General information for g13305.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative PDZ domain-containing protein 2.
Parent gene
- The parent gene g13305 is located on chr_1: 29040202..29047736 (- 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 | g13305 | g13305.t1 | TTS | g13305.t1 | 29034148 | 29034148 |
| chr_1 | g13305 | g13305.t1 | isoform | g13305.t1 | 29034766 | 29047736 |
| chr_1 | g13305 | g13305.t1 | exon | g13305.t1.exon1 | 29034766 | 29034911 |
| chr_1 | g13305 | g13305.t1 | cds | g13305.t1.CDS1 | 29034766 | 29034911 |
| chr_1 | g13305 | g13305.t1 | exon | g13305.t1.exon2 | 29035389 | 29035481 |
| chr_1 | g13305 | g13305.t1 | cds | g13305.t1.CDS2 | 29035389 | 29035481 |
| chr_1 | g13305 | g13305.t1 | exon | g13305.t1.exon3 | 29035557 | 29035746 |
| chr_1 | g13305 | g13305.t1 | cds | g13305.t1.CDS3 | 29035557 | 29035746 |
| chr_1 | g13305 | g13305.t1 | exon | g13305.t1.exon4 | 29040201 | 29041357 |
| chr_1 | g13305 | g13305.t1 | cds | g13305.t1.CDS4 | 29040201 | 29041357 |
| chr_1 | g13305 | g13305.t1 | exon | g13305.t1.exon5 | 29047694 | 29047736 |
| chr_1 | g13305 | g13305.t1 | cds | g13305.t1.CDS5 | 29047694 | 29047736 |
| chr_1 | g13305 | g13305.t1 | TSS | g13305.t1 | 29048038 | 29048038 |
Sequences
>g13305.t1 Gene=g13305 Length=1629
ATGGTTTTCTATGACACTGACAACGAACAATTGCCATCAGTCGACACACCAACTTCGAGT
TTGTCGAGGAAGTGGTGTAAATTGCGTCAACGTTGTGCGTCATTTCATGCGATGAAGACG
CTCGACTGCACATCGGCCGAGGGGCCATCTTCACTGCCTTATCAATTTTATGATAACGGT
ATGCTTGAAGTGACGACCCCACTACACGCACAAATGCCACATCATAGTAATAATTTCATC
TTAGCACACGACCCGCGCGCTCTAATGGACAATAAGCCAAAGATTTATGCTGTCATTGAT
GGTCGTAATGGTGGCTATTATACTACCGCTGCCAACTATCCTCTAATGTATGAGCCTATC
ATTGAACATCCAAAAATACAGAAAGTGTGTAAATGCAAGCACAATAAAACTTCTGCATCT
ACGACATCACTGAGCTATGATATGAGTGAGTCAACACAGTTCATGCACGTGCTGAATCAA
CAAACACGTCTACAATATTTCGATGGTGAAGATTTGAAAGCCAAATCAAAAACACGTCGT
CTAAGTCTCTTCGGCAGTGAAAGAAAGCCAAAGAAAGAAACGGCAAAGAATTTTGATATT
AAACAATTTAAATCAGTTTCTATGCGATGTCATCATCATCATCAACATCTTATGTATATA
AGAGAACAACAAATGTTGCAACAACAACAGCAGCAGCAACAGGAAGCTGAAAAGCAAGCT
CAATCAACTAAAAGCACAATGAAAATGAAATTTAATACTGTAGGTCGAAAGAAGAGATCA
ATCTACGATGTTTTCTTTAATAACAATAGCAGCAAAACACCAGCATCATCGTCATCATCG
AATGAACCAAATCTTAGACAACCGACATTTTACGTTCCATTACCAGATAAAGTAATTAAC
GATAACGAATTGCAGCATCATCATCATCGAAATAATAGTGTGAATCCGATTCGCTCGATT
CGTTCGCGTTCCGTTTGTGCAGGCGAGAGTAGTCAACAGATGCTCTTTCACAATGTCGAC
AATAGTCAGCATCAACAGAAAGAGCAAAAGAGTGAACGACGAAAATCAAATAGCTTCAAT
CCACGCGAATCACTCGAAATCACTTCATTTCTATTTAGCAAGCTCAAGATGGATCGCAAG
