Gene loci information

Transcript annotation

  • This transcript has been annotated as Carbohydrate-responsive element-binding protein.

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 g12005 g12005.t1 isoform g12005.t1 20292219 20300122
chr_1 g12005 g12005.t1 exon g12005.t1.exon1 20292219 20292225
chr_1 g12005 g12005.t1 cds g12005.t1.CDS1 20292219 20292225
chr_1 g12005 g12005.t1 exon g12005.t1.exon2 20294640 20294713
chr_1 g12005 g12005.t1 cds g12005.t1.CDS2 20294640 20294713
chr_1 g12005 g12005.t1 exon g12005.t1.exon3 20294775 20294894
chr_1 g12005 g12005.t1 cds g12005.t1.CDS3 20294775 20294894
chr_1 g12005 g12005.t1 exon g12005.t1.exon4 20297150 20297276
chr_1 g12005 g12005.t1 cds g12005.t1.CDS4 20297150 20297276
chr_1 g12005 g12005.t1 exon g12005.t1.exon5 20297336 20297422
chr_1 g12005 g12005.t1 cds g12005.t1.CDS5 20297336 20297422
chr_1 g12005 g12005.t1 exon g12005.t1.exon6 20297484 20297579
chr_1 g12005 g12005.t1 cds g12005.t1.CDS6 20297484 20297579
chr_1 g12005 g12005.t1 exon g12005.t1.exon7 20297634 20298015
chr_1 g12005 g12005.t1 cds g12005.t1.CDS7 20297634 20298015
chr_1 g12005 g12005.t1 exon g12005.t1.exon8 20298070 20299360
chr_1 g12005 g12005.t1 cds g12005.t1.CDS8 20298070 20299360
chr_1 g12005 g12005.t1 exon g12005.t1.exon9 20299419 20299546
chr_1 g12005 g12005.t1 cds g12005.t1.CDS9 20299419 20299546
chr_1 g12005 g12005.t1 exon g12005.t1.exon10 20299611 20299734
chr_1 g12005 g12005.t1 cds g12005.t1.CDS10 20299611 20299734
chr_1 g12005 g12005.t1 exon g12005.t1.exon11 20299794 20299923
chr_1 g12005 g12005.t1 cds g12005.t1.CDS11 20299794 20299923
chr_1 g12005 g12005.t1 exon g12005.t1.exon12 20299989 20300122
chr_1 g12005 g12005.t1 cds g12005.t1.CDS12 20299989 20300122
chr_1 g12005 g12005.t1 TTS g12005.t1 20300968 20300968
chr_1 g12005 g12005.t1 TSS g12005.t1 NA NA

