General information for g12506.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Balbiani ring protein 3.
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.t1 | TTS | g12506.t1 | 24090834 | 24090834 |
| chr_1 | g12506 | g12506.t1 | isoform | g12506.t1 | 24090910 | 24094576 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon1 | 24090910 | 24091145 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS1 | 24090910 | 24091145 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon2 | 24091207 | 24092421 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS2 | 24091207 | 24092421 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon3 | 24092717 | 24092860 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS3 | 24092717 | 24092860 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon4 | 24093276 | 24093337 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS4 | 24093276 | 24093337 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon5 | 24093409 | 24093457 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS5 | 24093409 | 24093457 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon6 | 24093695 | 24093844 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS6 | 24093695 | 24093844 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon7 | 24093970 | 24094055 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS7 | 24093970 | 24094055 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon8 | 24094112 | 24094247 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS8 | 24094112 | 24094247 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon9 | 24094305 | 24094466 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS9 | 24094305 | 24094466 |
| chr_1 | g12506 | g12506.t1 | exon | g12506.t1.exon10 | 24094537 | 24094576 |
| chr_1 | g12506 | g12506.t1 | cds | g12506.t1.CDS10 | 24094537 | 24094576 |
| chr_1 | g12506 | g12506.t1 | TSS | g12506.t1 | 24094597 | 24094597 |
Sequences
>g12506.t1 Gene=g12506 Length=2280
ATGAATAGACTTAACTTTGTTACTTTCTTTCTCATTTTGGGGAACAACTTAATTTATATT
GATGCAGTTCCACCTTGCAATGATCCACCACTATGCCAAGAACTTATGGTTCTTGATCCA
GCACAATGTAAATGTGTTTGTGTAGATAATAGTGGAAGCAAACCTTGTCCACTTCCTTTT
CCAACAGATTTTCCATGTCCATGTATTCAAGGACTTTCTACTGTAAATTCTACTACTGCT
GCTCCAGTTGCAACAATTGGTGCTCAAACAATTGGACCTGTTGTCATAAGTCCTTGTAAA
GTTAAACCAATAGCTTGTCCACCACCAAAAACATTTTGGGATTCAAATTCATGCAAATGT
ATCTGCGATCCAGGAGTCGATTGTCTTCATCCAACTTTTGTAATGAATCCAGACACTTGT
CTTTGTGAATGTGCAATTAAACCAACAACACCATGTCCATCAAATCAATTTTTTAATCCT
GCAACATGTAAATGTCAATGCAAAGACAATTGTTTGGGTAATGAATCAATCATGTGTGTT
AAACCGCAAGTTTGGTCAGAAGACTCTTGTACTTGTAATTGTCCAAGTCCAAATACGCAA
ATTTGTAAATCTAATAAATATTGGGATTTTGATACTTGTAACTGTGAATGCAAAAATAAA
CAAAAAACTTGTTGTAAACCAAAAATATGGGATCCAACCAGCTGTCAATGTATTTGTCCA
TTTATACAAGCATGTAAAGCACCTTTCATTTGGAGCGATGATTTATGCCAATGTGTTTGC
AAACAGATAGTTTCATGTAAACCACCACTTGTATGGAATCCAAAACTCTGCAAATGTACA
TGTCCACCAATAGATTGTCCACCTAATTTCATGCAAAATCCTTTTACTTGTCAATGTATG
TGCAATCAAGCAATGTCAAAAACTTGTGATACGTCAATTCAAGTGTGGAATCCAAAAAAA
TGTCAATGCGATTGCAAATTTCCAGTTGATTGCATACCAAACTACATTTTTAATCCAAAA
ACATGTAAATGTGAATGCAACCAAGCTCTTTCTACATCTTGTAAGCCACCATTATCAATT
TGGGATAAGACAAAATGTAAATGTGTTTGCAACATTGATTGTGCACCAAATTATATTCTT
AATGAAGCAACTTGCAGTTGTGATTGCAATAAAGAACTTGTGTTATCTACTTGTGATCTC
AACACTCATGTTTTTAATCCTGATAAATGTTCGTGTGATTGCAAACCAATTGTATGCCCT
CCCAACTTTATTCAAAATCCTAAGACATGCAAATGTGACTGTGCACTTACTCAAGCTAGC
TGTCCAGCTCCTCAAATTTTTGTACCCGAAAAATGTGCTTGCATTTGTGATCCAACGATT
TCATGTGCACCAAATTATATCATAGATCCAGCTACTTGTACATGTGTTTGTGATAGTAAA
ACAGTTGCTGCCACTTGCATTCCAAATGTTCAAATTTTTGTTCCTGACACTTGTAGCTGT
