General information for g16250.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Condensin complex subunit 3.
Parent gene
- The parent gene g16250 is located on chr_4: 8855420..8858291 (- 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_4 | g16250 | g16250.t1 | TTS | g16250.t1 | 8854283 | 8854283 |
| chr_4 | g16250 | g16250.t1 | isoform | g16250.t1 | 8854445 | 8858291 |
| chr_4 | g16250 | g16250.t1 | exon | g16250.t1.exon1 | 8854445 | 8857029 |
| chr_4 | g16250 | g16250.t1 | cds | g16250.t1.CDS1 | 8854445 | 8857029 |
| chr_4 | g16250 | g16250.t1 | exon | g16250.t1.exon2 | 8857563 | 8857609 |
| chr_4 | g16250 | g16250.t1 | cds | g16250.t1.CDS2 | 8857563 | 8857609 |
| chr_4 | g16250 | g16250.t1 | exon | g16250.t1.exon3 | 8857732 | 8858291 |
| chr_4 | g16250 | g16250.t1 | cds | g16250.t1.CDS3 | 8857732 | 8858291 |
| chr_4 | g16250 | g16250.t1 | TSS | g16250.t1 | NA | NA |
Sequences
>g16250.t1 Gene=g16250 Length=3192
ATGTCTTCATTTTCACAAAAGGCTGAATTGGATGAATCAATTATTGATAAAATAACTGAA
AGAATGCTTTATTTTATGAAAGATATTTCGCCCTTGGTGAGAACTCAAGCAGTTTTTGCA
TTACAAAGATTACAAGATCCAGACTCAAGTGAAGATCCAGTAACAAAATCTTTTATATAT
CACATGGAATCAGATCCAGCAGTGAAAGTTCGTCAAGCAACAATAACAGCAATTGCAAAG
AAATTACAAAATATTCCTGCTATACTTGATCGACTTCATGATGTTGATGAGAAAGTTCGT
CGTCATACATACTTACAAATGTCAAGTTATTCAGTCAAAAGCTACAAAATTGCAGATCGA
ATTGCTATTCTTAGTGCAGGCTTGAATGATCGTTCTGAAATTGTGAAAAAAGCAGTGACA
AATTTACTTCTTTCAAATTGGATTGGTGTTTATGATCATGATTATGCTGAATTTATTCGT
GCTATTAAATTAGACTCGAGTGAAAAGGAATTGATTAAATTTCGTAGTCTTGCTGAAACG
GCTTTGAGTGAAATTTTTAAAAAGCGAAAACTTAATGATTTAATTGCATACCTCAATGCA
TCCGAAATTGGAAAAGAAAGACTTCAAAAATTACTTAAAACAATTCTTTTATCCTATGAC
ATTTCTGAATTTGCAATTGAAGAAATTTCTCATGTCATTGAAAAAGTTATTCCAAATGTT
GAAAAACGTCTTGCATTCTTTAATCAAATTGTGACTGAAATGATAAAACCAGGTGTACCA
TCAGAATATAGTCGACAAACAATCATTGATGATCTTATAGATCGATCAGATATTGATAGA
AAAGTGCAGGCAAAAGCAATTAAACTTCGTATGATGGACTTGAAAGAACAAGAAAGTCAA
TTTGTTAAACAAAAGCAATATGCAGAATGTCAAAAAGTATCTGAAGAATTTCACAAATTA
AATGAAGAACTTATTGAATTGCTTAAACCTGTTGCTAAATCACATTCATCTGATTCAACA
CAATCACTTTTAGAAAATTTATCTTCTGTTGTCACATCTAAAAAAATTACATCAAATGAT
GTTCTTAAGAATTTACGTATTTGTTATTATGCTGTAATGACAAAAGGAGTTAAAACAATT
ACACACGACATACTACAAATTTACAATGAATTTGTTCGTTATCATTTGGAATCAACTGAT
TTAGCAACAAGAATTTGGGCATTAAAAACTACAACAGCTTATAGCTTGCTATATGAGTCA
ATTGCAAAAGAAATTTATTTGGTTATAAAATCTCAAGTTTTTAAAAGTACTCATGTCATT
