General information for g17518.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17518 is located on chr_4: 13770769..13773465 (- strand)
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 | g17518 | g17518.t1 | TTS | g17518.t1 | 13770594 | 13770594 |
| chr_4 | g17518 | g17518.t1 | isoform | g17518.t1 | 13770769 | 13773465 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon1 | 13770769 | 13771033 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS1 | 13770769 | 13771033 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon2 | 13771093 | 13771344 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS2 | 13771093 | 13771344 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon3 | 13771406 | 13771588 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS3 | 13771406 | 13771588 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon4 | 13771645 | 13771827 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS4 | 13771645 | 13771827 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon5 | 13771879 | 13772127 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS5 | 13771879 | 13772127 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon6 | 13772185 | 13772245 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS6 | 13772185 | 13772245 |
| chr_4 | g17518 | g17518.t1 | exon | g17518.t1.exon7 | 13773405 | 13773465 |
| chr_4 | g17518 | g17518.t1 | cds | g17518.t1.CDS7 | 13773405 | 13773465 |
| chr_4 | g17518 | g17518.t1 | TSS | g17518.t1 | 13773510 | 13773510 |
Sequences
>g17518.t1 Gene=g17518 Length=1254
ATGAGAAAATTAATAATTTTTAACATCATTATGGTTTTTGTGCTTAGTGTTAGTGCAAAA
AAGAATTGGTCTGATGAGAAGAAATGCAGTAAGGTTGAACAATGTGATGCAAAAACTAAA
GTATGGGATGAAGTTTTATGTAAATGCGTTTGTTGGTCTGATGGTTATAAATGTACATCT
GCACAGACATGGAATAATGAAACTTGTCAGTGCGAATGTCCGGGCATTACTTGTCCTGCA
ACAAAAGTTCTTGACAATAAATGCAGATGTTACTGTAAAGAAGATTGCAAAGATAAGAAC
TTGTTTGTACAAGATAAAAATACTTGTGGATGTTCTTGCAGAAAAGTTCAAAAATGTGCG
TTTAATGAAGTTTTCGATAATTTAGATTGCTCATGTAAATGCAATCTTACATGTCCAGCA
AATCAACATTTAGATAAAAATGAGTGTCGTTGTCGCTGCAATTCTGAATGTAGAGATAAA
AATATTTTCATCCAAGATCCAAAAACGTGTGCTTGTAACTGCAGAGAGGTTAAAAGATGT
TTACCAAATGAACATTTTGATGAATCAGAATGTCGATGCAAATGCAATCTTGTTTGTCCA
CCTAATCAATATCTAGATCGAGATTCTTGTGAATGTAAATGCAAAGAAAATTGCTTAAGA
CCACATTTGCATAATCAAGATCCTAACACATGTTGTTGTACTTGTAAAGATGTTAAAACT
TGCAGAGCAGTTGAATACTTTGATAACAAAACTTGCAACTGTCAATGTAAACTTACACCG
TTAGACTGTACAGCTAATCAGATTTTTGATCATCGGACTTGTCAATGTATTTGTAATCCA
AATATTGATTGTCCATGCAAAAAACATGCAGTAATGCCATCATGCGACTGTCAATGTGAA
CAAGGTTGTCCATTTTCTGCTATGGTTCAAAATAATGAAACATGTGATTGTAGATGTCCA
AATGCTACCGCTTGCAATGCTAGACAAATACTTGATGACAACTGCAACTGTGTCTGTGCT
ATTAAAGGAGTTTGTTCAGGTAAACAGCAATGGAATCCTGACTCATGTAGCTGTAGTTGC
AATACAACTTGCGATAATCCTAAAATTCAGGATTCAAATTGCAATTGTGTTTGCGACAAG
AGAGAAAAAGAAAAATGCTTGCATGGCGTAATTTTCAACGTCTGGCATAAAAATAATTGC
TCTTGCTCTTGGTCCTGGGGATTGTTGGGCACATTACTTCCATTTTTGAATTAA
>g17518.t1 Gene=g17518 Length=417
MRKLIIFNIIMVFVLSVSAKKNWSDEKKCSKVEQCDAKTKVWDEVLCKCVCWSDGYKCTS
AQTWNNETCQCECPGITCPATKVLDNKCRCYCKEDCKDKNLFVQDKNTCGCSCRKVQKCA
FNEVFDNLDCSCKCNLTCPANQHLDKNECRCRCNSECRDKNIFIQDPKTCACNCREVKRC
LPNEHFDESECRCKCNLVCPPNQYLDRDSCECKCKENCLRPHLHNQDPNTCCCTCKDVKT
CRAVEYFDNKTCNCQCKLTPLDCTANQIFDHRTCQCICNPNIDCPCKKHAVMPSCDCQCE
QGCPFSAMVQNNETCDCRCPNATACNARQILDDNCNCVCAIKGVCSGKQQWNPDSCSCSC
NTTCDNPKIQDSNCNCVCDKREKEKCLHGVIFNVWHKNNCSCSWSWGLLGTLLPFLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g17518.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 308 | 368 | 4.9E-15 |
| 5 | g17518.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 308 | 368 | 4.9E-15 |
| 3 | g17518.t1 | Pfam | PF03128 | CXCXC repeat | 62 | 73 | 0.021 |
| 2 | g17518.t1 | Pfam | PF03128 | CXCXC repeat | 266 | 278 | 7.1E-4 |
| 9 | g17518.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 10 | g17518.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 11 | g17518.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 12 | g17518.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 19 | - |
| 8 | g17518.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 417 | - |
| 7 | g17518.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 1 | g17518.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 6 | g17518.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 24 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K05449 (vascular endothelial growth factor C/D)
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.
