Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription initiation factor TFIID subunit 2.

Parent gene

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 g8868 g8868.t1 isoform g8868.t1 33592334 33596308
chr_2 g8868 g8868.t1 exon g8868.t1.exon1 33592334 33592489
chr_2 g8868 g8868.t1 cds g8868.t1.CDS1 33592334 33592489
chr_2 g8868 g8868.t1 exon g8868.t1.exon2 33592559 33595700
chr_2 g8868 g8868.t1 cds g8868.t1.CDS2 33592559 33595700
chr_2 g8868 g8868.t1 exon g8868.t1.exon3 33595761 33595924
chr_2 g8868 g8868.t1 cds g8868.t1.CDS3 33595761 33595924
chr_2 g8868 g8868.t1 exon g8868.t1.exon4 33595990 33596042
chr_2 g8868 g8868.t1 cds g8868.t1.CDS4 33595990 33596042
chr_2 g8868 g8868.t1 exon g8868.t1.exon5 33596302 33596308
chr_2 g8868 g8868.t1 cds g8868.t1.CDS5 33596302 33596308
chr_2 g8868 g8868.t1 TSS g8868.t1 NA NA
chr_2 g8868 g8868.t1 TTS g8868.t1 NA NA

Sequences

>g8868.t1 Gene=g8868 Length=3522
ATGAAAGCTCATCAAATTTTGGCATTGACTGGAATTTCATTTGAGAAAAAGAGCATAATT
GGTTTTGTTGAATTAACAATAGTTCCAGTAAGAGAAACACTCAAGTATATCAAACTAAAT
GCAAAACAGTGTCGAATTTATAAAGCGATTCTCAACGATACATATGAAGCTCAATTTTAT
TACTTTGATCCATTCACAAATGTCTGTCAGGAAAATCCTACAACACGAGCACTTGAACAA
TTTTCAAAATATCACTTGAATGCGGCTTTACAAGTTGATCCTGATGTGAACGCAGGTGAA
TTAATTATAGTCATACCTCAAGAAGCAAATCATCTAATTGGTGAAGGACGTGGATTAAGA
GTTGGTGTTGAATTTTCATTAGAAGAACCTGCTGGTGGCATTCATTTTGCAATTCCAGAT
CATGGCAATGAAAATTCAAATATGTTTGATCTTGGTGCTCATATGTTTACTTATGGACAT
GAAAATTCATCAAGATTATGGTTTCCTTGTGTCGATTCATATGCTGAACCATGCACTTGG
AAGCTTGAGTTTACAGTTGATGAAAAATTGACAGCAGTATCATGTGGAGAACTAACTGAA
GTTGTTTTGACACCAGATTTAAGGCGAAAAACTTTTCATTATGTAGTAAATACACCTATT
TGTGCACCAAATATTGCATTAGCAGTTGGACCATTTGAGATTTATGTCGATCCAAATATG
CATGAGGTTACACACTTTTGCTTACCAAATCTTCTTCCATTACTAAAAAATACTGTTCGT
TATGTTCATGAAGCATTTGAATTCTACGAAGAAGTGCTTGCATCTCGATTTCCATTTTCC
TGCTACAAACAAGTCTTTGTAGATGAACTTGAAGGAGGACAAGCTCATGCATATTCAACA
ATGACAATTTTGAGCACGCATCTCTTGCATTCGATTGCTATCATTGAACAAACTTTCATT
TCAAGAAAAATCATGTCAAAAGCAATTGCCGAACAATTTTTTGGATGCTTCATTACGATG
AAAAACTGGAATGACGTTTGGTTAGCTCGCGGTATAGCAGAATATTTAAATGGATTTTAT
AGCAAGAAATGTTTCGGAAATAATGCTTATCGTGCTTGGATTCGAAAAGAATTAGCAGAA
GTTGTGAGTTATGAAGAGAAATATGGAGGAATAATTTTAGATCCTAGTCAACCACCTGCT
CCACTACCCGTTGCCAATCAATCCACTAAAGTTGTGGAAATTCAAAAGATTGAGAATGTT
CATTATTTTCCTATCAAAAATCTTCATACAATGTCACCAAAATATGTAGAAATAATGAGA
