Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Hepatic leukemia 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_1 g11405 g11405.t4 TTS g11405.t4 16008070 16008070
chr_1 g11405 g11405.t4 isoform g11405.t4 16008195 16017690
chr_1 g11405 g11405.t4 exon g11405.t4.exon1 16008195 16008281
chr_1 g11405 g11405.t4 cds g11405.t4.CDS1 16008195 16008281
chr_1 g11405 g11405.t4 exon g11405.t4.exon2 16008346 16008599
chr_1 g11405 g11405.t4 cds g11405.t4.CDS2 16008346 16008599
chr_1 g11405 g11405.t4 exon g11405.t4.exon3 16008802 16009060
chr_1 g11405 g11405.t4 cds g11405.t4.CDS3 16008802 16009060
chr_1 g11405 g11405.t4 exon g11405.t4.exon4 16009328 16009488
chr_1 g11405 g11405.t4 cds g11405.t4.CDS4 16009328 16009488
chr_1 g11405 g11405.t4 exon g11405.t4.exon5 16016992 16017690
chr_1 g11405 g11405.t4 cds g11405.t4.CDS5 16016992 16017100
chr_1 g11405 g11405.t4 TSS g11405.t4 16018043 16018043

Sequences

>g11405.t4 Gene=g11405 Length=1460
TCAAAAGAAAATCGTCATCTTTCAGAATTGCTTTTAAACAATATTACACACTCAATCAAG
TTACAATAGTCCGATTAAAATTGTGATTTTCGTACTGATTTATTATGGAAAAGTTTTAAG
TGAAGAGCAAAGCGAGAGCATTAAAGAAGGAAGAAAATTTTTCGGTTGTGATAATTGGAT
TATCCTTTACCAAGTGGAACTTTATACATACATATATATACATTGTTAAGAATTTAAACG
AAAAAACACTTAACTAAACGCTCATTCATGTCATTTTGTTAAATAAAAAAAAGTGCAATA
ATAATTGTTATAAAAAAGTTAAATATTTTAAATATACTAAATAATAATAAAAATTATAAT
TAAAGAAATTGATAGTTAAACTATCGTTAAACAGTAAGCAAAGAGCTCTAAATACAGTTC
ATCACCATATAGTGCTATTAGTAAATTCAAAATCAATTAGGACTTTAACTGAACATTGTT
AACTAGTTGATAAAAAATTTCCCATACACTCTATTCAACCGAACATTCGAATTGTTTAGT
AAAAAATTGGAGGTTCAAAGATTAAAAAATATAACTTCAAAAGTGAAAACATGAGTGACA
GAGCATCATCGCCAAGCTTAATTGAATCAGGATTGAATGGATTAAAATCATTAATTGGAG
GAACAAGAGACAATTATCCTTTGATCAGCGGGACAAATGTCTTTTTATTTTCAGGAAAAA
CAAGTAATAAAGACATTTGCGGTGACGATAAACATAAAGAAGATGGTGATCCCTGGAATG
TGGAAGCACAAGCAGCATTTTTAGGACCGAACCTGTGGGATAAAACATTACCATACGACA
CAAATCTAAAAGTACATCAATACGCTGATTTGGATGAATTTTTATCGGAAAATGGTATAC
CAGTCGATGGCTTAAATGGCTTACCGAGCAGTCATTTGGGACATTCAGCGAGTATGGGTA
ATGGAAGCGGTGGCGGAGGTGGTGGTGTAACAAATAATCGCAACGATTTGGGCCTCTCAC
TAGGACTAAGTGCAGTTACAAAGCGAGAAAGATCTCCTTCACCATCTGATTGTATGAGTC
CCGATACTATAAACAATCCACCTTCTCCTGCAGACTCCATTTTCGATGTTACAGCATTTT
CAATGTCTTCTTCACGCGATTTTGATCCACGTACGCGTGCATTCTCGGATGAAGATTTAA
AACCGCAACCAATGATAAAAAAGTCTCGCAAGCAATTCGTACCCGATGAAATGAAAGATG
ACAAATACTGGGCGCGCAGACGAAAGAACAACATGGCCGCCAAGCGCTCGCGGGATGCTC
GCCGCATGAAAGAAAATCAAATAGCGCTTCGAGCCGGATATTTAGAAAAAGAAAACATGA
ATTTGCACCGTGAAGTTGAGCAGCTAAAACAAGAAAATATGGAGCTAAGAGCGCGTTTAT
CAAAATATCAAGAAGTGTAA

>g11405.t4 Gene=g11405 Length=289
MSDRASSPSLIESGLNGLKSLIGGTRDNYPLISGTNVFLFSGKTSNKDICGDDKHKEDGD
PWNVEAQAAFLGPNLWDKTLPYDTNLKVHQYADLDEFLSENGIPVDGLNGLPSSHLGHSA
SMGNGSGGGGGGVTNNRNDLGLSLGLSAVTKRERSPSPSDCMSPDTINNPPSPADSIFDV
TAFSMSSSRDFDPRTRAFSDEDLKPQPMIKKSRKQFVPDEMKDDKYWARRRKNNMAAKRS
RDARRMKENQIALRAGYLEKENMNLHREVEQLKQENMELRARLSKYQEV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11405.t4 CDD cd14695 bZIP_HLF 222 281 4.43862E-32
6 g11405.t4 Coils Coil Coil 255 289 -
5 g11405.t4 Gene3D G3DSA:1.20.5.170 - 210 287 7.9E-19
9 g11405.t4 MobiDBLite mobidb-lite consensus disorder prediction 150 172 -
2 g11405.t4 PANTHER PTHR11988 THYROTROPH EMBRYONIC FACTOR RELATED 44 289 4.2E-89
3 g11405.t4 PANTHER PTHR11988:SF27 GH27708P 44 289 4.2E-89
1 g11405.t4 Pfam PF07716 Basic region leucine zipper 222 275 3.6E-17
10 g11405.t4 ProSiteProfiles PS50217 Basic-leucine zipper (bZIP) domain profile. 223 286 11.668
8 g11405.t4 SMART SM00338 brlzneu 221 285 7.1E-8
4 g11405.t4 SUPERFAMILY SSF57959 Leucine zipper domain 222 283 6.88E-17

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:0006357 regulation of transcription by RNA polymerase II BP
GO:0006355 regulation of transcription, DNA-templated BP
GO:0003700 DNA-binding transcription factor activity MF

KEGG

Orthology

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.

Raw TPM values