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.t2 TTS g11405.t2 16008070 16008070
chr_1 g11405 g11405.t2 isoform g11405.t2 16008195 16011776
chr_1 g11405 g11405.t2 exon g11405.t2.exon1 16008195 16008281
chr_1 g11405 g11405.t2 cds g11405.t2.CDS1 16008195 16008281
chr_1 g11405 g11405.t2 exon g11405.t2.exon2 16008346 16008584
chr_1 g11405 g11405.t2 cds g11405.t2.CDS2 16008346 16008584
chr_1 g11405 g11405.t2 exon g11405.t2.exon3 16008802 16009060
chr_1 g11405 g11405.t2 cds g11405.t2.CDS3 16008802 16009060
chr_1 g11405 g11405.t2 exon g11405.t2.exon4 16009328 16009473
chr_1 g11405 g11405.t2 cds g11405.t2.CDS4 16009328 16009473
chr_1 g11405 g11405.t2 exon g11405.t2.exon5 16011335 16011776
chr_1 g11405 g11405.t2 cds g11405.t2.CDS5 16011335 16011776
chr_1 g11405 g11405.t2 TSS g11405.t2 16012647 16012647

Sequences

>g11405.t2 Gene=g11405 Length=1173
ATGGAATATCAGCAATTGCCGCCTGTTTCAATGATAATCGGAACACCGAATCAATCTCAA
TCACAAGCATCCCATTTACATAACTTGACAAACAGCAATAATAATAACAATAATGGATCA
AATAATCAACAGTTGCTTACAATGCAACCACCATTACTTCCACTACAAGTTGCTCACAAT
CTTCATCAGCTTACATCGCAGAATGGCAATTCACATGGTCTCGGCAATGCCACACAAAAT
CAAAACACTCAATCACTACCACCAACCACCCAGCTCTTGCAAGCAATTCACAACAATACT
CAGCAGCATCCAAATATGAATGGAAATGGCAATAATAACACAGGCAATAATACTAGTGAC
AATAACGCACCCAACGATGAGAATAATCGTTGGACACAATATCAAGTGCAACAATTATGG
CGACATCATGCATATTTGAACGGAAAAACAAGTAATAAAGACATTTGCGGTGACGATAAA
CATAAAGAAGATGGTGATCCCTGGAATGTGGAAGCACAAGCAGCATTTTTAGGACCGAAC
CTGTGGGATAAAACATTACCATACGACACAAATCTAAAAGTACATCAATACGCTGATTTG
GATGAATTTTTATCGGAAAATGGTATACCAGTCGATGGCTTAAATGGCTTACCGAGCAGT
CATTTGGGACATTCAGCGAGTATGGGTAATGGAAGCGGTGGCGGAGGTGGTGGTGTAACA
AATAATCGCAACGATTTGGGCCTCTCACTAGGACTAAGTGCAGTTACAAAGCGAGAAAGA
TCTCCTTCACCATCTGATTGTATGAGTCCCGATACTATAAACAATCCACCTTCTCCTGCA
GACTCCACATTTTCAATGTCTTCTTCACGCGATTTTGATCCACGTACGCGTGCATTCTCG
GATGAAGATTTAAAACCGCAACCAATGATAAAAAAGTCTCGCAAGCAATTCGTACCCGAT
GAAATGAAAGATGACAAATACTGGGCGCGCAGACGAAAGAACAACATGGCCGCCAAGCGC
TCGCGGGATGCTCGCCGCATGAAAGAAAATCAAATAGCGCTTCGAGCCGGATATTTAGAA
AAAGAAAACATGAATTTGCACCGTGAAGTTGAGCAGCTAAAACAAGAAAATATGGAGCTA
AGAGCGCGTTTATCAAAATATCAAGAAGTGTAA

>g11405.t2 Gene=g11405 Length=390
MEYQQLPPVSMIIGTPNQSQSQASHLHNLTNSNNNNNNGSNNQQLLTMQPPLLPLQVAHN
LHQLTSQNGNSHGLGNATQNQNTQSLPPTTQLLQAIHNNTQQHPNMNGNGNNNTGNNTSD
NNAPNDENNRWTQYQVQQLWRHHAYLNGKTSNKDICGDDKHKEDGDPWNVEAQAAFLGPN
LWDKTLPYDTNLKVHQYADLDEFLSENGIPVDGLNGLPSSHLGHSASMGNGSGGGGGGVT
NNRNDLGLSLGLSAVTKRERSPSPSDCMSPDTINNPPSPADSTFSMSSSRDFDPRTRAFS
DEDLKPQPMIKKSRKQFVPDEMKDDKYWARRRKNNMAAKRSRDARRMKENQIALRAGYLE
KENMNLHREVEQLKQENMELRARLSKYQEV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11405.t2 CDD cd14695 bZIP_HLF 323 382 4.64879E-32
6 g11405.t2 Coils Coil Coil 356 390 -
5 g11405.t2 Gene3D G3DSA:1.20.5.170 - 311 388 1.3E-18
9 g11405.t2 MobiDBLite mobidb-lite consensus disorder prediction 256 293 -
2 g11405.t2 PANTHER PTHR11988 THYROTROPH EMBRYONIC FACTOR RELATED 136 390 1.1E-89
3 g11405.t2 PANTHER PTHR11988:SF27 GH27708P 136 390 1.1E-89
1 g11405.t2 Pfam PF07716 Basic region leucine zipper 323 376 5.7E-17
10 g11405.t2 ProSiteProfiles PS50217 Basic-leucine zipper (bZIP) domain profile. 324 387 11.668
8 g11405.t2 SMART SM00338 brlzneu 322 386 7.1E-8
4 g11405.t2 SUPERFAMILY SSF57959 Leucine zipper domain 323 384 1.13E-16

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