General information for g5892.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Zinc finger protein 208.
Parent gene
- The parent gene g5892 is located on chr_2: 12629342..12630726 (+ 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 | g5892 | g5892.t1 | TSS | g5892.t1 | 12629253 | 12629253 |
| chr_2 | g5892 | g5892.t1 | isoform | g5892.t1 | 12629342 | 12630726 |
| chr_2 | g5892 | g5892.t1 | exon | g5892.t1.exon1 | 12629342 | 12629465 |
| chr_2 | g5892 | g5892.t1 | cds | g5892.t1.CDS1 | 12629342 | 12629465 |
| chr_2 | g5892 | g5892.t1 | exon | g5892.t1.exon2 | 12629527 | 12630240 |
| chr_2 | g5892 | g5892.t1 | cds | g5892.t1.CDS2 | 12629527 | 12630240 |
| chr_2 | g5892 | g5892.t1 | exon | g5892.t1.exon3 | 12630297 | 12630386 |
| chr_2 | g5892 | g5892.t1 | cds | g5892.t1.CDS3 | 12630297 | 12630386 |
| chr_2 | g5892 | g5892.t1 | exon | g5892.t1.exon4 | 12630443 | 12630726 |
| chr_2 | g5892 | g5892.t1 | cds | g5892.t1.CDS4 | 12630443 | 12630726 |
| chr_2 | g5892 | g5892.t1 | TTS | g5892.t1 | 12631586 | 12631586 |
Sequences
>g5892.t1 Gene=g5892 Length=1212
ATGGAGTATTTTGTAAAAACCGAGCCATTAGACTTGATAGAAGATGTTCATGAATGCATT
TTATGTGATGATGGCAAGAAATATTTAAATTTATTAGTTCAACATTTTCAAGAAAATCAC
AAAGACTATAACATGTTTGAAGATGGTCCAATTTTGCAATATTGTCGATGTCCAGAAAGC
CACCAACTTCAAATACATATTGTTACACATCTACTTAGTCATAGTATTCTAAATGACTAT
AATCAAAATAAAGATGAAGATATTACTACTTTAAAAGAAGATGCTGAACGTTATGAAGAA
GAATATTTAATAACTGAAGCAATTGAGGACGATTATGATAGATTTGAACAAAATGAAGAA
AATTATTCAATAGAGGAAGAAGAAGATTCAGTGCCATCCCCAATTCCAAATAAAAAAAGT
AGGAAGCGAAAGAATTCTTCGTCATCATCAGGAACAAAAAAGATTAAACGAGAAAAGAAT
CTCACATGCAAAGTATGTTTAAAAGATTTTGACAATCCGAAAAGATATTACAATCACACT
GCAGCAGCACATCGTGAAAAGTTTCAATGTGATAAATGTGAATTAAAATATAATTTCAAG
TATCAACTAAAGAAACACATTGAAATTGCACACCTTGATCATCCACGAACAAAAGTTAAC
AGACCTAAAAAGTTTCAATGTGATGTATGCAGTATGCAATTTACAGAGCTGAGAATTTTA
ACCGAGCATACCAATATTCATTTGGATTTGCGTCCATTTGTGTGTGAATTTTGTTCTGAA
GCCTTTCATAATTCTGCAAACTTAAGATATCATCGTAAAAGGCATTTAAATCCTAATGGA
TACAAATGCCCTGTGTGTCAGGAAAGTTTCGTTAATCAACAAAGTCTAAGAAAGCATCAT
GTACGACAACATGTTGAAATTGATTTGGATCCTCATCGTTTTGTCTGTGAATATCCTGAT
TGTGGAAGTTCGTTCAAATATGAAGATTTGCTTAAGCAACACATTAGAAAAATTCATTTC
AGAGTTTTGGGTGAATTTGTCTGTGAAATTTGCAATTTTGTAACAAACAATAAGCAAAAT
TATTTTCAACACCGACGACGATTACATGATATACGCAATAGAAAAGGAAATAGAGTATTC
CCATCAACATCAACAAGTCAACAACCAACCAAAGTTGAAATTGAACATGAGATTCATTTC
ACTACTTTATAG
>g5892.t1 Gene=g5892 Length=403
MEYFVKTEPLDLIEDVHECILCDDGKKYLNLLVQHFQENHKDYNMFEDGPILQYCRCPES
HQLQIHIVTHLLSHSILNDYNQNKDEDITTLKEDAERYEEEYLITEAIEDDYDRFEQNEE
NYSIEEEEDSVPSPIPNKKSRKRKNSSSSSGTKKIKREKNLTCKVCLKDFDNPKRYYNHT
AAAHREKFQCDKCELKYNFKYQLKKHIEIAHLDHPRTKVNRPKKFQCDVCSMQFTELRIL
TEHTNIHLDLRPFVCEFCSEAFHNSANLRYHRKRHLNPNGYKCPVCQESFVNQQSLRKHH
VRQHVEIDLDPHRFVCEYPDCGSSFKYEDLLKQHIRKIHFRVLGEFVCEICNFVTNNKQN
YFQHRRRLHDIRNRKGNRVFPSTSTSQQPTKVEIEHEIHFTTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5892.t1 | Coils | Coil | Coil | 81 | 101 | - |
| 14 | g5892.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 131 | 215 | 1.7E-8 |
