General information for g11970.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g11970 is located on chr_1: 20007751..20020803 (+ 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 | g11970 | g11970.t4 | isoform | g11970.t4 | 20007751 | 20020803 |
| chr_1 | g11970 | g11970.t4 | exon | g11970.t4.exon1 | 20007751 | 20007842 |
| chr_1 | g11970 | g11970.t4 | cds | g11970.t4.CDS1 | 20007751 | 20007842 |
| chr_1 | g11970 | g11970.t4 | exon | g11970.t4.exon2 | 20010255 | 20010404 |
| chr_1 | g11970 | g11970.t4 | cds | g11970.t4.CDS2 | 20010255 | 20010404 |
| chr_1 | g11970 | g11970.t4 | exon | g11970.t4.exon3 | 20014246 | 20014390 |
| chr_1 | g11970 | g11970.t4 | cds | g11970.t4.CDS3 | 20014246 | 20014390 |
| chr_1 | g11970 | g11970.t4 | exon | g11970.t4.exon4 | 20016395 | 20016610 |
| chr_1 | g11970 | g11970.t4 | cds | g11970.t4.CDS4 | 20016395 | 20016610 |
| chr_1 | g11970 | g11970.t4 | exon | g11970.t4.exon5 | 20019847 | 20020803 |
| chr_1 | g11970 | g11970.t4 | cds | g11970.t4.CDS5 | 20019847 | 20020803 |
| chr_1 | g11970 | g11970.t4 | TSS | g11970.t4 | NA | NA |
| chr_1 | g11970 | g11970.t4 | TTS | g11970.t4 | NA | NA |
Sequences
>g11970.t4 Gene=g11970 Length=1560
ATGTTCTTAAATGATGACGCGAATGATGTTAAAGGTGAAAAAAATATTGCTAACGTAGGT
GGCAAGAAGGAATATAAAGAATGCCTAACACGATCAAAATCCCCAACAGCAAAAGTACAA
CACAATACAATCAGTCGAATACCAATTCGTACTGCAAATGCTGAAAAACGTGCTCGTGAG
ATGGGTTTATTAGAGGATATCGATGAAACAAATTTGAGCCCATCGCAGCTCAGGGCACTT
AGAGCAGAAAAACGAGCAGCCTGGCGTCAAGCGAGACTTAAATCATTGGAGCAAGACGCA
ATACAGGCACAAATTATGATTCAAAGTTTGAACAGCGAAATTGCTAATAAACCTCGTGAC
AAACTAGATGGTGTAGAAGAGGAGGAGTCTAACGATGATTTAATAACAAAAACGACTACA
AAAAGCCGACTAAAGTTTCCTCGCATTGCAATAAAACTTCGTCCTGGTCAAGTGACAGTG
CGAGAAAAAGAGACGATTTTAGATGAAAAAGTTATTCAACGAACCGAAGAGGTTCCCGAT
CCAGTTAGTGGTGAACCAACGATACAAACATTCGAATATGTCGAGAAAGTCATCGAACGA
GAGGTTGAAACATGTCAGGAGAAAATTTTTTCTCTCGAACTTGAAGACCCAAAATCATTA
GAATCACCATCGACACCATCAACAGAGAGCTTTAGCATTACAGAGTCAATTATTGTCGAG
CAACAGCCACATGATGACAGCGATGATAATCAATCAATGATCACTGTCTGTCCAAACAAC
ACTGATGACACTTTTGTATTAAATCCAACAGATCCGGATGATTATATCAACGCTAATGTT
ATTGAAACATCCACGCAAATAAAAACAATTGTCGAGGTCATCAATCCGATGCTAACGGGC
GATGGAACAGCAACTGAAATTGCGGTTGGTCGGCCTGATGATCTTGAGTCCTTCAATCAA
GAAGTAGGCGATGATTTTGATGGTGTAACATTTCGTCGTGAGTTGTCACTGAACGACAAG
ATGAAAAATGTCCTCAAAGAGCTTAAAGAAAATGAAAAAGTTCGATTAAGTTTATCGCGT
AGTATGGAAGAAGATGAAGATGAAAATGAAAACGTAGAGAACGTGCCGGAATCAAGTGAA
AATGATGAAGCCGTGAGCACATCATATGAGGAAAAGCAGGGCAGTATAGGAACAGTTTTT
ATGGTTCGTGAGCGTCTTATAAACGATTTTTACGATCATCAGCAAGTGCCTGAGCATGCG
ACAGATGAAATTCAAGCAAGCATCGACAGTTGCCAAGTGATCTCAAATCCAAGTGTCGAT
GAGTTTCTTGCAAATGAAATTCGACACAGTCAAGATACAATGACTGCACGTAAAGAAACT
TTAACACTTGATTTAACGAAAACAACTGAAACGACACTACAAGACGATGACGACGATGAA
GAAGACGAGACGACCACTGAGAACACGCCAACAACACCAACGAAAATGCTACCAGGGAGC
AATGCGAGTTCAGGTGGAAAGAAAAAACGACGAAAGAGCAAGGGAAAGGCAAAGAAATAA
>g11970.t4 Gene=g11970 Length=519
MFLNDDANDVKGEKNIANVGGKKEYKECLTRSKSPTAKVQHNTISRIPIRTANAEKRARE
MGLLEDIDETNLSPSQLRALRAEKRAAWRQARLKSLEQDAIQAQIMIQSLNSEIANKPRD
KLDGVEEEESNDDLITKTTTKSRLKFPRIAIKLRPGQVTVREKETILDEKVIQRTEEVPD
PVSGEPTIQTFEYVEKVIEREVETCQEKIFSLELEDPKSLESPSTPSTESFSITESIIVE
QQPHDDSDDNQSMITVCPNNTDDTFVLNPTDPDDYINANVIETSTQIKTIVEVINPMLTG
DGTATEIAVGRPDDLESFNQEVGDDFDGVTFRRELSLNDKMKNVLKELKENEKVRLSLSR
SMEEDEDENENVENVPESSENDEAVSTSYEEKQGSIGTVFMVRERLINDFYDHQQVPEHA
TDEIQASIDSCQVISNPSVDEFLANEIRHSQDTMTARKETLTLDLTKTTETTLQDDDDDE
EDETTTENTPTTPTKMLPGSNASSGGKKKRRKSKGKAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11970.t4 | Coils | Coil | Coil | 93 | 113 | - |
| 7 | g11970.t4 | Coils | Coil | Coil | 355 | 375 | - |
| 3 | g11970.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 356 | 392 | - |
| 2 | g11970.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 363 | 377 | - |
| 5 | g11970.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 378 | 392 | - |
| 1 | g11970.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 466 | 519 | - |
| 6 | g11970.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 487 | 501 | - |
| 4 | g11970.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 505 | 519 | - |
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.
