General information for g6490.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription initiation factor TFIID subunit 3.
Parent gene
- The parent gene g6490 is located on chr_2: 17247233..17248926 (- 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 | g6490 | g6490.t1 | isoform | g6490.t1 | 17244171 | 17248926 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon1 | 17244171 | 17244315 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS1 | 17244171 | 17244315 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon2 | 17244507 | 17244607 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS2 | 17244507 | 17244607 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon3 | 17245368 | 17245813 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS3 | 17245368 | 17245813 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon4 | 17245877 | 17246037 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS4 | 17245877 | 17246037 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon5 | 17246099 | 17246292 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS5 | 17246099 | 17246292 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon6 | 17246352 | 17248705 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS6 | 17246352 | 17248705 |
| chr_2 | g6490 | g6490.t1 | exon | g6490.t1.exon7 | 17248764 | 17248926 |
| chr_2 | g6490 | g6490.t1 | cds | g6490.t1.CDS7 | 17248764 | 17248926 |
| chr_2 | g6490 | g6490.t1 | TSS | g6490.t1 | 17249160 | 17249160 |
| chr_2 | g6490 | g6490.t1 | TTS | g6490.t1 | NA | NA |
Sequences
>g6490.t1 Gene=g6490 Length=3564
ATGGAAACATACACACATCAAGTTTTAAGAGTGGTTGTAGCTCAAATATGTCAAACAATT
GGATGGCAGAGTGTTACAGCAACTTCATTAGAAATTTTGATTGACATCCTCGACCGATAT
ATTCGAGAAATTTGCAAAACTACTAAAGATTATGCAGAACACTATAATCGAACAGAAGGA
AATCTTGATGATTTAGAATTGGTATTTAGAGACATGGGCATTAATATGAATGAGATTATC
GAGTATATAACTTATGTGGATCCAATTTTACCTGCTGTTAATATTCCAAAATATCCAATT
CCTAAAGAATCACATTTCAATTTTCTAAAACCAGGAAGTAAAGAAATATTGACAAGACCA
GTGCATATCCATGAACATTTGCCACCACTCAATCCTGTCGAAGAAGAACCAATAATTGTG
AATGGTGAAAAAGAAATTGATGTAGTTGGTTTGCCTAATGATGATGTCTTCAAGAGACCA
GCTGACACAAGTAGTGAAGGAAATGCTGTAAAAAAAATAAAATTAGAGGAAGAAGGACGA
GCAACGAGAGAAATTTCATCTGTTATGATGACTACTTCAGGGTTTATTTCTCCTGCACGT
GAAGGAAAAGCTCCAGAATCAAGGCCTCCAAAATTACCAGATGAATTTCCTAAAACAATC
ACGACAACGCCACATATTTCGCCTGTTCCAGGATTTAAGACTAAAGATTCACAAAATTCT
ATACCGGGTATAATTGATAAGAAACTTGAGAAAAAATTAAAGAAAAAGAGTCACGATAAA
GAAAAGAAAAAGGATAAGCAACACAAAGAAAAATATACATTGCCAGATCCAATGGAATTG
TCTCAATATGATCCACTTCCACCACCACAACAGCAACAATCTATGATATCTCATTTGCCT
CCTGCACCAATGAGTGAAGAAATGCTAATGGCTGAACGCAAGAAAGAATTAAAGAAATTA
AAAATGCAGAAAAAAGAGGAAGCAAAGAAGAAGAAAGAAAAAACTCAAAAGTTAACAATG
AAAAGTCAATCAATCGATCCAGGATTTTTGGATACTAAACCACCTTTTGATCCATTTCAT
CATGTTATCACACCTTCTACTTTGCCACAACCTCTACCAACAAGCAGCAGTCAAGTTCAA
GCTCACAGTTATTTGACTGGAGCAGCTCATTCAAACATTTTCTCGAGCTCTATACTTGAT
CAAGCATTTGGTTCACAAGCACCCTCATTGATGTCTGCTCAAAATCCTTTGATTGAAGGA
AAATTAGTTTCTGAACCAGACAAACAAAAACTCAACATTTTCAAAAAGATTTCTAAACCG
AAAGAAGATTCAATAAAACAACAACCACTTGATTTTATGACACCCTCAAAATTAGATCGA
