Gene loci information

Transcript annotation

  • This transcript has been annotated as Host cell 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_4 g16840 g16840.t4 TSS g16840.t4 11359129 11359129
chr_4 g16840 g16840.t4 isoform g16840.t4 11359595 11361437
chr_4 g16840 g16840.t4 exon g16840.t4.exon1 11359595 11360084
chr_4 g16840 g16840.t4 cds g16840.t4.CDS1 11360065 11360084
chr_4 g16840 g16840.t4 exon g16840.t4.exon2 11360666 11360801
chr_4 g16840 g16840.t4 cds g16840.t4.CDS2 11360666 11360801
chr_4 g16840 g16840.t4 exon g16840.t4.exon3 11360871 11360909
chr_4 g16840 g16840.t4 cds g16840.t4.CDS3 11360871 11360909
chr_4 g16840 g16840.t4 exon g16840.t4.exon4 11360966 11361378
chr_4 g16840 g16840.t4 cds g16840.t4.CDS4 11360966 11361378
chr_4 g16840 g16840.t4 exon g16840.t4.exon5 11361436 11361437
chr_4 g16840 g16840.t4 cds g16840.t4.CDS5 11361436 11361436
chr_4 g16840 g16840.t4 TTS g16840.t4 NA NA

Sequences

>g16840.t4 Gene=g16840 Length=1080
ATGTTAAAGTGGAAGAAAGTTACAAACACTTCAGGCCCACAGCCGAGGTAAAAAAAAACA
AAATACGGGCCGAAAAAAATTTATTTTAAAAAAATATTTTAATTTTTAGACCACGGCATG
GACATCGCGCCGTTGCTATACGTGAACTTATGGTGGTCTTTGGTGGCGGCAATGAAGGAA
TTGTGGATGAACTTCATGTCTACAACACATGTAAGTACATGCCTGCATTTGTATGTGTGT
AATATTTTTTTTTGTATTAGTCAATTGAGGACGCCATTGGCCCGGCTTGTCATTCTCGGT
CGTTCTATCAACCCGGCCAACCATTGTTGTTGTTTCACACTGATGGAATTTTAGAAGAAA
AAAAATATTTTTTTTGTATGACTTGAAGAAAAAAATTTTCTTCTTTTTAAGCGACTTTTT
ACTATTCGTTGTGTGTTACGAGCGTAAAAATTTGCATGTTATGGTGAATGATGTATGAGA
GAAAAGAACGGTATGTGCCAGCAACAAAAGGAGAAGTGCCACCAGGATGTGCAGCTTATG
GATTTGTTGTTGATGGAACAAGAATTTTAATTTTTGGTGGCATGGTTGAATATGGAAAAT
ATTCAAATGACCTTTTTGAACTTCAAGCTACAAAATGGGAATGGAAAAAAATTCGACCAC
AAGCTCCATTTTCTGGAGATGCTCCATGTCCACGTTTAGGCCATTCATTTACACTTGTTG
GTGACAAAGTTTTTCTATTTGCTGGTCTAGCAAATGAGTCAGATGATCCAAAACACAATA
TCCCAAAATATCTCAATGACCTTTACATCCTAAATACAAAAAATGGCAATTACAGTTGGG
AAATACCAATAACATATGGAGAATGTCCACCACCTCGAGAATCACATACAGCAATAGCAT
GGAATGACAAATCAACTGGTCGCAATTATTTAGTCATTTATGGTGGCATGAGTGGTTGTC
GTTTGGGTGATTTGTGGATTCTCGATATTGAAACGCTCTCATGGAGCAAACCAAAGTGCT
CTGGAACACCACCATTACCTCGATCATTGCATTCAGCAACATTAATTAATGACAAAATGT

>g16840.t4 Gene=g16840 Length=203
MYERKERYVPATKGEVPPGCAAYGFVVDGTRILIFGGMVEYGKYSNDLFELQATKWEWKK
IRPQAPFSGDAPCPRLGHSFTLVGDKVFLFAGLANESDDPKHNIPKYLNDLYILNTKNGN
YSWEIPITYGECPPPRESHTAIAWNDKSTGRNYLVIYGGMSGCRLGDLWILDIETLSWSK
PKCSGTPPLPRSLHSATLINDKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16840.t4 Gene3D G3DSA:2.120.10.80 - 3 203 0.0e+00
4 g16840.t4 PANTHER PTHR46003 HOST CELL FACTOR 5 203 0.0e+00
5 g16840.t4 PANTHER PTHR46003:SF1 HOST CELL FACTOR 5 203 0.0e+00
1 g16840.t4 Pfam PF13854 Kelch motif 16 52 1.8e-05
2 g16840.t4 Pfam PF13418 Galactose oxidase, central domain 74 123 1.5e-05
3 g16840.t4 Pfam PF13415 Galactose oxidase, central domain 152 199 3.9e-05
6 g16840.t4 SUPERFAMILY SSF117281 Kelch motif 14 203 0.0e+00

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: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. There were no conditions that were differentially expressed