CGTTGTATTCATCCAATCGATTGTCTTCCAAATTATATTGGATTTTCATCAAATTGTAGC
TGTGTTTGCGATTGGTCACTTGCTGCACCATGTGTGGCTAATGGTGGAACTTTTGATTAT
GCTAATTGTAAATGTAATACAAATCCTTGTTCTGGAGTTGTTTGTCCACCAAATTTCATA
CCTGATGCTGCTTGTAATTGTGTTTGTAATCAAGCATTAGCAACATCTTGTGATCCAACT
ATTCAAAGATGGAATCCTGATCTTTGTAAATGTGAATGCATTAAAGTTAATGCAGATGGT
ACACCAATTTGCAATGGAAATCAAATTCAAGATCCTGTTTCTTGTAAATGCATTTGTGAT
CCAAATGCTGAAAAAAAATGCTTAACGCAACCAAATCATGTTTGGGATCCGAATACATGC
ACTTGCGTTTGCAAGCAACTTGTCGATTGTCCAACTGGTTTCAAATTTGATCAAGCATCA
TGCTCATGTGTTTGTGTACAACAAATAGATTGTGTTCAACCTTTGATTTTCAATACAACT
TTATGTAAATGTGCATGTCCAAAACCATGTCCTCCGAATTATATTCAAGATCCCTTAAAA
TGCACATGCACTTGTAATGAGAAACTTGTAGTATCAACCTGTGATTTAAACACTCACGTT
TTTAATTCAGCTTCATGTAGCTGTGACTGCAAACCAAATGGAATTGCGTGTCCAAATGGA
TCTATTTTAGATCCTATCAATTGTAAAGATTGCATTGTTGTTCCTCCTAATCCTGCATAA
>g12506.t1 Gene=g12506 Length=759
MNRLNFVTFFLILGNNLIYIDAVPPCNDPPLCQELMVLDPAQCKCVCVDNSGSKPCPLPF
PTDFPCPCIQGLSTVNSTTAAPVATIGAQTIGPVVISPCKVKPIACPPPKTFWDSNSCKC
ICDPGVDCLHPTFVMNPDTCLCECAIKPTTPCPSNQFFNPATCKCQCKDNCLGNESIMCV
KPQVWSEDSCTCNCPSPNTQICKSNKYWDFDTCNCECKNKQKTCCKPKIWDPTSCQCICP
FIQACKAPFIWSDDLCQCVCKQIVSCKPPLVWNPKLCKCTCPPIDCPPNFMQNPFTCQCM
CNQAMSKTCDTSIQVWNPKKCQCDCKFPVDCIPNYIFNPKTCKCECNQALSTSCKPPLSI
WDKTKCKCVCNIDCAPNYILNEATCSCDCNKELVLSTCDLNTHVFNPDKCSCDCKPIVCP
PNFIQNPKTCKCDCALTQASCPAPQIFVPEKCACICDPTISCAPNYIIDPATCTCVCDSK
TVAATCIPNVQIFVPDTCSCRCIHPIDCLPNYIGFSSNCSCVCDWSLAAPCVANGGTFDY
ANCKCNTNPCSGVVCPPNFIPDAACNCVCNQALATSCDPTIQRWNPDLCKCECIKVNADG
TPICNGNQIQDPVSCKCICDPNAEKKCLTQPNHVWDPNTCTCVCKQLVDCPTGFKFDQAS
CSCVCVQQIDCVQPLIFNTTLCKCACPKPCPPNYIQDPLKCTCTCNEKLVVSTCDLNTHV
FNSASCSCDCKPNGIACPNGSILDPINCKDCIVVPPNPA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 99 | 169 | 5.4E-46 |
| 16 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 99 | 169 | 5.4E-46 |
| 7 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 171 | 241 | 5.4E-46 |
| 14 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 171 | 241 | 5.4E-46 |
| 10 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 245 | 310 | 5.4E-46 |
| 17 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 245 | 310 | 5.4E-46 |
| 6 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 291 | 372 | 5.4E-46 |
| 13 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 291 | 372 | 5.4E-46 |
| 5 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 312 | 392 | 5.4E-46 |
| 12 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 312 | 392 | 5.4E-46 |
| 4 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 382 | 460 | 5.4E-46 |
| 11 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 382 | 460 | 5.4E-46 |
| 8 | g12506.t1 | PANTHER | PTHR11633:SF1 | LD28763P | 604 | 670 | 5.4E-46 |
| 15 | g12506.t1 | PANTHER | PTHR11633 | PLATELET-DERIVED GROWTH FACTOR | 604 | 670 | 5.4E-46 |
| 2 | g12506.t1 | Pfam | PF03128 | CXCXC repeat | 227 | 239 | 0.013 |
| 1 | g12506.t1 | Pfam | PF03128 | CXCXC repeat | 336 | 346 | 0.041 |
| 3 | g12506.t1 | Pfam | PF03128 | CXCXC repeat | 632 | 644 | 0.0096 |
| 20 | g12506.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 21 | g12506.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 22 | g12506.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 14 | - |
| 23 | g12506.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 22 | - |
| 19 | g12506.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 759 | - |
| 18 | g12506.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
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. There were no conditions that were differentially expressed