General information for g12001.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Smoothelin.
Parent gene
- The parent gene g12001 is located on chr_1: 20282853..20286592 (+ 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 | g12001 | g12001.t6 | TSS | g12001.t6 | 20280976 | 20280976 |
| chr_1 | g12001 | g12001.t6 | isoform | g12001.t6 | 20280992 | 20286592 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon1 | 20280992 | 20281058 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS1 | 20280992 | 20281058 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon2 | 20281145 | 20281235 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS2 | 20281145 | 20281235 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon3 | 20281670 | 20281829 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS3 | 20281670 | 20281829 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon4 | 20282498 | 20282543 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS4 | 20282498 | 20282543 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon5 | 20282680 | 20282785 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS5 | 20282680 | 20282785 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon6 | 20282843 | 20282890 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS6 | 20282843 | 20282890 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon7 | 20282988 | 20283590 |
| chr_1 | g12001 | g12001.t6 | cds | g12001.t6.CDS7 | 20282988 | 20283006 |
| chr_1 | g12001 | g12001.t6 | exon | g12001.t6.exon8 | 20286574 | 20286592 |
| chr_1 | g12001 | g12001.t6 | TTS | g12001.t6 | NA | NA |
Sequences
>g12001.t6 Gene=g12001 Length=1140
ATGACAAAGACTAGTTCGGAAGTGCATCAGCAGGGAGATAGAATTATTAAAACGACTACT
ACAGAAGTTATTACAAAATCATCAACAATGCAACCACAAAAAAAGGTATCACCATTCGAG
AAATTCCGTCAACTTGATCGTCAAAATTCCCTTCCAAATTCACCATCACCTCGAACACCA
ACAACACCCACTACTCCCGGAGGTTCTAAGAAAAATGGTCCACTTTTTTCCTTCACTGAT
CCAGCACTCGCTAAGCGAGCATCCACCGTCAAAGAACAATTATTACAATGGGCGCAGATG
AAGACGAAAGAATATGAGAACGTCAATATAGAAAATTTCAGTACAAGTTGGTCAGATGGA
TTAGCATTTGCCGCTCTTATACACCACTTTTTACCCGATGCATTTGATTATAGCAAATTA
ACACCTAAAGATAGAAGACATAATTTTACTTTGGCATTCCGGATTGCAGAAGAAAAAGCC
GGTATTTGTCCTTTGCTTGATGTTGACGATATGGTTATCATCAAAAAGGCTTTTTAAATG
GAAAATTTCTTCTTATTCATCACATTGATTTTAAGATAAAAAAAAGTTTTTATGACAATA
GTCTTTATGTTGAAATTTAAATTTGAGCAAGTCAAATGTATCATAATTTTTGTTGATTTA
TTCAATTTTATTTTCTTTTAAATTGTGATGTATAGAACGTGTATTAATTTTGTAAATTTT
AATTCATCTGACTTAATTTTTGATGATTTTTTCTCCTTTCTTTTTTACATTTTTGTCAAT
CTGTGGTTGTTGATTTTCTTTGAATGAAAAAATAATTTTTTATTTTAAAAGAAGATAATT
TTGTTTGCAAACATAAAACTCTCAAAATGGTGCAGGTTTATTGTACTAACTTTTCTATAA
CTATTTTTTTAATAAAACACTCATAACAGCAATGCTGTAATCAAAAAATTATGTGAAACT
AATCATTAGAGTTAATTAAAATATTTTTTGTAACTTGATAATCATGAAACCATTATGAAA
TTGTTGGAAAAAAAACTAAAACTATGAAACAAAAAAGCAATACAATTGTAAAAACTTTTT
ACTGATGACAATAAAAATATTTTATTGAATCAAATTTATGCATTGCTGTCATATACACAT
>g12001.t6 Gene=g12001 Length=178
MTKTSSEVHQQGDRIIKTTTTEVITKSSTMQPQKKVSPFEKFRQLDRQNSLPNSPSPRTP
TTPTTPGGSKKNGPLFSFTDPALAKRASTVKEQLLQWAQMKTKEYENVNIENFSTSWSDG
LAFAALIHHFLPDAFDYSKLTPKDRRHNFTLAFRIAEEKAGICPLLDVDDMVIIKKAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12001.t6 | CDD | cd00014 | CH | 91 | 172 | 4.23146E-20 |
| 5 | g12001.t6 | Gene3D | G3DSA:1.10.418.10 | - | 86 | 177 | 1.5E-33 |
| 8 | g12001.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 76 | - |
| 9 | g12001.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 2 | g12001.t6 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 62 | 176 | 6.0E-51 |
| 3 | g12001.t6 | PANTHER | PTHR23167:SF48 | AGAP011397-PA | 62 | 176 | 6.0E-51 |
| 1 | g12001.t6 | Pfam | PF00307 | Calponin homology (CH) domain | 90 | 173 | 2.2E-19 |
| 10 | g12001.t6 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 88 | 178 | 21.665 |
| 7 | g12001.t6 | SMART | SM00033 | ch_5 | 90 | 176 | 1.9E-11 |
| 4 | g12001.t6 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 87 | 172 | 1.96E-28 |
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 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. There were no conditions that were differentially expressed