AAGAAAGCTCATTTAGTAATAAGAATGCTGGAACATCGTATTGGACAAGAGTTGCTGTTA
CAAGTCTTTAATAAACAACTCGCATTAGCAACTAATGCTGCATCTACAAAAATTAGTAGT
GGACTCTGGCATCAACTTTTGATTTCAACAAATGTTTTTACAAAAGCAATTTTCACGGTG
ACAGGAAAAGATATGGCTGTTTTTATTGATCAATGGGTGAGAACAGGTGGCCATGCAAAA
TTTAGTCTTACATCTGTATTCAATCGTAAACGAAATACAATCGAATTAGAAATTCGTCAA
GATTCTGTCAATCAGAAGGGTGTTAGGAAATACGTTGGACCATTGCTTATTCAATTGCAA
GAATTAGACGGTACATTCAAACACACTTTACAAATTGAAAACACAATCGTTAAAGCTGAC
ATTACATGTCACAGTAAATCGCGACGAAATAAAAAAAAGAAAATTCCATTATGTACAGGT
GAAGAAGTTGATATGGATCTATCAGTGATGGATGAATCACCAGTATTATGGATAAGATTG
GATCCTGAAATGACTTTAATGAGACACGTTAATTGTGAGCAACCAGACTTTCAATGGCAA
TTTCAATTAAGACATGAACGTGATGTTACAGCTCAACTTGATGCAATTGATGCTCTTTCA
AAATATGCAACAGCAGCAACTCGAATGGCATTGACTGATGTAATTGAGCATGAATCTTGT
TTTTATGAAGTTCGATGTGAAGCTGCCAAATGCTTGACAAAAGTTGCAAACGCAATGCCT
CAATGGCAAGGACCACCTGCAATGTTGACAATTTTTAGAAAACTTTTTGGGTCATTTTCT
GCACCGCATATCGTAAGACAAAACAATTTTGACAATTTTCAACATTATTTCTTACAAAAA
ACTATACCTTTGGCAATGGCTGGATTACGAACAGCTCACGGAATTTGTCCACCAGAAATA
ATGAGATTCCTATTGGATTTGTTCAAATATAATGATAATGCAAAGAATCACTATTCTGAT
GTTTATTATCGTGCATCACTTGTTGATGCATTAGGTAATTCTATCACTCCTGTCATTTCA
ATGATTCAACAAGGAGCCAAAATTACTTCTGAAAATTTAACACCTGATGCGAAGCTGGTT
CTTGAAGAAATAACGAGAATTTTAAACTTGGAAAAGCATTTGCCTTCATATAAATATGGA
GTGTCTGTGTCATGCTTAAAAGTTATAAGAAAACTACAAAAATGTGGTCATCTTCCACCA
AGTTCAAAAATTTATAGAAGTTATTCAGAATATGGTCATTATATTGATGTTCGTTTAGCT
GCACTCGAATGTCTTGTTGATTATTTAAAAGTTGATGGAAAATGGGATGATATGATTTTT
ATTATTGACTTGCTTGAAAAAGATACAGATCCTGAAGTTCGACATCAATTGGCAAGATTA
ATTGTTGAAAATCCACCATTCGAAAGAAGTAAAGGTCATCGATTGAATCGTGAAGAATTA
CGTGAAAGAATATGGACTAGTATGAATTCAAAATTATCACATGATACCCGGCTTAGATGT
GATTTTGTTGATGTTTATTATGCATTATATGGCGTTAAGGAGCCACACATTGTCAAAAAC
ACAGAATTAGCTGCACTTTATCAGCCACAAAAAGTTGAAAATGATTACAAAGAAGATGAA
AATTTGAAAATCGAAATGGTTGATGCTAAAGAAGAACCAATAATTGAAGGTATTGAAGTT
GTAACTGAATCAATGGAAGAACATAATGATGATGCAATGATTATTGAAACACAACCTGAT
GAAGAAGTAGACTTGAAAATAGAAGCTGATTATGATAAAGTTATTGAAACAACGATAGTT
CCATCTACTACCGATTCATTCCAGTCTCAATTTGCTGAAAGTATTGAACAACCAAGTGTA
AAGAAAATCAAACTTGATTATGCTTCAGATTCACAATCACAGCCAAGCATTGATATGAAT
GAAGGACCTTCTAATTTAAGTATAAATGAAAATCCAAGTGAAGTGAGTGCTGTAAAAGAA
CATAAGAAAAAGAAAAAGAAGGATAAAAAGCGTCACAAGAAAAAGCATAAAAAAGAAAAG
AAACGTGAGAAACATAATCCCGAATCACACCCAAAACATAAAGAAGAAATCGAAATTGAG
ACATTATCTAGTGGTGGCGAAGGTGAAAGTTCATCATCATAA

