAGCAGGGATTAGAAAAGCAAGGTGTTCAG
CTAGAAAAAATGATAAGAGAACGTTGTGAAGGCGATAATCGTACAACTGAAGAACTTTTA
GAGCAATTACCCAATGCAAAGAATCCAAAGGAAGTTGAAGAACTCATATTACAATTATTT
GAGTTAGTGAATGAAAAAAATGAGCTATTTAGACGTCAAGCAGAGTTGATGTATTTAAGG
AGAGCCCATCGTCTTGAAGAAGAACAAGCGGATGTTGAATATGAAATAAGAAAGTTAATG
GCTCAACCTGAACATAATAAGACTGACTCAGATAAAGCTAGAGAAGAAGCATTGATAGCG
AGACTTGTGGAAATTGTTCAATTAAGAAATGAAGTTGTTGATTGTCTAGAAATGGATCGA
TTGCGAGAAGCAGAAGAAGATTTGAGTATTAAACAAAGAATGGAAAGTCACACAGCTAAA
CTTGACCAAGAATATCTTAATCAAACACCAACAAAATTATCGAAGAAAGAAAAGAAGAAA
CTAAAAGAGGCAAAAAAGATGAAAAACAAGAAACTCAATGATGCCGATAAAGTAAGAGAA
AACTAATTAGACAGCATGTGATGGAAAACTTAATATTTATTTCTTTCTTTCTATTTTAAT
AAGGATTTAGATACCAGTGAAATGAAAGCAGAAACGGGCGAAAAAAAGAAGAAGAAGAAA
AAATTTTTGTTCTAA
>g11954.t4 Gene=g11954 Length=208
MLPLQEIRHELEIIEVQQQGLEKQGVQLEKMIRERCEGDNRTTEELLEQLPNAKNPKEVE
ELILQLFELVNEKNELFRRQAELMYLRRAHRLEEEQADVEYEIRKLMAQPEHNKTDSDKA
REEALIARLVEIVQLRNEVVDCLEMDRLREAEEDLSIKQRMESHTAKLDQEYLNQTPTKL
SKKEKKKLKEAKKMKNKKLNDADKVREN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11954.t4 | Coils | Coil | Coil | 4 | 24 | - |
| 8 | g11954.t4 | Coils | Coil | Coil | 89 | 109 | - |
| 9 | g11954.t4 | Coils | Coil | Coil | 185 | 208 | - |
| 6 | g11954.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 164 | 208 | - |
| 5 | g11954.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 208 | - |
| 2 | g11954.t4 | PANTHER | PTHR23167:SF59 | MICAL-LIKE 1A-RELATED | 2 | 202 | 4.2E-57 |
| 3 | g11954.t4 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 2 | 202 | 4.2E-57 |
| 1 | g11954.t4 | Pfam | PF12130 | Bivalent Mical/EHBP Rab binding domain | 7 | 157 | 5.5E-48 |
| 10 | g11954.t4 | ProSiteProfiles | PS51848 | bMERB domain profile. | 1 | 159 | 50.035 |
| 4 | g11954.t4 | SMART | SM01203 | DUF3585_4 | 1 | 159 | 3.3E-64 |
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.
