General information for g11954.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g11954 is located on chr_1: 19775063..19776052 (+ 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 | g11954 | g11954.t3 | isoform | g11954.t3 | 19770721 | 19773167 |
| chr_1 | g11954 | g11954.t3 | TSS | g11954.t3 | 19770721 | 19770721 |
| chr_1 | g11954 | g11954.t3 | exon | g11954.t3.exon1 | 19770721 | 19770889 |
| chr_1 | g11954 | g11954.t3 | exon | g11954.t3.exon2 | 19771112 | 19771423 |
| chr_1 | g11954 | g11954.t3 | exon | g11954.t3.exon3 | 19771752 | 19771861 |
| chr_1 | g11954 | g11954.t3 | cds | g11954.t3.CDS1 | 19771752 | 19771861 |
| chr_1 | g11954 | g11954.t3 | exon | g11954.t3.exon4 | 19772519 | 19773167 |
| chr_1 | g11954 | g11954.t3 | cds | g11954.t3.CDS2 | 19772519 | 19773167 |
| chr_1 | g11954 | g11954.t3 | TTS | g11954.t3 | 19773481 | 19773481 |
Sequences
>g11954.t3 Gene=g11954 Length=1240
ACATCGAAACATTTAAAAAATTCTTTCGTGTGATTCACATTGTTTTGAGTATTTTAGTTG
ATAAGCCAGTTCTATTGTTGAAATTTTTGTTATCACTCGTTTCTCAGCATTGCTCCCTAA
GTGTTTAATATGAAGTGTAATATAAAAAAATTGATTTAAGTAACAAAAACAGGACGAAAG
TCTAAAAGGAACTTTTTTGCCCGAAATTATCTGTTAAGAATCATTTTTATTCACACAATT
GCAACAAAAAGTTTAATCTACGATTAAAGAAAGTATAAAAAAGTTTAAAATTAATTATTT
TTTGTCAATTAACTTGAGTTTGTCGTCTTATAAAGAAAAAAAAGTTTTTCAATAGTTTTA
TCGCATAGTTTTTAAAAGTAGTAATTTTCGATCGCAAAAAAGTCACTTGTCTGAGAGAAG
AAAGAAAGAGCTTCAGTCCTCATTATATCATTTCATACACAATTTATAATTCTGTTATCA
GATGGCAAATGTTGTACCGAAAAGAGAACCTTGCGTAAAATGCAATAATCCTGTATTTTT
TGCTGAACGACTTGTTATCGAAAATCATCTCTATCATCGGACATGTTTTAGATGTGCACG
ATGTCATTCAGTATTAACATTGGGCAATTTCTACCAAACAGAAAAAGACAATGAATTTTG
TTGTGAAACATGTCCAGATGAGGAACTTAAGACCAAACGCAAGGTCGATGAGTCAAATCG
TTTATCAATTGCACAGCGAATTGCATTGTTTGAGAAAACAGAGACATCAAGTGTTCTCAA
AAAATCATTGAGTGATGAAGAGAAAACAAAAAGTCTGAATCGCCAATTGCCATCATCAAC
AGCAGCAACATCTGTCAATTCCAATTCCAACGCGCTCAATAACTTTCTCACATCACAAAT
TGTCGACGATGATGAAAAAACAAATGAGTCACAATCTTCAGAGTCGGAAAGCGATGACGA
ATTAGTGAATGATGACAAGAAGCTCTTTGAAACAAAAAGTGACCATAGTAATTCAATTAA
TAATGACAGCAACATTATTTCAACCAAAGAACTAACACAGACGACACAAGCGCATCAAAA
TGAATCTCAAGAGCAACTAAAGCAAATAGTTAACGATATAATCTTAGTAAGTTCCAATGA
AAATGTAGATGATATAGAATTGGAATTTGAGAAACTTGCTGAGGAAGCTGTAAACAATCC
AATCCCATTGCTTGTATCACCTAACATAATAACAACAAAG
>g11954.t3 Gene=g11954 Length=253
MANVVPKREPCVKCNNPVFFAERLVIENHLYHRTCFRCARCHSVLTLGNFYQTEKDNEFC
CETCPDEELKTKRKVDESNRLSIAQRIALFEKTETSSVLKKSLSDEEKTKSLNRQLPSST
AATSVNSNSNALNNFLTSQIVDDDEKTNESQSSESESDDELVNDDKKLFETKSDHSNSIN
NDSNIISTKELTQTTQAHQNESQEQLKQIVNDIILVSSNENVDDIELEFEKLAEEAVNNP
IPLLVSPNIITTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11954.t3 | CDD | cd09400 | LIM_like_1 | 7 | 68 | 5.72468E-31 |
| 6 | g11954.t3 | Coils | Coil | Coil | 215 | 235 | - |
| 5 | g11954.t3 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 7 | 128 | 4.2E-15 |
| 11 | g11954.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 100 | 127 | - |
| 10 | g11954.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 127 | - |
| 12 | g11954.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 139 | 163 | - |
| 2 | g11954.t3 | PANTHER | PTHR23167:SF59 | MICAL-LIKE 1A-RELATED | 7 | 204 | 1.1E-23 |
| 3 | g11954.t3 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 7 | 204 | 1.1E-23 |
| 1 | g11954.t3 | Pfam | PF00412 | LIM domain | 11 | 64 | 1.8E-8 |
| 9 | g11954.t3 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 11 | 45 | - |
| 13 | g11954.t3 | ProSiteProfiles | PS50023 | LIM domain profile. | 9 | 71 | 11.355 |
| 8 | g11954.t3 | SMART | SM00132 | lim_4 | 10 | 64 | 1.6E-8 |
| 4 | g11954.t3 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 5 | 36 | 2.97E-7 |
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.
