General information for g13034.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Integrin beta-PS.
Parent gene
- The parent gene g13034 is located on chr_1: 27634379..27636423 (+ 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 | g13034 | g13034.t3 | TSS | g13034.t3 | 27624519 | 27624519 |
| chr_1 | g13034 | g13034.t3 | isoform | g13034.t3 | 27625536 | 27633733 |
| chr_1 | g13034 | g13034.t3 | exon | g13034.t3.exon1 | 27625536 | 27625834 |
| chr_1 | g13034 | g13034.t3 | exon | g13034.t3.exon2 | 27630743 | 27631277 |
| chr_1 | g13034 | g13034.t3 | cds | g13034.t3.CDS1 | 27630806 | 27631277 |
| chr_1 | g13034 | g13034.t3 | exon | g13034.t3.exon3 | 27631333 | 27631561 |
| chr_1 | g13034 | g13034.t3 | cds | g13034.t3.CDS2 | 27631333 | 27631561 |
| chr_1 | g13034 | g13034.t3 | exon | g13034.t3.exon4 | 27632576 | 27632660 |
| chr_1 | g13034 | g13034.t3 | cds | g13034.t3.CDS3 | 27632576 | 27632660 |
| chr_1 | g13034 | g13034.t3 | exon | g13034.t3.exon5 | 27633188 | 27633619 |
| chr_1 | g13034 | g13034.t3 | cds | g13034.t3.CDS4 | 27633188 | 27633619 |
| chr_1 | g13034 | g13034.t3 | exon | g13034.t3.exon6 | 27633676 | 27633733 |
| chr_1 | g13034 | g13034.t3 | cds | g13034.t3.CDS5 | 27633676 | 27633732 |
| chr_1 | g13034 | g13034.t3 | TTS | g13034.t3 | NA | NA |
Sequences
>g13034.t3 Gene=g13034 Length=1638
TTAATAAAAGCCAAAAATATTTCATTGATTTTCTTATTATTTCACTGAATATTTAAACAT
TAAAAGCCGTCATAAATTCCGTCCTTTCAGAAAAATACATCAAAACTAAAAGACCACAAG
TAATAGAGAACTCACTGTCATAGTACATTTTGTGAGTGTTGAAAAAGACTTCGTAAGGAC
AATTTTTAATCATAATTTAGTTTTATACGCATTTAAACGTTCTAAAAATCGTGAAAAAGT
ATTTTCGCGCATCTGTAAAATTCGAAATTGTTCAAGTGCAGATGAAATTTGATTAAATAA
AACACAAAAAAACCTCATCACAAAGTGCCACAGTAACTCACAGAATGTCTAGATACTCAA
TAATGTTATTTTCAATAGTGCTGATAAGCACATTAGTAGTTATAAATGCACAATTTGGCA
TTGACAAAGCTGCACTTTATCAAAATCCTTGTACAAGTAAAACATCATGTAGTGCTTGCA
TTCAAACACAAAAGTGTGCTTGGTGTATGCAGCCAGATTTTGGTGATCGTCCAAGATGTT
TCCAACCTGATTTGAAACCAGCAACCACATGTCCAGAAGAATTTGTTGTGAATCCAGACA
ATGAAGAAATTATGATTAGAAATTGGGCATTGAGCAGAGGAGGCCAAGTATTAACAGGTG
GTGGTGGAATAGCAAGCGGTGGAACTTATGAAGAAGAACATCAATCTTCAGGATCAATGT
CAGGTCATGGGTCATCAGCAAGTGGTGGTTCAGCGGCTGGAAGTGCATCAGGAAGTGGTC
ATGGAAGTGTTGTTCAAGTCAGTCCACAACATGTTAACTTAAAATTGAGAATTAATGAAA
AACATAGCATGAAAGTCAGTTATGCTCAAGCTGAAGATTATCCAGTAGATCTTTACTATC
TTATGGACTTGTCAAAATCTATGGAAGATGATAAAGAAAAATTGTCGCATTTGGGAAATT
TATTGTCAGACACAATGAGAAATATCACTTCAAATTTCCGTCTTGGTTTTGGATCATTTG
TTGATAAAGTTCTTATGCCTTATGTCTCAACTGTGCCTAAAAATTTGAGAGAACCATGTC
AAAATTGCGAAGCCCCATATGGATATCACAATGTCATGGCATTAAGCACTGACACATATC
GTTTTGCTGAAAATGTAAGAGATGCTCATGTCTCAGGAAATTTGGATGCACCAGAAGGTG
