Gene loci information

Transcript annotation

  • This transcript has been annotated as Suppressor of hairless 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_2 g6460 g6460.t1 isoform g6460.t1 17146407 17149523
chr_2 g6460 g6460.t1 exon g6460.t1.exon1 17146407 17146748
chr_2 g6460 g6460.t1 cds g6460.t1.CDS1 17146407 17146748
chr_2 g6460 g6460.t1 exon g6460.t1.exon2 17146972 17147514
chr_2 g6460 g6460.t1 cds g6460.t1.CDS2 17146972 17147514
chr_2 g6460 g6460.t1 exon g6460.t1.exon3 17147572 17148120
chr_2 g6460 g6460.t1 cds g6460.t1.CDS3 17147572 17148120
chr_2 g6460 g6460.t1 exon g6460.t1.exon4 17149236 17149523
chr_2 g6460 g6460.t1 cds g6460.t1.CDS4 17149236 17149523
chr_2 g6460 g6460.t1 TSS g6460.t1 17150264 17150264
chr_2 g6460 g6460.t1 TTS g6460.t1 NA NA

Sequences

>g6460.t1 Gene=g6460 Length=1722
ATGCCTTATGGGATTTCGACTTATGGCCAATCGGCGCAAATAGACTCTCCCTTACAGCAT
ACGGGTGCACTTATTCCACAACATATGGGAGGCACAACAATTTACGCTGGATCAGATAGT
AATAATGGAAGTCCGAGTGCTGTCTCATCAACAGCATTACAGACGACATCACAAGCAGTC
GCAACATCCTCTCTTTTTCGTAATGAAGATAAGCGACTCACACGTGAGGCTATGGAAAAA
TATCTTCGAAATCGCAATGACATGATCATTGTAATTTTACATGCTAAGGTAGCGCAAAAG
TCTTATGGCAACGAGAAAAGATTTTTTTGTCCACCACCATGTATTTATCTTTTTGGTGAT
GGTTGGCGGCTTAGACAGGAGCAAATGTTACGAAAAGGCGAAAGTGAGCAAGGCTCACAA
TTATGTGCCTTTATTGGAATAGGCAATTCAGATCATGATATGCAACAACTGGACCTCAAT
AATGGAAAACAGTACTGTGCCGCGAAAACTCTTTTCATCTCAGATTCTGACAAGCGAAAA
CATTTTATGTTGAGTGTAAAAATGTTCTATGGCAATGGCCATGATATTGGACTATTTAAT
TCAAAACGAATCAAAGTCATTTCGAAACCATCGAAAAAGAAACAATCTCTAAAAAATGCT
GATCTCTGTATAGCTAGTGGAACTAAAGTTGCTCTCTTCAATCGACTGCGATCACAAACT
GTCTCAACACGTTATCTTCATGTCGAAAATGGACATTTTCATGCGAGTTCAACGCAATGG
GGTGCATTTACAATTCATCTGCTAGATGACAATGAAAGTGAATCTGAAGAATTTGCGGTT
CGTGATGGATATGTGCATTATGGTGCTACAGTAAAATTAGTATGTAGTGTGACAGGTATG
GCATTACCAAGACTAATTATCAGGAAAGTAGACAAGCAAATGGCTCTGCTAGAGGCAGAT
GATCCAGTATCACAACTTCACAAGTGCGCATTTTACATGAAAGATACAGAACGAATGTAT
CTGTGTTTATCGCAAGAAAAAATTATTCAATTTCAAGCGACACCATGTCCAAAAGAGGCC
AATAAAGAAATGATCAATGATGGCGCATGTTGGACAATCATTTCTACAGATAAAGCAGAA
TATCAATTTTTTGAAGGCATGGGTCCAGTTAGGTCACCTGTAACTCCCGTTCCTGTAGTT
CATTCATTAAATCTCAATGGTGGAGGTGATGTTGCTATGTTGGAATTAACAGGCGATAAT
TTCACTCCTGCCCTTCAAGTATGGTTTGGTGATGTAGAAGCTGAAACAATGTATAGATGT
GCAGAAGCGCTCTTATGTGTCGTTCCAGACATCTCACAATTTCGTGGAGAATGGCTCTGG
GTTCGACAGCCCACCCAAGTGCCTGTTACACTAGTTAGAAATGATGGAATTATCTATGCA
ACAGGCCTCACATTCACATACACACCCGAACCTGGACCACGACAGCATTATGGTCAAGCA
GATGAAGTCATGAGAGCATCACAAAATCGTACGCGAACAGAAAATTCCGCAAATAATAAC
AATAATAGTCCAAGTAATACTGCAAATCATAATCCAAGTAGTAATAGTAGTAGCACACCA
TCAACAGCTACAATGTCACCAGTAAGTCTCAATCAAAGCTACTCATCACTACCATCAATC
TCAGAAATGTCATCATGGAATATGCATAGTGGACTTCAATAG

>g6460.t1 Gene=g6460 Length=573
MPYGISTYGQSAQIDSPLQHTGALIPQHMGGTTIYAGSDSNNGSPSAVSSTALQTTSQAV
ATSSLFRNEDKRLTREAMEKYLRNRNDMIIVILHAKVAQKSYGNEKRFFCPPPCIYLFGD
GWRLRQEQMLRKGESEQGSQLCAFIGIGNSDHDMQQLDLNNGKQYCAAKTLFISDSDKRK
HFMLSVKMFYGNGHDIGLFNSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQT
VSTRYLHVENGHFHASSTQWGAFTIHLLDDNESESEEFAVRDGYVHYGATVKLVCSVTGM
ALPRLIIRKVDKQMALLEADDPVSQLHKCAFYMKDTERMYLCLSQEKIIQFQATPCPKEA
NKEMINDGACWTIISTDKAEYQFFEGMGPVRSPVTPVPVVHSLNLNGGGDVAMLELTGDN
FTPALQVWFGDVEAETMYRCAEALLCVVPDISQFRGEWLWVRQPTQVPVTLVRNDGIIYA
TGLTFTYTPEPGPRQHYGQADEVMRASQNRTRTENSANNNNNSPSNTANHNPSSNSSSTP
STATMSPVSLNQSYSSLPSISEMSSWNMHSGLQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g6460.t1 CDD cd01176 IPT_RBP-Jkappa 393 489 2.00152E-67
12 g6460.t1 Gene3D G3DSA:2.60.40.1450 - 73 396 6.9E-173
10 g6460.t1 Gene3D G3DSA:2.80.10.50 - 218 375 6.9E-173
11 g6460.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 398 491 4.6E-41
9 g6460.t1 MobiDBLite mobidb-lite consensus disorder prediction 507 546 -
3 g6460.t1 PANTHER PTHR10665 RECOMBINING BINDING PROTEIN SUPPRESSOR OF HAIRLESS 45 495 1.2E-206
1 g6460.t1 Pfam PF09271 LAG1, DNA binding 90 221 4.5E-46
2 g6460.t1 Pfam PF09270 Beta-trefoil DNA-binding domain 249 371 1.8E-62
8 g6460.t1 SMART SM01267 LAG1_DNAbind_2 89 221 3.1E-86
7 g6460.t1 SMART SM01268 BTD_2 222 371 8.6E-94
6 g6460.t1 SUPERFAMILY SSF49417 p53-like transcription factors 72 221 3.23E-61
5 g6460.t1 SUPERFAMILY SSF110217 DNA-binding protein LAG-1 (CSL) 219 376 1.29E-66
4 g6460.t1 SUPERFAMILY SSF81296 E set domains 377 489 2.42E-40

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:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific MF
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding MF
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