Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Microphthalmia-associated transcription factor.

Parent gene

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.t5 isoform g9028.t5 34728047 34731468
chr_2 g9028 g9028.t5 exon g9028.t5.exon1 34728047 34728297
chr_2 g9028 g9028.t5 cds g9028.t5.CDS1 34728047 34728297
chr_2 g9028 g9028.t5 exon g9028.t5.exon2 34730582 34730750
chr_2 g9028 g9028.t5 cds g9028.t5.CDS2 34730582 34730750
chr_2 g9028 g9028.t5 exon g9028.t5.exon3 34730883 34731468
chr_2 g9028 g9028.t5 cds g9028.t5.CDS3 34730883 34730924
chr_2 g9028 g9028.t5 TSS g9028.t5 34731468 34731468
chr_2 g9028 g9028.t5 TTS g9028.t5 NA NA

Sequences

>g9028.t5 Gene=g9028 Length=1006
AGTTTACTTTCAATCGCCGGAGTGAGCGGATCACAAAAGCAAGACTAAAGACTTTATTTT
ATAAAAATCATATTTTTTTATTGCAAAATTATTTCTCGTATATGAAAAAGAATAAAAAAT
TCTAAAAAGCGATTGTTTTTTTGTTCTATCAATCAAAAAACAATTCGAGTGAACAAAAGA
GTGCAATGACTAATTATCAGTGAATCATATGAAATAATATTAATAAAATGAAATTATGTT
GATAAATATCAAATGAACAATGAATTGAACAATTTTTTGTATAATTATTGAATGATAGAG
AAAAAAAGACTTTTGACTAAAAAAAATATTTAGTGAGTGCTTCTATAATGTATTCCAATA
ATAATAATAATAGCTGATAAAAGGAAATTGATAATTCCGCCTTTCTTTGAAGCTCAATAA
TAAAAGACTCGATAAAGTGACATTTAAATTAAAAACAGAACTCTGCAATTAACTTGCATA
GATAGAGACTATATTTCTTTTTTTTATATTCAAAACTATTCATAATAATTTTCTATAAAC
CATAATGCCTGTCTATAATTTAAATGCTCGTAGACGACAAAATAAGTCAAAAGATTTCAT
TGATGAGATTCTAAACTTAGACTCGGGGTCACTGGATGAGGCATTAAAACTCGAGAAATT
TCTAGCAGACGATAGTATTCTCATTAAGCAAGAACCCGAAGAGCTCTCAATGGCCGAGGT
TCGTGACAGACAGAAGAAGGATAATCATAATATGATTGAACGACGACGACGTTTCAACAT
TAATGACAGAATAAAAGAACTTGGCACGTTATTACCGAAGACCAATGAATTTTTATTTGA
TATCATTCAGGACCTGCACATTCGACAACCTAATAAAGGTACAATTTTAAAATCATCAGT
AGACTATATCAAGTGTCTTAAACATGAAGTTAATCGTCTCAAGCGCAATGAACAGAAACA
AAAGGATTTGGATAATGTGAATCGGCGTCTGATAACGAGAATTCGG

>g9028.t5 Gene=g9028 Length=154
MPVYNLNARRRQNKSKDFIDEILNLDSGSLDEALKLEKFLADDSILIKQEPEELSMAEVR
DRQKKDNHNMIERRRRFNINDRIKELGTLLPKTNEFLFDIIQDLHIRQPNKGTILKSSVD
YIKCLKHEVNRLKRNEQKQKDLDNVNRRLITRIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9028.t5 CDD cd11397 bHLHzip_MITF_like 60 137 5.97978E-30
6 g9028.t5 Coils Coil Coil 122 142 -
5 g9028.t5 Gene3D G3DSA:4.10.280.10 HLH 62 142 1.9E-23
2 g9028.t5 PANTHER PTHR45776 MIP04163P 42 153 5.4E-43
3 g9028.t5 PANTHER PTHR45776:SF2 MIP04163P 42 153 5.4E-43
1 g9028.t5 Pfam PF00010 Helix-loop-helix DNA-binding domain 64 125 1.6E-14
9 g9028.t5 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 63 125 15.351
8 g9028.t5 SMART SM00353 finulus 69 131 8.6E-13
4 g9028.t5 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 60 134 2.75E-15

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:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific MF
GO:0046983 protein dimerization activity MF

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.

Raw TPM values