GATTTGATGCAATCATGCAAGCAGTTGTATGTAAGGATCACATTGGTTGGCGCGATCGTG
CTCGTCGTTTGCTCGTCTTCTCAACTGATGCTGGCTTCCATTATGCAGGAGATGGGAAAC
TTGGTGGTGTAATAACTCCAAATGATGGTGAATGCCACATGGCAAATAATATGTACACTC
ATTCTACTATTCAAGATTATCCCAGCATTTCACAAATCAATTTGAAAGTTAAAGAAAATG
CAATCAACATTATTTTTGCTGTTACACAATCACAGCATGAAGTTTATAAGAAACTTTCAA
GTCATATTGAAGGTTCATCAAGCGCTGTCTTATCAGAAGATTCATCAAATGTTGTTGAAC
TAGTTAGAGATGAATATAATAAAATCACATCATCAGTTGAAATGAAAGACACTGCATCAG
GTTCAGTAAAAGTTACAT
>g13034.t3 Gene=g13034 Length=425
MLFSIVLISTLVVINAQFGIDKAALYQNPCTSKTSCSACIQTQKCAWCMQPDFGDRPRCF
QPDLKPATTCPEEFVVNPDNEEIMIRNWALSRGGQVLTGGGGIASGGTYEEEHQSSGSMS
GHGSSASGGSAAGSASGSGHGSVVQVSPQHVNLKLRINEKHSMKVSYAQAEDYPVDLYYL
MDLSKSMEDDKEKLSHLGNLLSDTMRNITSNFRLGFGSFVDKVLMPYVSTVPKNLREPCQ
NCEAPYGYHNVMALSTDTYRFAENVRDAHVSGNLDAPEGGFDAIMQAVVCKDHIGWRDRA
RRLLVFSTDAGFHYAGDGKLGGVITPNDGECHMANNMYTHSTIQDYPSISQINLKVKENA
INIIFAVTQSQHEVYKKLSSHIEGSSSAVLSEDSSNVVELVRDEYNKITSSVEMKDTASG
SVKVT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g13034.t3 | Gene3D | G3DSA:2.60.40.1510 | ntegrin | 139 | 421 | 5.3E-132 |
| 12 | g13034.t3 | Gene3D | G3DSA:3.40.50.410 | - | 172 | 409 | 5.3E-132 |
| 19 | g13034.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 109 | 143 | - |
| 3 | g13034.t3 | PANTHER | PTHR10082 | INTEGRIN BETA SUBUNIT | 23 | 417 | 1.7E-127 |
| 4 | g13034.t3 | PRINTS | PR01186 | Integrin beta subunit signature | 32 | 48 | 9.6E-16 |
| 5 | g13034.t3 | PRINTS | PR01186 | Integrin beta subunit signature | 345 | 368 | 9.6E-16 |
| 6 | g13034.t3 | PRINTS | PR01186 | Integrin beta subunit signature | 381 | 405 | 9.6E-16 |
| 1 | g13034.t3 | Pfam | PF17205 | Integrin plexin domain | 28 | 70 | 1.2E-10 |
| 2 | g13034.t3 | Pfam | PF00362 | Integrin beta chain VWA domain | 170 | 412 | 2.3E-110 |
| 14 | g13034.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 15 | g13034.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 16 | g13034.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 12 | - |
| 17 | g13034.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 16 | - |
| 13 | g13034.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 425 | - |
| 18 | g13034.t3 | SMART | SM00187 | INB_2 | 35 | 424 | 1.5E-171 |
| 7 | g13034.t3 | SUPERFAMILY | SSF103575 | Plexin repeat | 27 | 78 | 1.62E-9 |
| 8 | g13034.t3 | SUPERFAMILY | SSF53300 | vWA-like | 170 | 410 | 1.11E-77 |
| 10 | g13034.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 9 | g13034.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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.