TTATGGGAATGTTCTATTGAATGCATTTTTGATCTACTTTTACATTATGGAATCGAAAAA
ATGGAAAATGAAAATAATGATGGAAATAATTTGAGCATTTCAATGAATTCACAACCAAAT
AGAAGCAAACGTGGTGGTAGAACATTGTATACAAATGTCGAAGATGATGATGATGAACAT
GATGAAATGAATATTGTCAAAACATTGGACATAATGCAAATGTTGCAACATTTATTGGAA
CAAAGTGATGACATGAGAATAACAAAAGTTTTAATTTGTGGCTTTTGTAAAATGATTTTA
CATGGTGCATACTGCACTCGTGATCTTATGTCGAAATTTCTTTTAATGTATTTTAATCCT
GCAATGCCTGCTGAAATAACTCAATTGTTGGGTGTTTTCTTGGAAAATGTAATTAAGAAA
AAGAAACAAGAATATTTGCATGATGCTTTGACTCCCACAATTTTTACATTAGTTGAAGCT
CCTTATGATTCACCATTGCGTGAAGTTAAACTTGAAACTGTTTTAAAATACATCGTTAAT
GCAACAAGACCAATTTTCTGTAGTAATGGACTTAATTTGCATAACACTCTTGGTATGGAA
TTTTTAAATGTTATGAAAGAAAATCCAGACAGTAAAGAAATTTTAAAGATTTTTGCTAAA
GAATTAGCTGAGCTTGAAATTGGTGAAGATGCAATTTTAAAGAAAGACATGACAAAACAA
ATTGAAACAATTTTAAAAGAATCATCAGCTGATGCTCGTACAAAGAAATATTTGACTGAT
TTTAGTAAAATATTGAATGGAACATATCGAACACCATTGACATTTTCAAGTACAGCAAAA
GCACCAAAAGGTAATGAAGAAGAAGAAGATGAAGATCAATTGGAAAATATTGAAGAAGAA
AATGAAGAAGAAGAGGAAGCAAAAACACAAGCAGAAAAATCACTTGATAAAATTCCCGAT
ATTGAAGTTCAAACAACATCAGAAGTTGAAATTAAAGAATTAGAAATTAAAGTTAAAAAA
GTTGATGTTCCAATTGATACTTCAATGATTTCCATTGCTGAAGTTTCAATTATAAAAGAT
GAAACACAGCAGCCAGAAGATTCTTTGAATGAAACTGAAATTCCACAATCACCCGCACAT
GTTGATTTGCCTGCAACACAAGCTATGGATAATGTTGAAATTGCTGCAACACAAAATATT
ACAAAAGTTGATCTTACTGTACTTGATAGTAGTCAAGAAGATATAAGCATAATTTCAAGT
GATGTTCCTATGACACCACAAACACCTTTGACTGTAAAAAGAACAGCACGACAGAAGCAA
AACATTTCGAGAAGTTCAATGTCAACTGTTAATGAGACTCAAGAAAATGTTGAAATTCCA
CCAACACCTGAAGCAAGATTAAGACGAAGTTTAATAAATAATGCTAAACGTCAATTGGAA
GTTTCAAAATCTACACCAGTTACACCTTCCCAAAGCTCACCGCTTCGTAAAAATCCTAAA
AAAATGCCAGTCTCTACTAAATTGAATTTACAGTCATCTCCTGAAGTTACACCACAATCA
ACTTCTCGCTTATCGCAAACAACTTCGACACCAAATACAAGTCGAATGACAAGAAATCAA
GCAAAAATTGAAATTGCTAAAAATACTACTTTGACACGTTCGGCATCGAAATCACTCAAT
GTTAAACCAAGTAAGGAAACTGAAAAAAGCAATAAAAAAGAATCTAAAGAAACCAAGAAG
CCAACAGCAACAAAAGCATCTAAACTTCCAATTCGCAAACCTTCAGTAGTAGTGAAACCA
ACTGCAACATCAGCATTAAGAGAAATGAGAGTAAAAAACTTACAAAATGCTTCAAGACCG
CCATGGAAATAA
>g16250.t1 Gene=g16250 Length=1063
MSSFSQKAELDESIIDKITERMLYFMKDISPLVRTQAVFALQRLQDPDSSEDPVTKSFIY
HMESDPAVKVRQATITAIAKKLQNIPAILDRLHDVDEKVRRHTYLQMSSYSVKSYKIADR
IAILSAGLNDRSEIVKKAVTNLLLSNWIGVYDHDYAEFIRAIKLDSSEKELIKFRSLAET
ALSEIFKKRKLNDLIAYLNASEIGKERLQKLLKTILLSYDISEFAIEEISHVIEKVIPNV
EKRLAFFNQIVTEMIKPGVPSEYSRQTIIDDLIDRSDIDRKVQAKAIKLRMMDLKEQESQ
