Gene loci information

Transcript annotation

  • This transcript has been annotated as Polynucleotide 5’-hydroxyl-kinase NOL9.

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 g8356 g8356.t1 TSS g8356.t1 29945212 29945212
chr_2 g8356 g8356.t1 isoform g8356.t1 29945274 29949075
chr_2 g8356 g8356.t1 exon g8356.t1.exon1 29945274 29945397
chr_2 g8356 g8356.t1 cds g8356.t1.CDS1 29945274 29945397
chr_2 g8356 g8356.t1 exon g8356.t1.exon2 29945454 29946203
chr_2 g8356 g8356.t1 cds g8356.t1.CDS2 29945454 29946203
chr_2 g8356 g8356.t1 TTS g8356.t1 29946310 29946310
chr_2 g8356 g8356.t1 exon g8356.t1.exon3 29946445 29946468
chr_2 g8356 g8356.t1 cds g8356.t1.CDS3 29946445 29946468
chr_2 g8356 g8356.t1 exon g8356.t1.exon4 29946560 29949075
chr_2 g8356 g8356.t1 cds g8356.t1.CDS4 29946560 29949075

Sequences

>g8356.t1 Gene=g8356 Length=3414
ATGGAAGAAGATGGCTGTCCTCGTTGTAAGACAACTAAATATAGAAATCCATCACTCAAG
CTGATGGTTAACATTTGTGGACATACACTTTGCGAGAATTGTGTTGAATTATTGTTTGTT
AAAGGCGCAAACAGCTGTCCAGAATGCAACATCCCACTTCGGCGTAATAATTTTAGAGTC
CAGCTCTTTGATCCAATGGTCGAAAAAGAACTAGAAATTCGAAAACGGATTCTCAAAGAT
TATAATAAGAAAGAAGAAGACTTTGCAACTCTTGAAGAATACAATGCATATTTAGAGGAG
ATTGAAGAAATTATTTTTAATTTATGTAATAATATTGATATATTAGAGACAAATAAGAGA
ATCGAACAGTATAAAAAAGAAAATCGAGAGATAACTATGAAAAATCGACAAAAAATCAGC
AGGGAAGAGTATGAACTTGAGATGTTACTTGAACAAGAGAAAGAAATTGCAGAAATTCGC
AAGAAAGAATTGGAATCACTTGAAGAACAATCAAAGAAAAAGAAGACACTTGAAAAAGAG
AAGTTAATTGATGAGTTGATGTTTAGTACTGAAAATGCTAAATCAATCGTTCAAACTTAT
GCAGAAAAGATTGAGGAAGAGAAGAAAGAGCAAGAACTTGCGCCACCACCACCGAAACTC
ACAAAATTCTCAACTGGCATTGGTTTCTCCTCAAATATGCAACAACAATATCTACCTATT
CCTAAAATTGAAGAAGGTCCATTATATATTTATGAGGAGCCAGAATTTGAGATTCATGGA
CCTGCAGTGCCACGATTTGAAGAATTAAGTGAAAAGAATTTCCTTAAACATATAAGACAA
GAGAGTAATTTAGAGCGCGCTGGTGGATTTCAAATTGATAAGAGTTTTTACTATCAAAAA
ATAATGGTCAGAAACCGAAATAAACACACGCCGAAGAATGGAAAAGACAATCACATGGAT
GCAAAGGCATCGACTAAGCGAAAGAAAAAATTTTCTAATCATCCCCCAGCAAAACGAACG
AAATTACATAAAGAAAATGATGAAGAACATTCTGAACGATTCAAATACATTCTTGCACCG
AAAACTGAAAAAAAGAAAAACATGAAAAAGAATAAATTAGCAACAAATGATACTGTCCAA
ACTAATGGTATTAATAAACAACGTAAAAAGTTGTATGGTAAAAAAGGTAAAGCAAATTTG
ATGGACATTTATGATTATAATGAAAATGGAGAAAGCAGTGACGATGAATGGGAAATGAGT
GATGAATATGAATCATTTGAAAGCGACATGAGCTTAATGGAAGAAGAAGAGTCATCATTA