TTTGATCCAAATCAACCATCTACTTCGGGAGAACCGCCATTTGATCCTCTTAAGAAAATT
CATAAATTACCAAAAGAAACAACACTAACAAGAGTTGATGACAGTAATGTACCAATGAAT
CTTTCTGGTAATTTATCAAGAAGTAATGAATCATCATTTGAAGAGATTACAAATATTCCT
AAAACACCCACTATTGCTCCTAAAACACCTGATTTCAAACTAACACAGAGCATAGAGAAA
AAAGAAAAGAAGGAACGCAAGAAAAAAGAAAAGAAAATGGAACAAACAGATTGGAATGCA
CAACAACAATTTACTAATCCGTTTGATATTCAAAATAATCCATTTTTACAAAATTTTCAA
AATACTGGTCTAATGGGTTTAATTCCAAACAGAAATATCTTTACGGCTGCTGCTGACCTT
TTTTCTTCAGGTCCTGGACTTTTACCGAGACAACCGCCATTTGGTATGCCTCAACCAACA
TTGAATCCTTATGGATTTCCATTATCTGGTATGGATAATTTATTACAGCAACAACATCAA
CAGCAGCCACCTAAACCAAAGAAGGTAAAACCTCCTAAAACACAAATTCCCCCAAAGGCT
GCAAATATAGACGATTTTCTACAAATGGGTAGCAAATTTTGCAATGTAGCACCTTTAGTT
CCATCAACCTCAACTCTTTTAAAGGACCGTTTTGATCCTCAATCATTCATGAATGTCGAT
ACTTTTCCATTACAGCAACAGAGTACTACTAGTAATAGTAGTCATATGAATACTACTTTT
GATCAACTCTTGAAAGATCAACATTCATCACAGCAATTTCAAGCATCGACATCGACTCCT
GTTAAGAAATTCAGTGAAGAGAAAATGGAAACTTTTGATCTTACGAAAGATTCATCTCCT
GAGCCTGTAATGAATACGCCATCATCGATTTCTAGACAAGAGCCACCACAGCAGCAACAT
CAGCCTGAAATTTTACCAACAATTCCAGAAAATCAAGAACTTCAATTACAACAACAGGAA
CAACAGCCAGTTGTGATGAAAGAGAAATCTAAAGAAAAGAAAAAGAAGAAAGACAAGGAT
AAGGACAAAGATAAAGACAAAGAAAAAGACCGTGGTGATAAAGAAGAACGTAAAAAGAAG
AAGAAAGAAAAGAAGAAAAAGAAGGAAAAACATAAGGATAAAGAGAAGCATCGTGCATCA
ATGTCGACTCTAGATAGTCAAAGTAATGACACAGAAGATACACTTGATAATAACTCTTCA
TCTTCAATTCCTAAATTGACATTAAAATTAAACTCGCCTCGACCGAATACACCTGACGCT
CATAAAAAGACATTATTACATCGTGCTAGAAATGAAGACTTTGAATTTCCATCTCCACAT
CAAGATGTTGTTTTACATCGTGAAGAGACACATGGATTTATGCGAGATCCATCACCAGAA
CTTGTTCGAATTTCGCCATTAGTCACTCGTCCACCGAAACTAAAGCAGTCAACTTCAATT
TATTCGTCGAGTGGTGGTGATTTTACTTCTACTTCTTCTTATCAAAATAATCCTTCACAC
CATCAACAAGTTCAACATCAAACGAGTTATGTAAATCAATATGATTATAATAATCAATAT
ATGGAATCACAATATCAGCAACCAAGCGGTACATATACTTCTCATCATTATCAACCTTCT
CCGCCGCCAATTCAACAAAATCCTTATCACTATCATCAGTCACATATGCCTTCTTCTCAA
TATCAGAGTGGTCATCAATATCAAGACATGAATATTTATAATCAGTCTGAACCACAACAG
CAATATCATCATCAACCTGTTTATCCTTCAGAAACACAGCATCATCATCAGCATCAGCAA
ACTGATTTTGGATACAGTAATATTTCAAATAATAATAATCAAACATGGAACATATCACAA
AATAAGTCATCATATGTTGATGCTGATGGTAGCACAGTTTGGATTTGTCCTGCTTGTGGA
AGTATTGATGATGGTTCGCCTATGATTGGATGCGATAGTTGTGATGCTTGGTATCATTGG
GCATGTGTTGGTATAAAAGTGGAGCCTAAAGAAAACGAAGACTGGTTCTGTAGAGCGTGT
ATTAGTCGTAAACAGAATGATCAGCTTGAAGGAAAGAAGAAGAAGCGCAAGAAGAAGGAT
AAGGAGAGTAAAAAAGATCTATAG
>g6490.t1 Gene=g6490 Length=1187
METYTHQVLRVVVAQICQTIGWQSVTATSLEILIDILDRYIREICKTTKDYAEHYNRTEG
NLDDLELVFRDMGINMNEIIEYITYVDPILPAVNIPKYPIPKESHFNFLKPGSKEILTRP
VHIHEHLPPLNPVEEEPIIVNGEKEIDVVGLPNDDVFKRPADTSSEGNAVKKIKLEEEGR
ATREISSVMMTTSGFISPAREGKAPESRPPKLPDEFPKTITTTPHISPVPGFKTKDSQNS
IPGIIDKKLEKKLKKKSHDKEKKKDKQHKEKYTLPDPMELSQYDPLPPPQQQQSMISHLP
PAPMSEEMLMAERKKELKKLKMQKKEEAKKKKEKTQKLTMKSQSIDPGFLDTKPPFDPFH
HVITPSTLPQPLPTSSSQVQAHSYLTGAAHSNIFSSSILDQAFGSQAPSLMSAQNPLIEG
KLVSEPDKQKLNIFKKISKPKEDSIKQQPLDFMTPSKLDRFDPNQPSTSGEPPFDPLKKI
HKLPKETTLTRVDDSNVPMNLSGNLSRSNESSFEEITNIPKTPTIAPKTPDFKLTQSIEK
KEKKERKKKEKKMEQTDWNAQQQFTNPFDIQNNPFLQNFQNTGLMGLIPNRNIFTAAADL
FSSGPGLLPRQPPFGMPQPTLNPYGFPLSGMDNLLQQQHQQQPPKPKKVKPPKTQIPPKA
ANIDDFLQMGSKFCNVAPLVPSTSTLLKDRFDPQSFMNVDTFPLQQQSTTSNSSHMNTTF
DQLLKDQHSSQQFQASTSTPVKKFSEEKMETFDLTKDSSPEPVMNTPSSISRQEPPQQQH
