General information for g5483.t1
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.t1 | TSS | g5483.t1 | 9832519 | 9832519 |
| chr_2 | g5483 | g5483.t1 | isoform | g5483.t1 | 9832768 | 9835346 |
| chr_2 | g5483 | g5483.t1 | exon | g5483.t1.exon1 | 9832768 | 9834353 |
| chr_2 | g5483 | g5483.t1 | cds | g5483.t1.CDS1 | 9832768 | 9834353 |
| chr_2 | g5483 | g5483.t1 | exon | g5483.t1.exon2 | 9834421 | 9834652 |
| chr_2 | g5483 | g5483.t1 | cds | g5483.t1.CDS2 | 9834421 | 9834652 |
| chr_2 | g5483 | g5483.t1 | exon | g5483.t1.exon3 | 9834708 | 9834876 |
| chr_2 | g5483 | g5483.t1 | cds | g5483.t1.CDS3 | 9834708 | 9834876 |
| chr_2 | g5483 | g5483.t1 | exon | g5483.t1.exon4 | 9834938 | 9835050 |
| chr_2 | g5483 | g5483.t1 | cds | g5483.t1.CDS4 | 9834938 | 9835050 |
| chr_2 | g5483 | g5483.t1 | exon | g5483.t1.exon5 | 9835107 | 9835346 |
| chr_2 | g5483 | g5483.t1 | cds | g5483.t1.CDS5 | 9835107 | 9835346 |
| chr_2 | g5483 | g5483.t1 | TTS | g5483.t1 | 9836018 | 9836018 |
Sequences
>g5483.t1 Gene=g5483 Length=2340
ATGCCGCGAAAAGCAAGAGGATCGGGAAGCTCACCCGAAAAGCAGACAACTACAAGAAGA
AATACTCGTCGAGGACAAAAAGTTTCTGAGCCAGCTGAAAACGAAATTACCGATGAAATC
CCGGCTCATTTGCTGAGAGGATCTGATGAATCTTCTGAACAATCTGATAATGATTCTGAT
TATGGCAGCCCAAAAAAGGGTAGAGGAAGAGCAGCTGCAACTAGGGGTCGTGGCAGAAAA
GCAAAAGAGGCAGAAGAAAAGACTGCACCTACTCCGAGTCGACCAAGACGCGGAAGACGA
GCAAGAGGAGAAAGTCCAGCAACAATAGATGAACAAGAACAAGAGCAAAACTCACAGGAA
GAATATGTTGAATCTGTTAACAGTCAAACAACAATTGAAGAACATGAAACTTCTACTATG
GAATCAACATCTGATCAACGAGTTGTTTCTGATGAAAAACAAGAAGAACAAGAAATAGAA
AATGTTCAAGAGTCTTTTCCTGAAAAAAGTGTTGAACCAGAGAAAGAATCGTCACCAAAG
AATGAGGAACCACAAGAAATCATTGAAGTGAAAGAGCAAGTAATTACTGCTGAAAAGGTA
AGTGAAGTAACAATTGAACAGGATCAATCGAATAATGATCAAGCAACTGTTAACGAAGAA
GTTGTTGCTGATGATGATGAAAGTAAACAAAATGAAGAGAGTCAAAATGATGACAATGTA
GAACAGGTAACTGTAACAGTCGAAAAGGAAAAATCTTCTTCACCTGAAGTTACTGCTGAT
GATGAAGTATCAAAAGATGCACCAGACATTTCAATGGAAGTTGATCAGAGCGATTCTCGT
TCTAGTTCACCTCAACAACATACGAAAAATCAATTACAACGTTCAAGATCAAGTTCAGGA
GAAATCCATGAAGATAGCAGAGATGAATCTATGAAAGAAAGTTCGCCAAAAAAGCCACAA
GAATCATCTCCAAAGAGAAATCAATCTCCAATAAAGCAGCCGTCACCAAAAGAGACAGAG
CCTAAACCTGTGACTCAAAGAAAACGAAAATGGGGTGCACGTAAAGATGATGAAAAAGTT
ATTGCTATAACTACAGATTCATTGGCAAATATTATCGCTGAAGAAGTTAAACCAGTTCCT
TTAAGTGATGTAAAATTAGCAATGAGTCCATCACCTGAACCAGAAGAAAAAAGACCAAGA
GTTAGACTTTCATCGGAAGATCGTGATGCAAAAAAGAAACTTTTAAAGGAACGTTTGAGA
AAACAAGAAGAAGAAGAGGAACGTCGAAATGAGCAAATTGCTAAAGCTAGTGAACGCAGT
CAAGTATCTCCGACAATTGTTGTCACAAATGGAGGTGCTGGAAAAGATCGTAAAGTGTCA
CTTGTTAGCAATGAAGAAGCGATTGCAAAAACTTCATCCTCGCCAATATCGAAAAATCAA
TGCTCAAAAGTTATATGTATCACAAATTTGGTACGTCCTCTAACATTTTTAGCTGTCAAA
TCTTTGGTCTCACGAACTGGTGAACTTGATGATTTTTGGATAGATTCTATCAAATCAAAA
TGCTTTGTAAAGTACAAAACAGAAGATGAAGCTATTGAAACTCGTCATGCGTTGCATGGT
GTAAAATGGCCAGAACATAATTTGAAAACTTTAAATGTTGAATTTTCAACTGATGAAGAA
ATGTATCGAATTATTGAATCTACTCCTGGTGAACGTATTAAAACAGCACTAACAGAAGCT
CGAGAAGAGGAATCAAAAGTGCAGGAAAAGAGTTTTGGATGGTCGAAAGGTGATGCTTCG
GTTGATGATCGATCAAGAGTTTCAAAAAGAGTTCGTGAATGGGATGTTGGAAAGAAAGAA
GATTTAGAGCATGATGAAAGCAGAGAAAGGCGTCGTCGAAGATCTTCAGAACGAGAAAAT
CGTCGAGAGAAGGAGCGAAAACAATTGGAAGAGTCTACTGTAGAGAGACGACATAGTGTT
ACACCTGGACGAGAAGATAAAGATGCAATTCCATCACAGCCTGGTCGTTTATTAGATGAT
TTGTTCCGGAAATCTAAAGCTGTTCCATGCATTTATTGGCTACCACTTTCTGAAGAACAG
