General information for g4130.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein spaetzle.
Parent gene
- The parent gene g4130 is located on chr_3: 30817473..30818103 (- 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_3 | g4130 | g4130.t1 | TTS | g4130.t1 | 30816231 | 30816231 |
| chr_3 | g4130 | g4130.t1 | isoform | g4130.t1 | 30817172 | 30818103 |
| chr_3 | g4130 | g4130.t1 | exon | g4130.t1.exon1 | 30817172 | 30817421 |
| chr_3 | g4130 | g4130.t1 | cds | g4130.t1.CDS1 | 30817172 | 30817421 |
| chr_3 | g4130 | g4130.t1 | exon | g4130.t1.exon2 | 30817473 | 30817813 |
| chr_3 | g4130 | g4130.t1 | cds | g4130.t1.CDS2 | 30817473 | 30817813 |
| chr_3 | g4130 | g4130.t1 | exon | g4130.t1.exon3 | 30817874 | 30817939 |
| chr_3 | g4130 | g4130.t1 | cds | g4130.t1.CDS3 | 30817874 | 30817939 |
| chr_3 | g4130 | g4130.t1 | exon | g4130.t1.exon4 | 30818062 | 30818103 |
| chr_3 | g4130 | g4130.t1 | cds | g4130.t1.CDS4 | 30818062 | 30818103 |
| chr_3 | g4130 | g4130.t1 | TSS | g4130.t1 | 30818292 | 30818292 |
Sequences
>g4130.t1 Gene=g4130 Length=699
ATGAAAATATTATTGTTTTTGCTCGTGTTTTTATTTGAAGAACTTCTGGCAAGTCCGGTA
GCACAAAATCATGCCTCTTTTTATAACTATGGCACGAATACACGTAATCCTTATCCATAC
TATATTCAAAATCAGACATATGCGAGGAAAATTGATGTCTTCGATCCAGCACAACAAAGA
CCATGTACAGAAAAATTCTGTACTGACTACGCTGACTATCCTAAAGATTACATTCAATCA
TTAAATCTCGAAAAGTATGAACACTTGTTTGTAGACGATTTTATTGACACAATCTCAACA
AGATTTGATGCTGATGAAAATGGTTTGTGCCAAAGTCGTAAAAGATTAATTCATCCTAAG
CGGGGTGTCACAGCACAAGGCACATGGCTCACGATTGTAAATAACGACGATAGTAAATAT
AGACAAGGAATATTAATTGAAGAATGCTCAAGTCAAAACCAACCATGTGATTATGCTCAA
AATTTCCCACTGAGCGTTGATTCAAAATGCAAGCAGAGTTTTATTTATAGAAGTTTACTT
GCAATCAATATTGATGGGCGTCCTGTTATGGAACATTTTCAATTTCCTTCATGTTGTAAA
TGTGTCGTGACAATTGGACATGGACATCGATCTAATACAAATCGCTTTGGTGTCGAAGAA
AAACAAAAAGCGGATCCTCCTCTTGTATATCCAAATTAG
>g4130.t1 Gene=g4130 Length=232
MKILLFLLVFLFEELLASPVAQNHASFYNYGTNTRNPYPYYIQNQTYARKIDVFDPAQQR
PCTEKFCTDYADYPKDYIQSLNLEKYEHLFVDDFIDTISTRFDADENGLCQSRKRLIHPK
RGVTAQGTWLTIVNNDDSKYRQGILIEECSSQNQPCDYAQNFPLSVDSKCKQSFIYRSLL
AINIDGRPVMEHFQFPSCCKCVVTIGHGHRSNTNRFGVEEKQKADPPLVYPN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4130.t1 | Gene3D | G3DSA:2.10.90.10 | - | 102 | 211 | 3.7E-33 |
| 2 | g4130.t1 | PANTHER | PTHR23199:SF4 | PROTEIN SPAETZLE | 36 | 204 | 4.1E-35 |
| 3 | g4130.t1 | PANTHER | PTHR23199 | UNCHARACTERIZED | 36 | 204 | 4.1E-35 |
| 1 | g4130.t1 | Pfam | PF16077 | Spaetzle | 109 | 203 | 1.4E-28 |
| 9 | g4130.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 10 | g4130.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 11 | g4130.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 12 | - |
| 12 | g4130.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 8 | g4130.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 232 | - |
| 4 | g4130.t1 | SUPERFAMILY | SSF57501 | Cystine-knot cytokines | 79 | 203 | 1.15E-26 |
| 6 | g4130.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 13 | g4130.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 5 | g4130.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 25 | - |
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 K20694 (protein spaetzle)
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.