GCAGATGGAAGTGAAAAATGTGAGCAACAAGGCGACGAAATAAAGAAAAATGATAAACGA
GAAACGAGTGATGAAGTAATTAGCAAACCAAAGGATGTTGTTGATGGAAAAGGCAAAGAG
TGCGATAATTCACCCAAAATAGCAACAACAACAGCGAAAGCAAATACAATCCCAAAAAAT
TCTCTAGTGCTAAAGAAAGTGCAATTTGTAAAAAATCCTGGATCTAAAGCGCTCGGCTTC
TCAATTGTTGGTGGAATTGATTCACCAAAAGGGAAAATGGGTATTTTCGTAAAGACTATT
TATCCGTATGGTCAAGCAGCAGCAAGTGGACAGTTGAAAGAAGGTGATTTAATATTGTCA
GTAAATAATCAAGCACTTCATGGTGTTACCCATCAAGAAGCAATAAATGTTTTTAAAGGA
ATAAAAACAGGATTAGTTGAAATGATTGTTGGCCGGCAACAGCAAGTAGCAGCAGTCAAT
GGGCAATGA
>g13305.t1 Gene=g13305 Length=542
MVFYDTDNEQLPSVDTPTSSLSRKWCKLRQRCASFHAMKTLDCTSAEGPSSLPYQFYDNG
MLEVTTPLHAQMPHHSNNFILAHDPRALMDNKPKIYAVIDGRNGGYYTTAANYPLMYEPI
IEHPKIQKVCKCKHNKTSASTTSLSYDMSESTQFMHVLNQQTRLQYFDGEDLKAKSKTRR
LSLFGSERKPKKETAKNFDIKQFKSVSMRCHHHHQHLMYIREQQMLQQQQQQQQEAEKQA
QSTKSTMKMKFNTVGRKKRSIYDVFFNNNSSKTPASSSSSNEPNLRQPTFYVPLPDKVIN
DNELQHHHHRNNSVNPIRSIRSRSVCAGESSQQMLFHNVDNSQHQQKEQKSERRKSNSFN
PRESLEITSFLFSKLKMDRKADGSEKCEQQGDEIKKNDKRETSDEVISKPKDVVDGKGKE
CDNSPKIATTTAKANTIPKNSLVLKKVQFVKNPGSKALGFSIVGGIDSPKGKMGIFVKTI
YPYGQAAASGQLKEGDLILSVNNQALHGVTHQEAINVFKGIKTGLVEMIVGRQQQVAAVN
GQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13305.t1 | CDD | cd00992 | PDZ_signaling | 444 | 530 | 6.34402E-19 |
| 6 | g13305.t1 | Coils | Coil | Coil | 219 | 246 | - |
| 5 | g13305.t1 | Gene3D | G3DSA:2.30.42.10 | - | 419 | 540 | 3.7E-30 |
| 10 | g13305.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 250 | - |
| 11 | g13305.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 253 | - |
| 13 | g13305.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 340 | 360 | - |
| 12 | g13305.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 343 | 360 | - |
| 9 | g13305.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 420 | - |
| 2 | g13305.t1 | PANTHER | PTHR19964 | MULTIPLE PDZ DOMAIN PROTEIN | 327 | 533 | 2.7E-32 |
| 3 | g13305.t1 | PANTHER | PTHR19964:SF69 | ARC, ISOFORM A | 327 | 533 | 2.7E-32 |
| 1 | g13305.t1 | Pfam | PF00595 | PDZ domain | 448 | 527 | 7.2E-15 |
| 14 | g13305.t1 | ProSiteProfiles | PS50106 | PDZ domain profile. | 446 | 519 | 19.4 |
| 8 | g13305.t1 | SMART | SM00228 | pdz_new | 456 | 534 | 1.8E-15 |
| 4 | g13305.t1 | SUPERFAMILY | SSF50156 | PDZ domain-like | 443 | 536 | 9.86E-24 |
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 transcript has been annotated with K22628 (interleukin 16)
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.