>g8868.t1 Gene=g8868 Length=1173
MKAHQILALTGISFEKKSIIGFVELTIVPVRETLKYIKLNAKQCRIYKAILNDTYEAQFY
YFDPFTNVCQENPTTRALEQFSKYHLNAALQVDPDVNAGELIIVIPQEANHLIGEGRGLR
VGVEFSLEEPAGGIHFAIPDHGNENSNMFDLGAHMFTYGHENSSRLWFPCVDSYAEPCTW
KLEFTVDEKLTAVSCGELTEVVLTPDLRRKTFHYVVNTPICAPNIALAVGPFEIYVDPNM
HEVTHFCLPNLLPLLKNTVRYVHEAFEFYEEVLASRFPFSCYKQVFVDELEGGQAHAYST
MTILSTHLLHSIAIIEQTFISRKIMSKAIAEQFFGCFITMKNWNDVWLARGIAEYLNGFY
SKKCFGNNAYRAWIRKELAEVVSYEEKYGGIILDPSQPPAPLPVANQSTKVVEIQKIENV
HYFPIKNLHTMSPKYVEIMRKKAHLVIRMLEHRIGQELLLQVFNKQLALATNAASTKISS
GLWHQLLISTNVFTKAIFTVTGKDMAVFIDQWVRTGGHAKFSLTSVFNRKRNTIELEIRQ
DSVNQKGVRKYVGPLLIQLQELDGTFKHTLQIENTIVKADITCHSKSRRNKKKKIPLCTG
EEVDMDLSVMDESPVLWIRLDPEMTLMRHVNCEQPDFQWQFQLRHERDVTAQLDAIDALS
KYATAATRMALTDVIEHESCFYEVRCEAAKCLTKVANAMPQWQGPPAMLTIFRKLFGSFS
APHIVRQNNFDNFQHYFLQKTIPLAMAGLRTAHGICPPEIMRFLLDLFKYNDNAKNHYSD
VYYRASLVDALGNSITPVISMIQQGAKITSENLTPDAKLVLEEITRILNLEKHLPSYKYG
VSVSCLKVIRKLQKCGHLPPSSKIYRSYSEYGHYIDVRLAALECLVDYLKVDGKWDDMIF
IIDLLEKDTDPEVRHQLARLIVENPPFERSKGHRLNREELRERIWTSMNSKLSHDTRLRC
DFVDVYYALYGVKEPHIVKNTELAALYQPQKVENDYKEDENLKIEMVDAKEEPIIEGIEV
VTESMEEHNDDAMIIETQPDEEVDLKIEADYDKVIETTIVPSTTDSFQSQFAESIEQPSV
KKIKLDYASDSQSQPSIDMNEGPSNLSINENPSEVSAVKEHKKKKKKDKKRHKKKHKKEK
KREKHNPESHPKHKEEIEIETLSSGGEGESSSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8868.t1 CDD cd09839 M1_like_TAF2 3 513 2.81252E-162
12 g8868.t1 Coils Coil Coil 1122 1142 -
10 g8868.t1 Gene3D G3DSA:2.60.40.1730 tricorn interacting facor f3 domain 3 230 5.8E-25
11 g8868.t1 Gene3D G3DSA:1.10.390.60 - 236 517 2.9E-42
8 g8868.t1 MobiDBLite mobidb-lite consensus disorder prediction 1088 1173 -
9 g8868.t1 MobiDBLite mobidb-lite consensus disorder prediction 1088 1114 -
7 g8868.t1 MobiDBLite mobidb-lite consensus disorder prediction 1122 1143 -
6 g8868.t1 MobiDBLite mobidb-lite consensus disorder prediction 1144 1161 -
2 g8868.t1 PANTHER PTHR15137 TRANSCRIPTION INITIATION FACTOR TFIID 3 1155 0.0
1 g8868.t1 Pfam PF01433 Peptidase family M1 domain 262 512 9.1E-12
5 g8868.t1 SUPERFAMILY SSF63737 Leukotriene A4 hydrolase N-terminal domain 4 231 2.88E-26
4 g8868.t1 SUPERFAMILY SSF55486 Metalloproteases (zincins), catalytic domain 239 518 1.61E-27
3 g8868.t1 SUPERFAMILY SSF48371 ARM repeat 634 923 1.15E-7

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:0008237 metallopeptidase activity MF
GO:0008270 zinc ion binding MF
GO:0005669 transcription factor TFIID complex CC

KEGG

Orthology

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.

Raw TPM values