Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S9.

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 g7115 g7115.t1 TTS g7115.t1 21263047 21263047
chr_2 g7115 g7115.t1 isoform g7115.t1 21263156 21266725
chr_2 g7115 g7115.t1 exon g7115.t1.exon1 21263156 21263254
chr_2 g7115 g7115.t1 cds g7115.t1.CDS1 21263156 21263254
chr_2 g7115 g7115.t1 exon g7115.t1.exon2 21263795 21263831
chr_2 g7115 g7115.t1 cds g7115.t1.CDS2 21263795 21263831
chr_2 g7115 g7115.t1 exon g7115.t1.exon3 21264028 21264446
chr_2 g7115 g7115.t1 cds g7115.t1.CDS3 21264028 21264446
chr_2 g7115 g7115.t1 exon g7115.t1.exon4 21264852 21264902
chr_2 g7115 g7115.t1 cds g7115.t1.CDS4 21264852 21264902
chr_2 g7115 g7115.t1 TSS g7115.t1 21264887 21264887
chr_2 g7115 g7115.t1 exon g7115.t1.exon5 21265141 21266250
chr_2 g7115 g7115.t1 cds g7115.t1.CDS5 21265141 21266250
chr_2 g7115 g7115.t1 exon g7115.t1.exon6 21266304 21266443
chr_2 g7115 g7115.t1 cds g7115.t1.CDS6 21266304 21266443
chr_2 g7115 g7115.t1 exon g7115.t1.exon7 21266530 21266725
chr_2 g7115 g7115.t1 cds g7115.t1.CDS7 21266530 21266725

Sequences

>g7115.t1 Gene=g7115 Length=2052
ATGGAAGGAAACAAAGAAGGTACAGACAAAAAGGATGAATCTTTAGAGAGTAATGAAAAC
TCACAAGACAGTGAAATCTCTTCAAAAAAATCAGAAAATAGTGATAAAGTTGAAGAAGAG
CAACAACAACAACAGACAGCAAATCCTGATTTAAACGATGAAGATATTGATGAAGATCTT
CAGAAAAAAATTAAGGGTGATGCGATTGGTGATACTCTTTACTCAGAACGATTCATTTTA
AAGACACTGATGGAATTAAAAGATATGGATTATCAGAAATTAGATAAAGAAATGGAATCT
AAACTCGAAATTTTATGGGATACAACTATTGAGAAAGCGGTTGTCGAAGTATTGCTCCAA
TACGGATTTCTTGAAATTGCTGGCATAATATTGGATAGTGCTAGTGATGAACGTTTGATT
GAGATTATGCTCGGTATTATAGCTAATATGGGCTGCATGAGCGAAACTAGAGAACAACTT
TGCGATAATGAGGACGTCATGGCATCTATCCTCAATCAACTTTCTAGTAGTGATCCACTT
ATATTACATCAACTCATGAGGCTATTTCATTCTGCAATTCTGTTTGAAAATAAATGCGAT
GAAAAGATATGGTTTTCTCACTTCCAAAAATGCGAAAACTTCGTTGAAAAGTTCAGTTAT
ATTTTCGCTAATTCAACTAGTAACACATTGCTAACAAGTTCCTTTGAAGCTCTAAATGGT
ATTTGTGCTAAGTTTGCAGCAATTGAATGTCAATCGGATTCAGAGAAAGACTCAAGTTTT
CCACAACTTTTTGTGAAAAAATGCTTAGTAGACTCAATGATTGAAGCATTCAATACTGTC
ATACCACAATTGAATGAAAGTGAATGTGGAAGTAGTAGTAGTACCACAACTGATGTAATA
CCTACTCAAAGCCAAATTAAATTTATGAACCTCTTTCTTGAACTCAATATGGTCATCTCA
CAATATGAATCATTATCGATGGAAGCATACAAAACTTCACTAACCGACTTTCAAAGATGT
TTAAGTAGAATTTTATTTCCTTTATGTCACAAAATGTATCTACTGCCGCTCTCTTCAATT
CATCAAGGGGTCATTGAAAATATAAATGACATCACACAAGCTCTTTCTGATCCATTTGAT
AAGCAAATTTTTTCACAGATGATTCAAATATGGGATCTCATTGAAGAAGACAAAGGAAAA
GATCGATCAAATTCTGATTGGGATGATGAAGAAGATTCTACTTTTATAGACAGCGATGAT
TTTATGGAGAGTATATCAATGACAATTTTAGAATTTTTAACACGAACCGGATTCAATGCT
GAACAAGAGAATTTCACTGCATCACTTAAGAAATTAAATTTAGATTTAGTGATGAAGCTT
TTTGAGCGGATTAATGATAATGACGATCCCGAAGATGAAATTAAATCTGTTATACAGAAA
ATGAAACGCGATTTTCTCTTTCTTTTCGAAAAATTCTTGCAAAAAGAATTTTGTCAAGTT
TTCATCATGGTTAATCACAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGA
CGTCCATATGAAAAACCTCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTC
CGTAACAAGCGTGAGGTATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCT
CGTGAATTGCTTACACTTGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTT
CTTCGTCGTCTTGTTCGTATTGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTT
CTTGGTTTAAAAATTGAAGATTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTC
GGTTTGGCTAAATCTTATCATCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGTT
CGTAAACAAGTCGTCAACATCCCATCATTTGTCTCACCATTCGGTGGTGGACGACCAGGT
CGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGAAGAA
GAAGAGGATTAA