Sequences

>g12005.t1 Gene=g12005 Length=2700
ATGCAATTTATCTTGAAGAAACGACCATCTGTGTGTCAATTTGCATCTCCATTAGACGTC
GATTTACACAACACACCTCAAGCAATAATCTTAGAGGGAAAATACTGGAAACGAAAGTGG
AAGGTTATTACAGCTGAGTACAAAAAGTGGCGACGTTATAATGTCACTAAAGCTCTTGGT
ACTTCTAACATTTTAGATACGAAAAGTGAATTAGATATACTAGAATGGTCAACAAATGAT
AATTTGTTGATGTTATCAGATAATATGTCCAGTGATACATTGTTTTCATCGATTTCACAA
TTTCCATTTCCTGATTCTCGAGAAATTGCACGTGCTGGACGAGCGGATTTTATTCAACCA
AGTTTAGGCCCATTGCAGCCATGCAACTTTGATGATTTTATGGATTTTGATATAGATATT
TTAAATAGTTTAACAAATAATCGTTTAGCACCAGTACAAGAAGTTCCAGAAACTGAGGAA
CTACTGAAAGCTATCGAGTTTCCTATGATAGCTTCAATAGACACGATGCAGGATATAATG
AATTCAAATTCTTCAACACAACAAAGTGTGATACAACAAGCAAATTCATCGCAAATGAAT
GTAGATCAGCAAGGCACTTCAAATAATGGACAATTGTTATTTACTGCAACAATTTTTACA
CAAGACATGTCACAATCTGGAGGTGGTAATCAGCAAATCATGTCACAAAACAATGATTCA
TCATCGATAATGTCAGAGCTAAATTCATTTATTAATGCTAATGATATGGATATGAGTCAT
CAAGCACAACAAGCCCCCAATAATGAACATTTGATGGCACCCCCAACTGAACCTGATGTC
AAAGATGCATATAAAGGAAAATTTTCACGAAACAATTGGAAAGCTCAATTACCAAAACGT
GAGCCACACAATTATGATAAAGTTCAAAATACTGCTCATCAAACTACTTTTTATAATCAA
ATGCTTGCACAACAGCAACAACAAGCCCCTGCACCTTCTGCTCAAATGTACAACACAAAT
CATCCTTATGGAAATATGACTGATGTAAATCATATGTCACCGATTCAGACGACTACGAAT
AATTTTAATGTGTCACAAAGTGTACTAAACTTATCAAATTCGCAAATTTATGCCAAAAAT
TTGCTTATGCAGCAACAACAAAACTTGCAAAACCAAATGAATATTGAACAACAACAACAG
CAGCAAACAATGAGCACAACGCATGATAACAGTAGCAGTAATTATAAATCCCCACAGAGC
CCATCATTTAGATCTTATCACCATAGTAATCAGCAACCATATAAAATCCCATCACAGAAT
TCTGGTTACAATGCCACAAGTCGCATAATTATGCGCCAACAATCTCCACCTCATCAAATG
AGTGGCCAAGTATGCAAATCAATGTCTTTTCAACAGCAGCAGCAACAACAGCAGAATGCC
ACAGCAGCAGCAATCAAAGAAATGTATCGTTCAAATAGTTTACCAATAAATGCCAATATT
CAATTACCAAAGGATATAATAAATAATACATGCGAGAATTTTGTTATTCCAAAATATCCA
AATGCATCCGCTGCGACAATGTCGTCGTCAGCGGTAAAGGGACGAAATTCGAGATCGCGC
AGTAATTCAATCAATTTACGTCATAATCAATTGATTATGACCCCAATTCAATCAGCAACA
AGTGAACCAACATTAAATGCAAGCAGTGCCTTGGCTCAATTATTAACAAACTCGTCAAAT
ACGAGTTTAATTGGACAAAAAGCTCATAGTATCTCATCAAGTGCCATGTCAATTCAACAG
CAACAACAACAAATTCAACCACAAAGAGCTAATAGTTTCACTTCATCTTCATTAGTACAA
AATTCAATTTTGATGGCAGTTTCATCTGCTGCTGCAAACAATAAACAAGTTGCTACTAGC
AGCACATCATCTACTCCAATGTATCAAACACCAACTTTATCGCCTGAATCAACATATCAT
GAAGGTGGAAATTCTCAACATGAAACGCCATCATTATCACCAGAACGATGCATCAGTATC
GGAAAATATTCGTCATCACGTGAGAATAATAATCGACGAGCTGGTCACATTCACGCAGAA
CAAAAACGACGTTACAACATTAAAAACGGTTTTGATATGCTCCATAGTTTAATTCCACAA
CTACAACAAAATCCTAATGCAAAATTAAGTAAAGCAGCAATGCTCCAAAAAGGTGCTGAT
TATATTAAACAGTTAAGGTCTGAACGATCAGCTATTACAGAACAAATGGAAGGACTTAGA
AAAGAAATCGAGACTTTGACAAATTCGTTAAATCATTTGCAAAATGCATTACCAGCAAAT
GGTGCACCAGTTAGTCGTCAACGAACAGGAAGAACTCGCGAAATGTATCAAGATTATGTA
ATGCAGAGGACACAAAATAATTGGAAGTTTTGGATTTTTGGTCTCATTTGTGAACCTCTA
TTAAACACGTTCAATACAACTGTATCAACCGCAAGTATGGATGAATTATATCGCACTACA
ATGTTGTGGATTGATAACAGCTGTTCCCTTGCAACAATACGACCAGCTGTTTCAAATAAA
CTTCGAGAACTATCAACGACAACGGATATTCTCTCTGATAATCCAACAACATTGCAAGAG
GAAGTAAAGAAAGCTGTGCAGAATGCAACAAGGAATTCAAGAGATCAAAGTCCTAGATAA