QPEILPTIPENQELQLQQQEQQPVVMKEKSKEKKKKKDKDKDKDKDKEKDRGDKEERKKK
KKEKKKKKEKHKDKEKHRASMSTLDSQSNDTEDTLDNNSSSSIPKLTLKLNSPRPNTPDA
HKKTLLHRARNEDFEFPSPHQDVVLHREETHGFMRDPSPELVRISPLVTRPPKLKQSTSI
YSSSGGDFTSTSSYQNNPSHHQQVQHQTSYVNQYDYNNQYMESQYQQPSGTYTSHHYQPS
PPPIQQNPYHYHQSHMPSSQYQSGHQYQDMNIYNQSEPQQQYHHQPVYPSETQHHHQHQQ
TDFGYSNISNNNNQTWNISQNKSSYVDADGSTVWICPACGSIDDGSPMIGCDSCDAWYHW
ACVGIKVEPKENEDWFCRACISRKQNDQLEGKKKKRKKKDKESKKDL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6490.t1 | CDD | cd15522 | PHD_TAF3 | 1115 | 1160 | 6.69132E-28 |
| 7 | g6490.t1 | Coils | Coil | Coil | 310 | 338 | - |
| 9 | g6490.t1 | Coils | Coil | Coil | 534 | 554 | - |
| 8 | g6490.t1 | Coils | Coil | Coil | 825 | 858 | - |
| 5 | g6490.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 1 | 86 | 4.4E-25 |
| 6 | g6490.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 1099 | 1169 | 8.3E-20 |
| 24 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 280 | - |
| 20 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 220 | 241 | - |
| 16 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 350 | - |
| 17 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 339 | - |
| 15 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 536 | 556 | - |
| 18 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 727 | 742 | - |
| 21 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 727 | 746 | - |
| 23 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 751 | 781 | - |
| 25 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 758 | 781 | - |
| 19 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 795 | 898 | - |
| 28 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 805 | 837 | - |
| 27 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 838 | 854 | - |
| 29 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 862 | 898 | - |
| 14 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 942 | 967 | - |
| 26 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 951 | 967 | - |
| 22 | g6490.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1167 | 1187 | - |
| 3 | g6490.t1 | PANTHER | PTHR46452 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 3 | 1 | 1181 | 5.0E-108 |
| 1 | g6490.t1 | Pfam | PF07524 | Bromodomain associated | 4 | 78 | 1.1E-20 |
| 2 | g6490.t1 | Pfam | PF00628 | PHD-finger | 1115 | 1162 | 3.7E-11 |
| 13 | g6490.t1 | ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 1116 | 1160 | - |
| 30 | g6490.t1 | ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 1113 | 1163 | 9.775 |
| 12 | g6490.t1 | SMART | SM00576 | 17neu3 | 2 | 78 | 5.8E-25 |
| 11 | g6490.t1 | SMART | SM00249 | PHD_3 | 1115 | 1161 | 3.0E-12 |
| 4 | g6490.t1 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 1104 | 1165 | 2.88E-17 |
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:0046982 | protein heterodimerization activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14650 (transcription initiation factor TFIID subunit 3)
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.
