General information for g5778.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Spectrin alpha chain.
Parent gene
- The parent gene g5778 is located on chr_2: 11908393..11910177 (- 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_2 | g5778 | g5778.t2 | isoform | g5778.t2 | 11908393 | 11910177 |
| chr_2 | g5778 | g5778.t2 | exon | g5778.t2.exon1 | 11908393 | 11909522 |
| chr_2 | g5778 | g5778.t2 | cds | g5778.t2.CDS1 | 11908393 | 11909454 |
| chr_2 | g5778 | g5778.t2 | exon | g5778.t2.exon2 | 11910148 | 11910177 |
| chr_2 | g5778 | g5778.t2 | TSS | g5778.t2 | 11910181 | 11910181 |
| chr_2 | g5778 | g5778.t2 | TTS | g5778.t2 | NA | NA |
Sequences
>g5778.t2 Gene=g5778 Length=1160
ATCGCTAAGTTCTATTAAAGTAAAGTCGAGAAAAACAAATAATTTGAAAAACGATAAAGA
AGGAATTTTTTTATTAAAGAAGAAGAAATAAAAGAAAAATGGAACAGTTTACACCAAAAG
AAGTTCGCATTCTTGAGAGTGCGGAAGACATTCAGGAACGTCGTGAGCAAGTATTGAACC
GTTATGGTGAATTCAAATTGGAAACACGTTTGAAGAGAGAAAAACTTGAAGATTCACGAC
GATTCCAGTATTTTAAGCGTGACTCTGATGAGTTGGAAAGCTGGATACATGAAAAATTGC
AAGCAGCTAGCGAAGAAAGCTATCGTGATCCAACAAATTTACAAGCAAAAATTCAAAAAC
ATCAATCATTTGAAGCTGAAGTTGCTGCACATTCAAATGCAATTGTTTCACTCGATCACA
CTGGTCAAGAAATGATCAATCAAAACCATTTTGCCTCTGATGTCATTCAAAAACGTCTTG
ATGAATTGCATCGTCTTTGGGAGTTATTACTCTCTCGTCTTGCTGAGAAGGGAATGAAAT
TACAACAAGCACTCGTACTCGTTCAATATCTTCGTCATTGCGAAGAAGTAATGTTCTGGA
TTAAGGACAAAGAAGCATTTGTTACAGCTGATGAATTTGGTCATGACCTTGAACATGTCG
AAGTATTACAACGTAAATTTGATGAATTCCAAAAAGATATGGCATCGCAAGAATATCGTG
TTATTGAAGTCAATGATTTGGCTGATAAATTGATTCAAGATGGTCATCCAGAACGCGATT
CGATCATTAAACGTAAAGAAGAACTCAATGAGGCTTGGCAACGATTGAAGCAATTGGCAA
TTATGCGTCAAGAAAAGCTTTTCGGTGCTCATGAAATTCAAAGATTTAACCGTGATGCTG
ATGAAACTGTTGCATGGATAGCAGAAAAAGATGTCGTATTATCATCTGACGATTATGGTC
GTGATTTAGCAAGTGTTCAAGCACTCCAAAGAAAACATGAAGGTGTTGAACGTGACTTGG
CAGCTTTAGAAGACAAAGTTGCAACTCTTGGAACAGAAGCCGGTCGCTTATGCAGTATTC
ACTCAGACCATAGTGATCAAATTCGTGAAAAACAATCAGAAATTGCAGATTACTGGCAAT
CATTGACAGCAAAAGCAAAA
>g5778.t2 Gene=g5778 Length=354
MEQFTPKEVRILESAEDIQERREQVLNRYGEFKLETRLKREKLEDSRRFQYFKRDSDELE
SWIHEKLQAASEESYRDPTNLQAKIQKHQSFEAEVAAHSNAIVSLDHTGQEMINQNHFAS
DVIQKRLDELHRLWELLLSRLAEKGMKLQQALVLVQYLRHCEEVMFWIKDKEAFVTADEF
GHDLEHVEVLQRKFDEFQKDMASQEYRVIEVNDLADKLIQDGHPERDSIIKRKEELNEAW
QRLKQLAIMRQEKLFGAHEIQRFNRDADETVAWIAEKDVVLSSDDYGRDLASVQALQRKH
EGVERDLAALEDKVATLGTEAGRLCSIHSDHSDQIREKQSEIADYWQSLTAKAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5778.t2 | CDD | cd00176 | SPEC | 48 | 258 | 1.1513E-40 |
| 14 | g5778.t2 | Coils | Coil | Coil | 15 | 35 | - |
| 15 | g5778.t2 | Coils | Coil | Coil | 293 | 320 | - |
| 12 | g5778.t2 | Gene3D | G3DSA:1.20.58.60 | - | 3 | 148 | 1.5E-52 |
| 13 | g5778.t2 | Gene3D | G3DSA:1.20.58.1940 | - | 149 | 354 | 4.6E-74 |
| 4 | g5778.t2 | PANTHER | PTHR23064 | TROPONIN | 2 | 354 | 4.7E-217 |
| 5 | g5778.t2 | PANTHER | PTHR23064:SF26 | SPECTRIN ALPHA, NON-ERYTHROCYTIC 1 | 2 | 354 | 4.7E-217 |
| 1 | g5778.t2 | Pfam | PF00435 | Spectrin repeat | 48 | 150 | 3.8E-23 |
| 3 | g5778.t2 | Pfam | PF00435 | Spectrin repeat | 154 | 254 | 4.8E-25 |
| 2 | g5778.t2 | Pfam | PF00435 | Spectrin repeat | 258 | 353 | 5.5E-23 |
| 9 | g5778.t2 | SMART | SM00150 | SPEC_4 | 50 | 149 | 1.3E-30 |
| 11 | g5778.t2 | SMART | SM00150 | SPEC_4 | 155 | 255 | 2.1E-31 |
| 10 | g5778.t2 | SMART | SM00150 | SPEC_4 | 261 | 354 | 5.3E-23 |
| 7 | g5778.t2 | SUPERFAMILY | SSF46966 | Spectrin repeat | 14 | 144 | 4.32E-28 |
| 6 | g5778.t2 | SUPERFAMILY | SSF46966 | Spectrin repeat | 104 | 230 | 6.28E-30 |
| 8 | g5778.t2 | SUPERFAMILY | SSF46966 | Spectrin repeat | 210 | 353 | 8.11E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5778/g5778.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5778.t2.fa.iupred3.txt does not exist
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.
