General information for g9028.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Microphthalmia-associated transcription factor.
Parent gene
- The parent gene g9028 is located on chr_2: 34730880..34731939 (- 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 | g9028 | g9028.t3 | isoform | g9028.t3 | 34726498 | 34731939 |
| chr_2 | g9028 | g9028.t3 | exon | g9028.t3.exon1 | 34726498 | 34727698 |
| chr_2 | g9028 | g9028.t3 | TTS | g9028.t3 | 34726516 | 34726516 |
| chr_2 | g9028 | g9028.t3 | cds | g9028.t3.CDS1 | 34727042 | 34727698 |
| chr_2 | g9028 | g9028.t3 | exon | g9028.t3.exon2 | 34727764 | 34727955 |
| chr_2 | g9028 | g9028.t3 | cds | g9028.t3.CDS2 | 34727764 | 34727955 |
| chr_2 | g9028 | g9028.t3 | exon | g9028.t3.exon3 | 34728047 | 34728297 |
| chr_2 | g9028 | g9028.t3 | cds | g9028.t3.CDS3 | 34728047 | 34728297 |
| chr_2 | g9028 | g9028.t3 | exon | g9028.t3.exon4 | 34730582 | 34730750 |
| chr_2 | g9028 | g9028.t3 | cds | g9028.t3.CDS4 | 34730582 | 34730750 |
| chr_2 | g9028 | g9028.t3 | exon | g9028.t3.exon5 | 34730883 | 34731939 |
| chr_2 | g9028 | g9028.t3 | cds | g9028.t3.CDS5 | 34730883 | 34730924 |
| chr_2 | g9028 | g9028.t3 | TSS | g9028.t3 | NA | NA |
Sequences
>g9028.t3 Gene=g9028 Length=2870
TGTCAATGATATAAAATATTTTAGTTGTACAACACAAAAAGAATTTTTTTTTTTGCTTTT
CGATTCAATGAATGTGAATGTTTCAAATGTGGGTACCAACATTATATTTTTATTTAATGC
CCATTAGCAATTATCAATGATTATGTATCAAATAACACATATTGTGTATCTTACCATTAG
CAATGATGCTTGTCACAAAAGAGTCTTCTTTTTCATTGATATATATGTTTGCTGCTGCTG
TGCTGTGATAACAGCTCTCACATACATATATATTAATTTTTATTGTGAGAGCGAGAGCGA
AGTTTTTTTTTTGTAAATGTTGAGAGCGACATTATCTCTTAATAGTCGAGACTGACTCTC
AACTCTACATTCACAATAACAACTTGTGATTGTATGCAGGCAGTCAATGAGTAGAGTAAT
TATCCAAAAAAAATATATTAAAATAATTTTTAATTTTTTTTCACAACATTCAGTTTACTT
TCAATCGCCGGAGTGAGCGGATCACAAAAGCAAGACTAAAGACTTTATTTTATAAAAATC
ATATTTTTTTATTGCAAAATTATTTCTCGTATATGAAAAAGAATAAAAAATTCTAAAAAG
CGATTGTTTTTTTGTTCTATCAATCAAAAAACAATTCGAGTGAACAAAAGAGTGCAATGA
CTAATTATCAGTGAATCATATGAAATAATATTAATAAAATGAAATTATGTTGATAAATAT
CAAATGAACAATGAATTGAACAATTTTTTGTATAATTATTGAATGATAGAGAAAAAAAGA
CTTTTGACTAAAAAAAATATTTAGTGAGTGCTTCTATAATGTATTCCAATAATAATAATA
ATAGCTGATAAAAGGAAATTGATAATTCCGCCTTTCTTTGAAGCTCAATAATAAAAGACT
CGATAAAGTGACATTTAAATTAAAAACAGAACTCTGCAATTAACTTGCATAGATAGAGAC
TATATTTCTTTTTTTTATATTCAAAACTATTCATAATAATTTTCTATAAACCATAATGCC
TGTCTATAATTTAAATGCTCGTAGACGACAAAATAAGTCAAAAGATTTCATTGATGAGAT
TCTAAACTTAGACTCGGGGTCACTGGATGAGGCATTAAAACTCGAGAAATTTCTAGCAGA
CGATAGTATTCTCATTAAGCAAGAACCCGAAGAGCTCTCAATGGCCGAGGTTCGTGACAG
ACAGAAGAAGGATAATCATAATATGATTGAACGACGACGACGTTTCAACATTAATGACAG
AATAAAAGAACTTGGCACGTTATTACCGAAGACCAATGAATTTTTATTTGATATCATTCA
GGACCTGCACATTCGACAACCTAATAAAGGTACAATTTTAAAATCATCAGTAGACTATAT
CAAGTGTCTTAAACATGAAGTTAATCGTCTCAAGCGCAATGAACAGAAACAAAAGGATTT
GGATAATGTGAATCGGCGTCTGATAACGAGAATTCGGGAGCTAGAGGCTTTAGCACGAAA
GCATGGACTCTCAATCAAGGAATTTGATCTCAATGACGTGGAATCTTCTGCTCAAGTACT
TTGTGAGGAAGAAGAAGCAGAAATAATCGAAAATAATGATGAGGAGGTTGATGAAGATGA
TGAAGAAGAAGAAAATGAAGTGAAAAGAAATCAACAAAATTCAATTGAGCGAGAGTTTAC
GACGACGACAACAAAACTAGAGATAATCGATGCTGATGATGCAAAAAAAGTTATCAATTT