AACTCTTTAGACGAGGAGTACGATGATTCATATGACGAAGAATATGAAAGTGGAACTGAT
TATTCAGAAGCATCTTTTCATGAGAGTGATTGCGAAAGTTGTGATAATGATTTCAATATG
GAGTATCATTCATCAGAAGATGGCGATTATGTTCCATTCATTCAAGATATTTATGTTAAG
AAAGGAGAAGCAGTGCTCTACGAAGCAAAAGGTCTTGATTTAGCATTTGGCGATACGACA
GAAAGTCAAATTGTAGAGATAAATGAAATTGAAGCTGAAATACATGTTCAAAGTGATGAA
GAAATACCAACATTAGTACCAATTAATGAAAATCAAGAAGATGAAGTTATGCAAGCAGAA
CCAACTCTTGCTGAACTCAATATTGATGATGATGATGAAGAAAATTTAAAATCATCTCAT
CTCTTGGAAAAAGTTACATTCTATGACTGTATTGATGATAAAGGTGTAATTATGCGATTA
AATTCAAAAATTCATTTCCACGGTATTTTAATTATTCGCCCGCTTGTCAATAAAATTCAA
ATTAATGGCTATACACTCAATACAAATGAATCAGTCACAACTGCTTCGATTTCGCGAGCT
GATTATTATCTAAACCTTACACCTATCATTGATGAGAACGTTAGTTTCAACAAAACTGTG
CTATCTGAAACTTTGAAAGAACTGCTTGATCCAAATTTTGACGTTAAAAATTTTATAAAA
GAATTTGATAATACAAAAGAAGTTTTAGTTCATCTTCAACAAGGTCTTCCAGATTCAATT
TTGTCAACATTAGAAACCTATTCACCTCATTCGATTCTGCCACATAAAAATATGATTCTC
AAAAATAGTCCATGTCCTAGCAGCGAATTGATATTGCGTACGAAATTTTTTATTGACTCG
GAAAATCCAAAATTTAGTGGCTTTAAGGTCAATCATGATTGGGATTATATTGAAATGACA
TCAAATATGAAGTTGATAGTTGTTGGTGGTAAAAATGTTGGAAAATCAGCTTTTACTCAA
TACATAATAAATAAGAATGTCTCAAAATTTCAAAAGATTCTTCTCATTGATCTGGATATT
GGACAACCAATTGCATCACCATGTCAAACTGTGAGCGCTACAATTATAAAAAAACCCATT
ATCGGTGCTGGTTATTTATCTGATTTGACTCCTGAAAAAAGTTTTCTTTTTGGTAATGTA
TCAGTTATGGTTGATCCATTCAGATATGTCAAATGTGTCGAGGAGCTGATAAAATTCTGC
AATGAAAATGAAGAGTATAAAAACATTCCTTGGATTATAAATACAATGGGTTATCAAAAA
GGCTTTGGACTGCCATTAATGTGCGTTTTATTACGAATAATTCAACCAACGGATGTAATT
CAAATTCAGCATTCAAATAATAGCTACAATTTCAAAAGCATCCTCAAAGCTGAATTTGTT
AATAATTTTCAATACTTCTTTTTCACAAAGAAATTTCTTGATGAATTTCCAACTATGGTT
TCTTACACAACACATGTTCTAGATTCAATTGTTAATAATTCACCCATAATTGATGATGAT
AGAAAGCAAGATAGTGAAGGCAAATGGATTTCAAATGCATCTGAAAAGCGAAAAATGTCA
ATGATTGCACAAATGGGAAAACTAATGAAAGGTGGTCAAAAATATTTAAATGATGTCGTA
CCATTTTCTGCATTAATTGATTCAATTCGTATGGTAGTACTTGATGAAGAATATCAATCG
AACGATAAAGATATTGATTTGAAGTTATTCAATGGGAATTTAGTTTATCTGTGTCATGAT
GATGGCAGCAGTAAAATTAACAAGAAACCAATTGAGTGCTTTGGGTTTGGAATCGTTCGA
GCAATTGACAAAATTCATGGAAAAATTTATATCATCTTACCAGAAAGTAAAAACGCTCAG
AAAATGCAATCGAATATAAATATGCTTGCTTTAGGATATAACTGCATGCCACAAGAAATA
CTCTTGAAACAAAATTTCGGAATCGATGGAACAGTTCCTTACGTGACTTTCTTCAAGGAA
CGCAATATTAGCAAAAAGTATATCAATAGACGAAATATTAAGGACTGTTTTTAA