ATCAAAGAGAAGGAAGAACAACGACAAAAAAATATTGCTGAACATAATCGTCGCATGGAA
GAAATAATAAAAAATAGGGAATTACAGCGTGAGAAAATGAATGAAGAAAGACGCGAACGC
GAAGCAAAGCGTCGTGAGGAGAGAAAAGATCGCGAAAGAAAGCGTACAAGATCACGTAGC
CGTAGTGTTCGTCGTTATTCGCGTGAGAGACATCGTGATCGACGATACGATCGTCGATAA
>g5483.t1 Gene=g5483 Length=779
MPRKARGSGSSPEKQTTTRRNTRRGQKVSEPAENEITDEIPAHLLRGSDESSEQSDNDSD
YGSPKKGRGRAAATRGRGRKAKEAEEKTAPTPSRPRRGRRARGESPATIDEQEQEQNSQE
EYVESVNSQTTIEEHETSTMESTSDQRVVSDEKQEEQEIENVQESFPEKSVEPEKESSPK
NEEPQEIIEVKEQVITAEKVSEVTIEQDQSNNDQATVNEEVVADDDESKQNEESQNDDNV
EQVTVTVEKEKSSSPEVTADDEVSKDAPDISMEVDQSDSRSSSPQQHTKNQLQRSRSSSG
EIHEDSRDESMKESSPKKPQESSPKRNQSPIKQPSPKETEPKPVTQRKRKWGARKDDEKV
IAITTDSLANIIAEEVKPVPLSDVKLAMSPSPEPEEKRPRVRLSSEDRDAKKKLLKERLR
KQEEEEERRNEQIAKASERSQVSPTIVVTNGGAGKDRKVSLVSNEEAIAKTSSSPISKNQ
CSKVICITNLVRPLTFLAVKSLVSRTGELDDFWIDSIKSKCFVKYKTEDEAIETRHALHG
VKWPEHNLKTLNVEFSTDEEMYRIIESTPGERIKTALTEAREEESKVQEKSFGWSKGDAS
VDDRSRVSKRVREWDVGKKEDLEHDESRERRRRRSSERENRREKERKQLEESTVERRHSV
TPGREDKDAIPSQPGRLLDDLFRKSKAVPCIYWLPLSEEQIKEKEEQRQKNIAEHNRRME
EIIKNRELQREKMNEERREREAKRREERKDRERKRTRSRSRSVRRYSRERHRDRRYDRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g5483.t1 | CDD | cd12432 | RRM_ACINU | 482 | 566 | 1.02227E-32 |
| 25 | g5483.t1 | Coils | Coil | Coil | 109 | 129 | - |
| 24 | g5483.t1 | Coils | Coil | Coil | 405 | 441 | - |
| 23 | g5483.t1 | Coils | Coil | Coil | 619 | 639 | - |
| 22 | g5483.t1 | Coils | Coil | Coil | 705 | 753 | - |
| 21 | g5483.t1 | Gene3D | G3DSA:3.30.70.330 | - | 460 | 563 | 4.2E-6 |
| 7 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 443 | - |
| 14 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 17 | 65 | - |
| 13 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 109 | - |
| 11 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 137 | - |
| 6 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 196 | - |
| 5 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 200 | 218 | - |
| 17 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 237 | 252 | - |
| 18 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 273 | - |
| 8 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 297 | - |
| 4 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 298 | 320 | - |
| 19 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 335 | - |
| 15 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 341 | 362 | - |
| 9 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 390 | 435 | - |
| 16 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 619 | 672 | - |
| 12 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 724 | 779 | - |
| 20 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 724 | 753 | - |
| 10 | g5483.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 754 | 773 | - |
| 2 | g5483.t1 | PANTHER | PTHR46589 | APOPTOTIC CHROMATIN CONDENSATION INDUCER IN THE NUCLEUS | 266 | 765 | 1.9E-71 |
| 1 | g5483.t1 | Pfam | PF16294 | RNSP1-SAP18 binding (RSB) motif | 610 | 714 | 7.0E-24 |
| 3 | g5483.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 474 | 560 | 1.77E-8 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5483/g5483.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5483.t1.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.