FVKQKQYAECQKVSEEFHKLNEELIELLKPVAKSHSSDSTQSLLENLSSVVTSKKITSND
VLKNLRICYYAVMTKGVKTITHDILQIYNEFVRYHLESTDLATRIWALKTTTAYSLLYES
IAKEIYLVIKSQVFKSTHVILWECSIECIFDLLLHYGIEKMENENNDGNNLSISMNSQPN
RSKRGGRTLYTNVEDDDDEHDEMNIVKTLDIMQMLQHLLEQSDDMRITKVLICGFCKMIL
HGAYCTRDLMSKFLLMYFNPAMPAEITQLLGVFLENVIKKKKQEYLHDALTPTIFTLVEA
PYDSPLREVKLETVLKYIVNATRPIFCSNGLNLHNTLGMEFLNVMKENPDSKEILKIFAK
ELAELEIGEDAILKKDMTKQIETILKESSADARTKKYLTDFSKILNGTYRTPLTFSSTAK
APKGNEEEEDEDQLENIEEENEEEEEAKTQAEKSLDKIPDIEVQTTSEVEIKELEIKVKK
VDVPIDTSMISIAEVSIIKDETQQPEDSLNETEIPQSPAHVDLPATQAMDNVEIAATQNI
TKVDLTVLDSSQEDISIISSDVPMTPQTPLTVKRTARQKQNISRSSMSTVNETQENVEIP
PTPEARLRRSLINNAKRQLEVSKSTPVTPSQSSPLRKNPKKMPVSTKLNLQSSPEVTPQS
TSRLSQTTSTPNTSRMTRNQAKIEIAKNTTLTRSASKSLNVKPSKETEKSNKKESKETKK
PTATKASKLPIRKPSVVVKPTATSALREMRVKNLQNASRPPWK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g16250.t1 | Coils | Coil | Coil | 303 | 323 | - |
| 14 | g16250.t1 | Coils | Coil | Coil | 723 | 757 | - |
| 13 | g16250.t1 | Gene3D | G3DSA:1.25.10.10 | - | 4 | 235 | 1.9E-10 |
| 10 | g16250.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 716 | 761 | - |
| 11 | g16250.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 728 | 746 | - |
| 8 | g16250.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 874 | 898 | - |
| 9 | g16250.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 874 | 1063 | - |
| 12 | g16250.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 915 | 1001 | - |
| 7 | g16250.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1002 | 1023 | - |
| 2 | g16250.t1 | PANTHER | PTHR14418:SF5 | CONDENSIN COMPLEX SUBUNIT 3 | 3 | 192 | 2.9E-108 |
| 4 | g16250.t1 | PANTHER | PTHR14418 | CONDENSIN COMPLEX SUBUNIT 3-RELATED | 3 | 192 | 2.9E-108 |
| 3 | g16250.t1 | PANTHER | PTHR14418:SF5 | CONDENSIN COMPLEX SUBUNIT 3 | 194 | 1021 | 2.9E-108 |
| 5 | g16250.t1 | PANTHER | PTHR14418 | CONDENSIN COMPLEX SUBUNIT 3-RELATED | 194 | 1021 | 2.9E-108 |
| 1 | g16250.t1 | Pfam | PF12719 | Nuclear condensing complex subunits, C-term domain | 365 | 667 | 6.5E-43 |
| 6 | g16250.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 14 | 616 | 1.61E-13 |
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:0000796 | condensin complex | CC |
| GO:0007076 | mitotic chromosome condensation | BP |
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.
