General information for g5483.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Apoptotic chromatin condensation inducer in the nucleus.
Parent gene
- The parent gene g5483 is located on chr_2: 9835346..9836011 (+ 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 | g5483 | g5483.t10 | isoform | g5483.t10 | 9833786 | 9836011 |
| chr_2 | g5483 | g5483.t10 | exon | g5483.t10.exon1 | 9833786 | 9834353 |
| chr_2 | g5483 | g5483.t10 | cds | g5483.t10.CDS1 | 9833929 | 9834353 |
| chr_2 | g5483 | g5483.t10 | exon | g5483.t10.exon2 | 9834421 | 9834652 |
| chr_2 | g5483 | g5483.t10 | cds | g5483.t10.CDS2 | 9834421 | 9834652 |
| chr_2 | g5483 | g5483.t10 | exon | g5483.t10.exon3 | 9834708 | 9834876 |
| chr_2 | g5483 | g5483.t10 | cds | g5483.t10.CDS3 | 9834708 | 9834876 |
| chr_2 | g5483 | g5483.t10 | exon | g5483.t10.exon4 | 9834938 | 9835054 |
| chr_2 | g5483 | g5483.t10 | cds | g5483.t10.CDS4 | 9834938 | 9835054 |
| chr_2 | g5483 | g5483.t10 | exon | g5483.t10.exon5 | 9835107 | 9836011 |
| chr_2 | g5483 | g5483.t10 | cds | g5483.t10.CDS5 | 9835107 | 9835147 |
| chr_2 | g5483 | g5483.t10 | TTS | g5483.t10 | 9836018 | 9836018 |
| chr_2 | g5483 | g5483.t10 | TSS | g5483.t10 | NA | NA |
Sequences
>g5483.t10 Gene=g5483 Length=1991
AGCCTAAACCTGTGACTCAAAGAAAACGAAAATGGGGTGCACGTAAAGATGATGAAAAAG
TTATTGCTATAACTACAGATTCATTGGCAAATATTATCGCTGAAGAAGTTAAACCAGTTC
CTTTAAGTGATGTAAAATTAGCAATGAGTCCATCACCTGAACCAGAAGAAAAAAGACCAA
GAGTTAGACTTTCATCGGAAGATCGTGATGCAAAAAAGAAACTTTTAAAGGAACGTTTGA
GAAAACAAGAAGAAGAAGAGGAACGTCGAAATGAGCAAATTGCTAAAGCTAGTGAACGCA
GTCAAGTATCTCCGACAATTGTTGTCACAAATGGAGGTGCTGGAAAAGATCGTAAAGTGT
CACTTGTTAGCAATGAAGAAGCGATTGCAAAAACTTCATCCTCGCCAATATCGAAAAATC
AATGCTCAAAAGTTATATGTATCACAAATTTGGTACGTCCTCTAACATTTTTAGCTGTCA
AATCTTTGGTCTCACGAACTGGTGAACTTGATGATTTTTGGATAGATTCTATCAAATCAA
AATGCTTTGTAAAGTACAAAACAGAAGATGAAGCTATTGAAACTCGTCATGCGTTGCATG
GTGTAAAATGGCCAGAACATAATTTGAAAACTTTAAATGTTGAATTTTCAACTGATGAAG
AAATGTATCGAATTATTGAATCTACTCCTGGTGAACGTATTAAAACAGCACTAACAGAAG
CTCGAGAAGAGGAATCAAAAGTGCAGGAAAAGAGTTTTGGATGGTCGAAAGGTGATGCTT
CGGTTGATGATCGATCAAGAGTTTCAAAAAGAGTTCGTGAATGGGATGTTGGAAAGAAAG
AAGATTTAGAGCATGATGAAAGCAGAGAAAGGCGTCGTCGAAGATCTTCAGAACGAGAAA
ATCGTCGAGAGAAGGAGCGAAAACAATTGGAAGAGTCTACTGTAGAGAGACGACATAGTG
TTACACCTGGACGAGAAGATAAAGATGCAATTCCATCACAGCCTGGTCGTTTATTAGATG
ATTTGTTCCGGAAATCTAAAGCTGTTCCATGCATTTATTGGCTACCACTTTCTGAAGAAC
AGGTTAATCAAAGAGAAGGAAGAACAACGACAAAAAAATATTGCTGAACATAATCGTCGC
