General information for g12506.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12506 is located on chr_1: 24093277..24094576 (- 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_1 | g12506 | g12506.t4 | isoform | g12506.t4 | 24091912 | 24094576 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon1 | 24091912 | 24092421 |
| chr_1 | g12506 | g12506.t4 | cds | g12506.t4.CDS1 | 24091913 | 24092421 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon2 | 24092717 | 24092860 |
| chr_1 | g12506 | g12506.t4 | cds | g12506.t4.CDS2 | 24092717 | 24092860 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon3 | 24093276 | 24093337 |
| chr_1 | g12506 | g12506.t4 | cds | g12506.t4.CDS3 | 24093276 | 24093337 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon4 | 24093409 | 24093457 |
| chr_1 | g12506 | g12506.t4 | cds | g12506.t4.CDS4 | 24093409 | 24093457 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon5 | 24093691 | 24093844 |
| chr_1 | g12506 | g12506.t4 | cds | g12506.t4.CDS5 | 24093691 | 24093748 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon6 | 24093966 | 24094055 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon7 | 24094112 | 24094247 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon8 | 24094305 | 24094466 |
| chr_1 | g12506 | g12506.t4 | exon | g12506.t4.exon9 | 24094537 | 24094576 |
| chr_1 | g12506 | g12506.t4 | TSS | g12506.t4 | 24094597 | 24094597 |
| chr_1 | g12506 | g12506.t4 | TTS | g12506.t4 | NA | NA |
Sequences
>g12506.t4 Gene=g12506 Length=1347
ATGAATAGACTTAACTTTGTTACTTTCTTTCTCATTTTGGGGAACAACTTAATTTATATT
GATGCAGTTCCACCTTGCAATGATCCACCACTATGCCAAGAACTTATGGTTCTTGATCCA
GCACAATGTAAATGTGTTTGTGTAGATAATAGTGGAAGCAAACCTTGTCCACTTCCTTTT
CCAACAGATTTTCCATGTCCATGTATTCAAGGACTTTCTACTGTAAATTCTACTACTGCT
GCTCCAGTTGCAACAATTGGTGCTCAAACAATTGGACCTGTTGTCATAAGTCCTTGTAAA
GTTAAACCAATAGCTTGTCCACCACCAAAAACATTTTGGGATTCAAATTCATGCAAATGT
ATCTGCGATCCAGGAGTCGATTGTCTTCATCCAACTTTTGTAATGAATCCAGACACTTGT
CTTTGTAAGTGAATGTGCAATTAAACCAACAACACCATGTCCATCAAATCAATTTTTTAA
TCCTGCAACATGTAAATGTCAATGCAAAGACAATTGTTTGGGTAATGAATCAATCATGTG
TGTTAAACCGCAAGTTTGGTCAGAAGACTCTTGTACTTGTAAGTAATTGTCCAAGTCCAA
ATACGCAAATTTGTAAATCTAATAAATATTGGGATTTTGATACTTGTAACTGTGAATGCA
AAAATAAACAAAAAACTTGTTGTAAACCAAAAATATGGGATCCAACCAGCTGTCAATGTA
TTTGTCCATTTATACAAGCATGTAAAGCACCTTTCATTTGGAGCGATGATTTATGCCAAT
GTGTTTGCAAACAGATAGTTTCATGTAAACCACCACTTGTATGGAATCCAAAACTCTGCA
AATGTACATGTCCACCAATAGATTGTCCACCTAATTTCATGCAAAATCCTTTTACTTGTC
AATGTATGTGCAATCAAGCAATGTCAAAAACTTGTGATACGTCAATTCAAGTGTGGAATC
CAAAAAAATGTCAATGCGATTGCAAATTTCCAGTTGATTGCATACCAAACTACATTTTTA
ATCCAAAAACATGTAAATGTGAATGCAACCAAGCTCTTTCTACATCTTGTAAGCCACCAT
TATCAATTTGGGATAAGACAAAATGTAAATGTGTTTGCAACATTGATTGTGCACCAAATT
ATATTCTTAATGAAGCAACTTGCAGTTGTGATTGCAATAAAGAACTTGTGTTATCTACTT
GTGATCTCAACACTCATGTTTTTAATCCTGATAAATGTTCGTGTGATTGCAAACCAATTG
TATGCCCTCCCAACTTTATTCAAAATCCTAAGACATGCAAATGTGACTGTGCACTTACTC
AAGCTAGCTGTCCAGCTCCTCAAATTT
>g12506.t4 Gene=g12506 Length=274
MNQSCVLNRKFGQKTLVLVSNCPSPNTQICKSNKYWDFDTCNCECKNKQKTCCKPKIWDP
TSCQCICPFIQACKAPFIWSDDLCQCVCKQIVSCKPPLVWNPKLCKCTCPPIDCPPNFMQ
NPFTCQCMCNQAMSKTCDTSIQVWNPKKCQCDCKFPVDCIPNYIFNPKTCKCECNQALST
SCKPPLSIWDKTKCKCVCNIDCAPNYILNEATCSCDCNKELVLSTCDLNTHVFNPDKCSC
DCKPIVCPPNFIQNPKTCKCDCALTQASCPAPQI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g12506.t4 | PANTHER | PTHR11633:SF1 | LD28763P | 22 | 69 | 0.000 |
| 7 | g12506.t4 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 22 | 69 | 0.000 |
| 5 | g12506.t4 | PANTHER | PTHR11633:SF1 | LD28763P | 73 | 139 | 0.000 |
| 9 | g12506.t4 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 73 | 139 | 0.000 |
| 4 | g12506.t4 | PANTHER | PTHR11633:SF1 | LD28763P | 119 | 200 | 0.000 |
| 8 | g12506.t4 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 119 | 200 | 0.000 |
| 6 | g12506.t4 | PANTHER | PTHR11633:SF1 | LD28763P | 140 | 220 | 0.000 |
| 10 | g12506.t4 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 140 | 220 | 0.000 |
| 1 | g12506.t4 | Pfam | PF03128 | CXCXC repeat | 55 | 67 | 0.004 |
| 2 | g12506.t4 | Pfam | PF03128 | CXCXC repeat | 164 | 174 | 0.013 |
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 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