>g8356.t1 Gene=g8356 Length=1137
MEEDGCPRCKTTKYRNPSLKLMVNICGHTLCENCVELLFVKGANSCPECNIPLRRNNFRV
QLFDPMVEKELEIRKRILKDYNKKEEDFATLEEYNAYLEEIEEIIFNLCNNIDILETNKR
IEQYKKENREITMKNRQKISREEYELEMLLEQEKEIAEIRKKELESLEEQSKKKKTLEKE
KLIDELMFSTENAKSIVQTYAEKIEEEKKEQELAPPPPKLTKFSTGIGFSSNMQQQYLPI
PKIEEGPLYIYEEPEFEIHGPAVPRFEELSEKNFLKHIRQESNLERAGGFQIDKSFYYQK
IMVRNRNKHTPKNGKDNHMDAKASTKRKKKFSNHPPAKRTKLHKENDEEHSERFKYILAP
KTEKKKNMKKNKLATNDTVQTNGINKQRKKLYGKKGKANLMDIYDYNENGESSDDEWEMS
DEYESFESDMSLMEEEESSLNSLDEEYDDSYDEEYESGTDYSEASFHESDCESCDNDFNM
EYHSSEDGDYVPFIQDIYVKKGEAVLYEAKGLDLAFGDTTESQIVEINEIEAEIHVQSDE
EIPTLVPINENQEDEVMQAEPTLAELNIDDDDEENLKSSHLLEKVTFYDCIDDKGVIMRL
NSKIHFHGILIIRPLVNKIQINGYTLNTNESVTTASISRADYYLNLTPIIDENVSFNKTV
LSETLKELLDPNFDVKNFIKEFDNTKEVLVHLQQGLPDSILSTLETYSPHSILPHKNMIL
KNSPCPSSELILRTKFFIDSENPKFSGFKVNHDWDYIEMTSNMKLIVVGGKNVGKSAFTQ
YIINKNVSKFQKILLIDLDIGQPIASPCQTVSATIIKKPIIGAGYLSDLTPEKSFLFGNV
SVMVDPFRYVKCVEELIKFCNENEEYKNIPWIINTMGYQKGFGLPLMCVLLRIIQPTDVI
QIQHSNNSYNFKSILKAEFVNNFQYFFFTKKFLDEFPTMVSYTTHVLDSIVNNSPIIDDD
RKQDSEGKWISNASEKRKMSMIAQMGKLMKGGQKYLNDVVPFSALIDSIRMVVLDEEYQS
NDKDIDLKLFNGNLVYLCHDDGSSKINKKPIECFGFGIVRAIDKIHGKIYIILPESKNAQ
KMQSNINMLALGYNCMPQEILLKQNFGIDGTVPYVTFFKERNISKKYINRRNIKDCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8356.t1 CDD cd16517 RING-HC_MAT1 6 54 2.68363E-32
10 g8356.t1 Coils Coil Coil 98 134 -
12 g8356.t1 Coils Coil Coil 147 180 -
9 g8356.t1 Coils Coil Coil 190 210 -
11 g8356.t1 Coils Coil Coil 433 453 -
8 g8356.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 1 65 3.8E-22
7 g8356.t1 Gene3D G3DSA:3.40.50.300 - 752 931 3.4E-21
18 g8356.t1 MobiDBLite mobidb-lite consensus disorder prediction 307 352 -
16 g8356.t1 MobiDBLite mobidb-lite consensus disorder prediction 309 323 -
17 g8356.t1 MobiDBLite mobidb-lite consensus disorder prediction 338 352 -
15 g8356.t1 MobiDBLite mobidb-lite consensus disorder prediction 409 444 -
4 g8356.t1 PANTHER PTHR12683 CDK-ACTIVATING KINASE ASSEMBLY FACTOR MAT1 1 293 3.4E-76
5 g8356.t1 PANTHER PTHR12683:SF13 CDK-ACTIVATING KINASE ASSEMBLY FACTOR MAT1 1 293 3.4E-76
1 g8356.t1 Pfam PF17121 Zinc finger, C3HC4 type (RING finger) 3 48 3.6E-12
3 g8356.t1 Pfam PF06391 CDK-activating kinase assembly factor MAT1 53 252 1.4E-58
2 g8356.t1 Pfam PF16575 mRNA cleavage and polyadenylation factor CLP1 P-loop 769 916 4.2E-29
14 g8356.t1 ProSitePatterns PS00518 Zinc finger RING-type signature. 26 35 -
20 g8356.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 6 50 10.35
6 g8356.t1 SUPERFAMILY SSF57850 RING/U-box 2 60 5.02E-10
19 g8356.t1 TIGRFAM TIGR00570 cdk7: CDK-activating kinase assembly factor MAT1 1 292 2.5E-111

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:0005675 transcription factor TFIIH holo complex CC
GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity BP
GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity MF
GO:0006289 nucleotide-excision repair 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.

Raw TPM values