AACAGAGCTTGAAAGTCTAATAGATTGTGATACCGATCTCAAGCTAAATGATCCATTACT
CTCATCATTCCCACTGTTTGACACTCCACCATCATCTTCGCATTCCAACTCAATTCCTTC
ATCACCATCTTCAATATCCACCGTATCAAGCAGCAGTAAACGAAGGCGAACTACTTTGTC
GTCATCATCAAAGCATCAGTACAAGCAATCAACATCATTTCTCAGTAGTGACGATGAAGA
TGTTATAGATGATGATTTCGATGAGAAATCACGGCATAAACATAAAAAGAACAAATATTA
TAGCAGTAATAGTAGTACAAGTGCAAATGCAAGCAATAACAGTGGCAGTTGCAATATTAG
TGAACGATCAAGTGCCTTGAGTTTAAAAGATCCAATGATGATGTCGGCCTCGCATTCTCC
AGCGCATTTTACAAGTGATTTAAGCAGTTATATGGATCAAATGTTTTTCTCATCGTCGCA
ATATCTCTCGCCAAGTTTAGCAGCTGATGACACTATAGATTTGTGCACGATTTTGAAAAC
TGAAAATCCATTAGGATATGATAATGATATGATCATGATTGGATGATTATTTCTCATGCT
GGTGTGATTTTTTCTTTCTATTTTTCATTCAAATGAATGAAAAAATTCTCTTTTGATAAT
GATGAGGCAAAACGCACCAGTTGGACTTAAAAATGTGAAATCTTGTTTTATGTTGAAAGA
AGTGATCACAATTTGAATTCTGTCTTGCTATGCAATCGTTTGGACAGTATTTTTCAGACT
ACTAATTATCTTATAAGATAAAAAAATTATGGAAAAGTATTATCGCTTATGAGCTAGTGC
AATCAATGAATTAAAAGTTGAAGAAGTAATTTTTATTGTTAATTAATTGATAAGATTATA
TAAGTATTTAACCTTAAGAGTAATTCGTTAAGTTTCCTTTTATTTGCCAGTCGAATTGTA
TTGTATTGTATTTTTAAAAAGAGTTTTTTTTTCTTTTTCTTCTTTTTAACCATCTTGTCT
TAGATTTATTTAGTCAAACAAAAAAACCATTAGACTTAGAGAGTGAAAATAAAGTGTTAA
GTAGAATAAATATCAAAAGCTAAAAACAAACAAAAACAACCTTCACATGC
>g9028.t3 Gene=g9028 Length=436
MPVYNLNARRRQNKSKDFIDEILNLDSGSLDEALKLEKFLADDSILIKQEPEELSMAEVR
DRQKKDNHNMIERRRRFNINDRIKELGTLLPKTNEFLFDIIQDLHIRQPNKGTILKSSVD
YIKCLKHEVNRLKRNEQKQKDLDNVNRRLITRIRELEALARKHGLSIKEFDLNDVESSAQ
VLCEEEEAEIIENNDEEVDEDDEEEENEVKRNQQNSIEREFTTTTTKLEIIDADDAKKVI
NLTELESLIDCDTDLKLNDPLLSSFPLFDTPPSSSHSNSIPSSPSSISTVSSSSKRRRTT
LSSSSKHQYKQSTSFLSSDDEDVIDDDFDEKSRHKHKKNKYYSSNSSTSANASNNSGSCN
ISERSSALSLKDPMMMSASHSPAHFTSDLSSYMDQMFFSSSQYLSPSLAADDTIDLCTIL
KTENPLGYDNDMIMIG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9028.t3 | CDD | cd11397 | bHLHzip_MITF_like | 60 | 137 | 5.21724E-33 |
| 6 | g9028.t3 | Coils | Coil | Coil | 122 | 142 | - |
| 5 | g9028.t3 | Coils | Coil | Coil | 200 | 220 | - |
| 4 | g9028.t3 | Gene3D | G3DSA:4.10.280.10 | HLH | 73 | 164 | 3.0E-23 |
| 10 | g9028.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 218 | - |
| 12 | g9028.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 207 | - |
| 9 | g9028.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 273 | 316 | - |
| 13 | g9028.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 328 | 360 | - |
| 11 | g9028.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 342 | 360 | - |
| 2 | g9028.t3 | PANTHER | PTHR45776 | MIP04163P | 43 | 288 | 1.5E-48 |
| 1 | g9028.t3 | Pfam | PF00010 | Helix-loop-helix DNA-binding domain | 64 | 125 | 1.0E-13 |
| 14 | g9028.t3 | ProSiteProfiles | PS50888 | Myc-type, basic helix-loop-helix (bHLH) domain profile. | 63 | 125 | 15.351 |
| 8 | g9028.t3 | SMART | SM00353 | finulus | 69 | 131 | 8.6E-13 |
| 3 | g9028.t3 | SUPERFAMILY | SSF47459 | HLH, helix-loop-helix DNA-binding domain | 60 | 134 | 1.7E-14 |
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:0046983 | protein dimerization activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09455 (microphthalmia-associated transcription factor)
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.