>g12005.t1 Gene=g12005 Length=899
MQFILKKRPSVCQFASPLDVDLHNTPQAIILEGKYWKRKWKVITAEYKKWRRYNVTKALG
TSNILDTKSELDILEWSTNDNLLMLSDNMSSDTLFSSISQFPFPDSREIARAGRADFIQP
SLGPLQPCNFDDFMDFDIDILNSLTNNRLAPVQEVPETEELLKAIEFPMIASIDTMQDIM
NSNSSTQQSVIQQANSSQMNVDQQGTSNNGQLLFTATIFTQDMSQSGGGNQQIMSQNNDS
SSIMSELNSFINANDMDMSHQAQQAPNNEHLMAPPTEPDVKDAYKGKFSRNNWKAQLPKR
EPHNYDKVQNTAHQTTFYNQMLAQQQQQAPAPSAQMYNTNHPYGNMTDVNHMSPIQTTTN
NFNVSQSVLNLSNSQIYAKNLLMQQQQNLQNQMNIEQQQQQQTMSTTHDNSSSNYKSPQS
PSFRSYHHSNQQPYKIPSQNSGYNATSRIIMRQQSPPHQMSGQVCKSMSFQQQQQQQQNA
TAAAIKEMYRSNSLPINANIQLPKDIINNTCENFVIPKYPNASAATMSSSAVKGRNSRSR
SNSINLRHNQLIMTPIQSATSEPTLNASSALAQLLTNSSNTSLIGQKAHSISSSAMSIQQ
QQQQIQPQRANSFTSSSLVQNSILMAVSSAAANNKQVATSSTSSTPMYQTPTLSPESTYH
EGGNSQHETPSLSPERCISIGKYSSSRENNNRRAGHIHAEQKRRYNIKNGFDMLHSLIPQ
LQQNPNAKLSKAAMLQKGADYIKQLRSERSAITEQMEGLRKEIETLTNSLNHLQNALPAN
GAPVSRQRTGRTREMYQDYVMQRTQNNWKFWIFGLICEPLLNTFNTTVSTASMDELYRTT
MLWIDNSCSLATIRPAVSNKLRELSTTTDILSDNPTTLQEEVKKAVQNATRNSRDQSPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12005.t1 CDD cd11405 bHLHzip_MLXIP_like 691 763 7.62932E-36
9 g12005.t1 Coils Coil Coil 379 402 -
8 g12005.t1 Coils Coil Coil 742 776 -
7 g12005.t1 Gene3D G3DSA:4.10.280.10 HLH 703 777 1.1E-20
12 g12005.t1 MobiDBLite mobidb-lite consensus disorder prediction 393 435 -
14 g12005.t1 MobiDBLite mobidb-lite consensus disorder prediction 637 675 -
13 g12005.t1 MobiDBLite mobidb-lite consensus disorder prediction 872 899 -
3 g12005.t1 PANTHER PTHR15741:SF32 LD38259P 1 355 1.7E-98
5 g12005.t1 PANTHER PTHR15741 BASIC HELIX-LOOP-HELIX ZIP TRANSCRIPTION FACTOR 1 355 1.7E-98
2 g12005.t1 PANTHER PTHR15741:SF32 LD38259P 246 872 1.7E-98
4 g12005.t1 PANTHER PTHR15741 BASIC HELIX-LOOP-HELIX ZIP TRANSCRIPTION FACTOR 246 872 1.7E-98
1 g12005.t1 Pfam PF00010 Helix-loop-helix DNA-binding domain 692 746 3.4E-13
15 g12005.t1 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 691 745 15.224
11 g12005.t1 SMART SM00353 finulus 697 751 6.4E-12
6 g12005.t1 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 689 774 3.01E-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:0046983 protein dimerization 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