ATGGAAGAAATAATAAAAAATAGGGAATTACAGCGTGAGAAAATGAATGAAGAAAGACGC
GAACGCGAAGCAAAGCGTCGTGAGGAGAGAAAAGATCGCGAAAGAAAGCGTACAAGATCA
CGTAGCCGTAGTGTTCGTCGTTATTCGCGTGAGAGACATCGTGATCGACGATACGATCGT
CGATAAATTTGTATTTTACTCTCATCCTTTTTCACAGCTTGTCAAAAAAAAATTAATAAT
TATATTAATTGCACTCATTTGTAACTATACAAGTTTATGGTTGCATTTTTAAATTTTTAA
GAGTGCTTTTTACTTCAACTACTATTTCAATAACATCAAAATTTAAGTTCAAGTGATTGT
TTTCATATTTCAATATTGGATCAAATTTGATTCTAAAATTCTTAATACTTTTTCTTTTTC
TAACCATATCCATTTTTCCTTTTAAAATTTTCTGTCCCTCATCAAGACTATTACATACCA
TACACACAAAATTTTGGTTCTGTTTGCTTTTTCTTCTTTTCTTCTATATACCAGAGTTTA
AATTAGAATATAAGTGTTTAAACCGAGAAACAGGACGAAAATTGAGAGAGAGAGACGAAG
TAATGTTGTCGACTACAATATTGAGAAAAGGATTCAATGTGAAACTTATGCAAAAAAAAT
TATCAGTGAAATGGATCGTTTACGAAGATAACTAATACTAAATAATATATGCCACCTAGT
GTAGTAAAACACGCTCGTGTTCATCGTGGGAGTTGATCGAAATTTGAATCATCAGATTAT
GAATCACAACTTAAAATGAATATGTGCGGTTTATGAATTTAAATTTTTCTTCTTATTAAA
TAAAACTAAAT
>g5483.t10 Gene=g5483 Length=327
MSPSPEPEEKRPRVRLSSEDRDAKKKLLKERLRKQEEEEERRNEQIAKASERSQVSPTIV
VTNGGAGKDRKVSLVSNEEAIAKTSSSPISKNQCSKVICITNLVRPLTFLAVKSLVSRTG
ELDDFWIDSIKSKCFVKYKTEDEAIETRHALHGVKWPEHNLKTLNVEFSTDEEMYRIIES
TPGERIKTALTEAREEESKVQEKSFGWSKGDASVDDRSRVSKRVREWDVGKKEDLEHDES
RERRRRRSSERENRREKERKQLEESTVERRHSVTPGREDKDAIPSQPGRLLDDLFRKSKA
VPCIYWLPLSEEQVNQREGRTTTKKYC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5483.t10 | CDD | cd12432 | RRM_ACINU | 95 | 179 | 1.52406E-34 |
| 8 | g5483.t10 | Coils | Coil | Coil | 18 | 54 | - |
| 9 | g5483.t10 | Coils | Coil | Coil | 232 | 252 | - |
| 7 | g5483.t10 | Gene3D | G3DSA:3.30.70.330 | - | 73 | 176 | 1.0E-6 |
| 4 | g5483.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 48 | - |
| 6 | g5483.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 63 | - |
| 5 | g5483.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 232 | 285 | - |
| 2 | g5483.t10 | PANTHER | PTHR46589 | APOPTOTIC CHROMATIN CONDENSATION INDUCER IN THE NUCLEUS | 29 | 320 | 8.2E-60 |
| 1 | g5483.t10 | Pfam | PF16294 | RNSP1-SAP18 binding (RSB) motif | 223 | 322 | 2.8E-21 |
| 3 | g5483.t10 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 87 | 173 | 3.41E-9 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5483/g5483.t10; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5483.t10.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12875 (apoptotic chromatin condensation inducer in the nucleus)
Pathway
- This transcript belongs to the following pathways
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.