>g7115.t1 Gene=g7115 Length=683
MEGNKEGTDKKDESLESNENSQDSEISSKKSENSDKVEEEQQQQQTANPDLNDEDIDEDL
QKKIKGDAIGDTLYSERFILKTLMELKDMDYQKLDKEMESKLEILWDTTIEKAVVEVLLQ
YGFLEIAGIILDSASDERLIEIMLGIIANMGCMSETREQLCDNEDVMASILNQLSSSDPL
ILHQLMRLFHSAILFENKCDEKIWFSHFQKCENFVEKFSYIFANSTSNTLLTSSFEALNG
ICAKFAAIECQSDSEKDSSFPQLFVKKCLVDSMIEAFNTVIPQLNESECGSSSSTTTDVI
PTQSQIKFMNLFLELNMVISQYESLSMEAYKTSLTDFQRCLSRILFPLCHKMYLLPLSSI
HQGVIENINDITQALSDPFDKQIFSQMIQIWDLIEEDKGKDRSNSDWDDEEDSTFIDSDD
FMESISMTILEFLTRTGFNAEQENFTASLKKLNLDLVMKLFERINDNDDPEDEIKSVIQK
MKRDFLFLFEKFLQKEFCQVFIMVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGL
RNKREVWRVKYTLAKIRKAARELLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYV
LGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIRVRKQVVNIPSFVSPFGGGRPG
RVKRKNMKKGQGGSGGADEEEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t1 CDD cd00165 S4 611 650 2.67597E-6
5 g7115.t1 Gene3D G3DSA:3.10.290.10 - 612 655 8.6E-9
10 g7115.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 39 -
11 g7115.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
9 g7115.t1 MobiDBLite mobidb-lite consensus disorder prediction 657 683 -
2 g7115.t1 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 510 683 5.7E-80
3 g7115.t1 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 510 683 5.7E-80
1 g7115.t1 Pfam PF01479 S4 domain 611 650 1.9E-7
7 g7115.t1 ProSitePatterns PS00632 Ribosomal protein S4 signature. 609 633 -
8 g7115.t1 SMART SM01390 Ribosomal_S4_2 506 610 2.3E-17
4 g7115.t1 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 514 650 1.7E-30
12 g7115.t1 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 513 651 3.6E-58

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:0003723 RNA binding MF
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0015935 small ribosomal subunit CC
GO:0019843 rRNA binding 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