General information for g2410.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein polybromo-1.
Parent gene
- The parent gene g2410 is located on chr_3: 17768025..17769463 (- 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_3 | g2410 | g2410.t3 | isoform | g2410.t3 | 17768025 | 17769463 |
| chr_3 | g2410 | g2410.t3 | exon | g2410.t3.exon1 | 17768025 | 17768116 |
| chr_3 | g2410 | g2410.t3 | cds | g2410.t3.CDS1 | 17768025 | 17768116 |
| chr_3 | g2410 | g2410.t3 | exon | g2410.t3.exon2 | 17768340 | 17769463 |
| chr_3 | g2410 | g2410.t3 | cds | g2410.t3.CDS2 | 17768340 | 17769282 |
| chr_3 | g2410 | g2410.t3 | TSS | g2410.t3 | 17769706 | 17769706 |
| chr_3 | g2410 | g2410.t3 | TTS | g2410.t3 | NA | NA |
Sequences
>g2410.t3 Gene=g2410 Length=1216
ATGAGTAAAAGAAGAAGAACATCATCTGATATTGAAACAGATGACTCAGACGATGATTCT
GAACAATTTCCAACCACTCCAGCTATTAGAAAAAAGAAAAAATTAGATCCGGTATGTTTT
CAGGTTTTATTATTTTTATCCTTATTATTACCCTATGTATAAAATGTAAAAATTTTTTTA
GATGGAGCAATGTCAATCTCTTTATGAATCAATCAGAAATTTTAAGAAAGAAGATGGTAC
ACAACTCTGTGACAGCTTTATACGCGCACCAAAGCGTCGTCAAGAACCAAATTATTATGA
AATTGTCACCAACCCGATAGATTTATTGCGCGTACAACAAAAACTTAAAACTGATTCATA
TGAAGACATCGATGATCTTACAAATGACATTGAGTTGCTAGTGAAAAATGCAAAAGCATT
CTATAAACCAGATAGTGTTGAGTATAAAGATGCATGCACATTATGGGATGTGTACAATTC
TAATAAAGTGAAACTCATTGAAAGTCTAAATGAAGAGTCAACTCCTGTTGCTTTTGATTC
TTCAAAACCACGTCGAATTGGACGTCCAAGAAAATCAACTACAGTTGATGATGATCAAAT
TTCAGAAAATTCATCTGAAAATAATGACTTTGATGCATATGAAGAACTTTTTGCTTCAAT
AATGACAGCTACTGATCCACTTGATGATCGTGCTCTTCATACAATGTTTCAGCTTTTACC
ATCAAAGAGAACTTTTCCTAGTTATTATGAAGTCATCGATCATCCAATTGATCTCAAATT
TATAGCCAATAAAATTCAAACAAACGCTTATACAAGTCTCAATGAGATGGAAAAAGATGT
CCTGCAAATGGTTAAAAATACACAAATTTTCAATGAACCTGGCAGTCAAATTTACAAAGA
TGCAAAAACTATCAAGAAAATTTTCTTGCAAAAGAAACTTGATATTGAAACTGGAAAATA
CAAGAAACCTATGAGAAGAGGCCGTCAAATTAGTTATAGCGCGGCATGTGCTGCACTTAA
AGAGGAGCTTGAATCATCTGAAGAAGAAATGGACATGGATGATGAGGAGCAAACTGGACC
ATTGTGGCAGCTATTTGATTCTCTCTACCAACAACCAAATTCAGATGGATCTTTAGGGGG
TAATTCACCTTTAGGTGAGAGTTTGTGGAAACTACCGAATAAAAGATTTCATCCTGAGTA
TTACACGCTTATCAAA
>g2410.t3 Gene=g2410 Length=345
MEQCQSLYESIRNFKKEDGTQLCDSFIRAPKRRQEPNYYEIVTNPIDLLRVQQKLKTDSY
EDIDDLTNDIELLVKNAKAFYKPDSVEYKDACTLWDVYNSNKVKLIESLNEESTPVAFDS
SKPRRIGRPRKSTTVDDDQISENSSENNDFDAYEELFASIMTATDPLDDRALHTMFQLLP
SKRTFPSYYEVIDHPIDLKFIANKIQTNAYTSLNEMEKDVLQMVKNTQIFNEPGSQIYKD
AKTIKKIFLQKKLDIETGKYKKPMRRGRQISYSAACAALKEELESSEEEMDMDDEEQTGP
LWQLFDSLYQQPNSDGSLGGNSPLGESLWKLPNKRFHPEYYTLIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g2410.t3 | CDD | cd05524 | Bromo_polybromo_I | 1 | 107 | 1.64479E-56 |
| 16 | g2410.t3 | CDD | cd05517 | Bromo_polybromo_II | 151 | 252 | 3.06582E-44 |
| 14 | g2410.t3 | Coils | Coil | Coil | 276 | 296 | - |
| 13 | g2410.t3 | Gene3D | G3DSA:1.20.920.10 | Histone Acetyltransferase; Chain A | 1 | 109 | 3.5E-35 |
| 12 | g2410.t3 | Gene3D | G3DSA:1.20.920.10 | Histone Acetyltransferase; Chain A | 142 | 260 | 9.3E-32 |
| 20 | g2410.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 117 | 146 | - |
| 19 | g2410.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 123 | 137 | - |
| 3 | g2410.t3 | PANTHER | PTHR16062:SF19 | POLYBROMO | 3 | 94 | 3.0E-96 |
| 5 | g2410.t3 | PANTHER | PTHR16062 | SWI/SNF-RELATED | 3 | 94 | 3.0E-96 |
| 4 | g2410.t3 | PANTHER | PTHR16062:SF19 | POLYBROMO | 30 | 345 | 3.0E-96 |
| 6 | g2410.t3 | PANTHER | PTHR16062 | SWI/SNF-RELATED | 30 | 345 | 3.0E-96 |
| 9 | g2410.t3 | PRINTS | PR00503 | Bromodomain signature | 185 | 201 | 2.0E-10 |
| 8 | g2410.t3 | PRINTS | PR00503 | Bromodomain signature | 201 | 219 | 2.0E-10 |
| 7 | g2410.t3 | PRINTS | PR00503 | Bromodomain signature | 219 | 238 | 2.0E-10 |
| 2 | g2410.t3 | Pfam | PF00439 | Bromodomain | 21 | 91 | 3.4E-18 |
| 1 | g2410.t3 | Pfam | PF00439 | Bromodomain | 165 | 242 | 5.7E-20 |
| 22 | g2410.t3 | ProSiteProfiles | PS50014 | Bromodomain profile. | 18 | 88 | 16.625 |
| 21 | g2410.t3 | ProSiteProfiles | PS50014 | Bromodomain profile. | 168 | 238 | 17.384 |
| 17 | g2410.t3 | SMART | SM00297 | bromo_6 | 1 | 107 | 4.6E-25 |
| 18 | g2410.t3 | SMART | SM00297 | bromo_6 | 149 | 257 | 1.3E-23 |
| 11 | g2410.t3 | SUPERFAMILY | SSF47370 | Bromodomain | 3 | 108 | 3.4E-25 |
| 10 | g2410.t3 | SUPERFAMILY | SSF47370 | Bromodomain | 145 | 253 | 3.79E-28 |
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:0016586 | RSC-type complex | CC |
| GO:0006338 | chromatin remodeling | BP |
| 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. There were no conditions that were differentially expressed