| 13 | g5892.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 216 | 277 | 2.9E-12 |
| 12 | g5892.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 278 | 345 | 1.5E-10 |
| 30 | g5892.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 121 | 155 | - |
| 5 | g5892.t1 | PANTHER | PTHR24384:SF223 | ZINC FINGER PROTEIN | 55 | 301 | 1.5E-40 |
| 7 | g5892.t1 | PANTHER | PTHR24384 | FINGER PUTATIVE TRANSCRIPTION FACTOR FAMILY-RELATED | 55 | 301 | 1.5E-40 |
| 6 | g5892.t1 | PANTHER | PTHR24384:SF223 | ZINC FINGER PROTEIN | 222 | 367 | 1.5E-40 |
| 8 | g5892.t1 | PANTHER | PTHR24384 | FINGER PUTATIVE TRANSCRIPTION FACTOR FAMILY-RELATED | 222 | 367 | 1.5E-40 |
| 2 | g5892.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 188 | 211 | 0.0067 |
| 1 | g5892.t1 | Pfam | PF13894 | C2H2-type zinc finger | 281 | 304 | 3.0E-4 |
| 4 | g5892.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 314 | 339 | 3.1E-4 |
| 3 | g5892.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 346 | 369 | 0.011 |
| 17 | g5892.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 163 | 184 | - |
| 19 | g5892.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 190 | 211 | - |
| 18 | g5892.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 227 | 247 | - |
| 21 | g5892.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 255 | 275 | - |
| 20 | g5892.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 283 | 304 | - |
| 16 | g5892.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 316 | 339 | - |
| 32 | g5892.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 225 | 252 | 11.302 |
| 31 | g5892.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 253 | 280 | 10.845 |
| 34 | g5892.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 281 | 304 | 9.91 |
| 33 | g5892.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 314 | 339 | 10.803 |
| 25 | g5892.t1 | SMART | SM00355 | c2h2final6 | 17 | 40 | 27.0 |
| 24 | g5892.t1 | SMART | SM00355 | c2h2final6 | 161 | 184 | 6.4 |
| 22 | g5892.t1 | SMART | SM00355 | c2h2final6 | 188 | 211 | 0.94 |
| 26 | g5892.t1 | SMART | SM00355 | c2h2final6 | 225 | 247 | 0.21 |
| 23 | g5892.t1 | SMART | SM00355 | c2h2final6 | 253 | 275 | 0.012 |
| 29 | g5892.t1 | SMART | SM00355 | c2h2final6 | 281 | 304 | 0.0014 |
| 28 | g5892.t1 | SMART | SM00355 | c2h2final6 | 314 | 339 | 0.0015 |
| 27 | g5892.t1 | SMART | SM00355 | c2h2final6 | 346 | 369 | 0.0078 |
| 11 | g5892.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 223 | 275 | 4.13E-12 |
| 9 | g5892.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 261 | 305 | 1.54E-6 |
| 10 | g5892.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 297 | 352 | 1.05E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5892/g5892.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5892.t1.fa.iupred3.txt does not exist
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.
