Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein SMG5.

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 g5201 g5201.t2 TSS g5201.t2 7627601 7627601
chr_2 g5201 g5201.t2 isoform g5201.t2 7627787 7629164
chr_2 g5201 g5201.t2 exon g5201.t2.exon1 7627787 7627818
chr_2 g5201 g5201.t2 cds g5201.t2.CDS1 7627787 7627818
chr_2 g5201 g5201.t2 exon g5201.t2.exon2 7628086 7629164
chr_2 g5201 g5201.t2 cds g5201.t2.CDS2 7628086 7629163
chr_2 g5201 g5201.t2 TTS g5201.t2 7629844 7629844

Sequences

>g5201.t2 Gene=g5201 Length=1111
ATGGAAAATTCAGAATTGAAAGCAAAAACAAAGAATGTTTATCAGATAATTAAAGCACTG
GATGAGCATAAACAAACATCAAAAACAATTTCATCGCTATTCAGTGACATTGGAGTAGAG
GTCTTACGCAAGAAACTTGTAATTTTAATAGAATCAATTTTGTTAGAGGATTTTGAGACC
ATCGGGAAGAAAACAAGAGATATATTATGGCGAAAAATGTATTACGATCCAATTTCAACA
TCAAAAAAATTATGGAAGAAGAGTGAAAGGGAGTTGACTGACTCGGAAGCGACTGTTTTA
TATGAGTTTATCAAAAGTGGGATAAAGCACTACAAGACATTGATTCTTAAATTTGAAGAT
ATTTTCAATCTTGATATACGCTACATCATTGACTTTAGTATCATCGCTAATGGTGCTGAT
CCTTTTGAGAAACGCAGTGAAAAAGAAATTTATACAGTGAATGAGACGAATCATGCAATT
GAGACTATACATAACTTTTTAATCAGTCTCGGTGACCTTCATCGTTATTGCATTGAATTT
AAATTTGCTGAAAGAGAAAAATTTTTAGCATGTGGCAATAAACAACTTGCTGCTAGCTAC
TACATTGAGGCGTTCAAGTTAAATCCAAAAGTTGGAATGCCACATAATCAACTTGGAACA
TTGTTGTCTGGTGAAAATTATGAGATTGATTCAATTTTTCACTATCTTTATTCACTTTGT
TCACCTATTCCCGTTGAATTGAGTGAAGCAAATGTCAGCAAAATTTTTCAACAAAATAAC
GAAATGCTTGTCACTATAGAGCCTTCTTGCGATGGATTTAACATTCGAGACTTTATGATG
CAAGTTATTCTTCTCATTGACATTTTTTTCTACGATAAAGAAATTGTTGACTTTAATTCG
ATCTGCTTTAGTGTTCTTTTGAATTTTAAAGATTATTTAATCAAATGCAATCGCAACTCA
CAATCTGATGTTACTTTTCAACTTACATCAATCTTTATGCTTTGCTTATTAAAGCTCAAA
CGAAATAATTCTCCAAAGGTTCAGTGCTTGAATGCCTTTCTTGTAGCATTTTGTGCAAAA
ATTGTTGATATTGTCATTGAGAAAATTGACG

>g5201.t2 Gene=g5201 Length=370
MENSELKAKTKNVYQIIKALDEHKQTSKTISSLFSDIGVEVLRKKLVILIESILLEDFET
IGKKTRDILWRKMYYDPISTSKKLWKKSERELTDSEATVLYEFIKSGIKHYKTLILKFED
IFNLDIRYIIDFSIIANGADPFEKRSEKEIYTVNETNHAIETIHNFLISLGDLHRYCIEF
KFAEREKFLACGNKQLAASYYIEAFKLNPKVGMPHNQLGTLLSGENYEIDSIFHYLYSLC
SPIPVELSEANVSKIFQQNNEMLVTIEPSCDGFNIRDFMMQVILLIDIFFYDKEIVDFNS
ICFSVLLNFKDYLIKCNRNSQSDVTFQLTSIFMLCLLKLKRNNSPKVQCLNAFLVAFCAK
IVDIVIEKID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g5201.t2 PANTHER PTHR15696:SF7 PROTEIN SMG5 15 369 0
4 g5201.t2 PANTHER PTHR15696 SMG-7 SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN 7 15 369 0
1 g5201.t2 Pfam PF10374 Telomerase activating protein Est1 64 180 0
2 g5201.t2 Pfam PF10373 Est1 DNA/RNA binding domain 197 369 0
5 g5201.t2 SUPERFAMILY SSF48452 TPR-like 11 361 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5201/g5201.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5201.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein 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