General information for g3020.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nucleolar protein 6.
Parent gene
- The parent gene g3020 is located on chr_3: 22170387..22171940 (- 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 | g3020 | g3020.t1 | TTS | g3020.t1 | 22166847 | 22166847 |
| chr_3 | g3020 | g3020.t1 | isoform | g3020.t1 | 22166895 | 22170387 |
| chr_3 | g3020 | g3020.t1 | exon | g3020.t1.exon1 | 22166895 | 22167588 |
| chr_3 | g3020 | g3020.t1 | cds | g3020.t1.CDS1 | 22166895 | 22167588 |
| chr_3 | g3020 | g3020.t1 | exon | g3020.t1.exon2 | 22167659 | 22169115 |
| chr_3 | g3020 | g3020.t1 | cds | g3020.t1.CDS2 | 22167659 | 22169115 |
| chr_3 | g3020 | g3020.t1 | exon | g3020.t1.exon3 | 22169173 | 22170306 |
| chr_3 | g3020 | g3020.t1 | cds | g3020.t1.CDS3 | 22169173 | 22170306 |
| chr_3 | g3020 | g3020.t1 | exon | g3020.t1.exon4 | 22170364 | 22170387 |
| chr_3 | g3020 | g3020.t1 | cds | g3020.t1.CDS4 | 22170364 | 22170387 |
| chr_3 | g3020 | g3020.t1 | TSS | g3020.t1 | 22170456 | 22170456 |
Sequences
>g3020.t1 Gene=g3020 Length=3309
ATGGCAAAAGTTAAACAATCTGCTGGACTTTTTGTTCGCAATCCAAATTTTGTTAAAAAT
GATTCTGAAAGTGATATTGATGACGATGAATTCAATGATTCTGGAGTAAGTGATGATCAT
GCAATAGAAGAAAAACCTACGAAAAAGAGAAAGAATAAATCAAAAGATGGTAAGAAGGCA
AAGAAAATAAAGTCTGATGAAAAATTGACTGCTGAAGAAATTAATGAGTTGAAAGAAACC
GAAGAACTTTATCATTCAAGTCTTTTTCGTATGCAAATTGATGAAACGCTGAAAGAAGTT
CAATTGAGCAACGATCAACAGGAGTTTGTGAAAAAATGGCTAACAACTTTCAAAAAGTTT
CTAAATAAATTACCATCAGTTGAAATTAGTGGATTTGCAAAGAATTTGAAAGTGATTGAT
GGCACTAAGAAGCCACAATTCAATTATAAACCACCGGAAGATGCCATTTTATTTGGATCT
CATGCTATAGAAACTAATATAGAAGCAAAATCAAGTGTTGATGTTCTGTTAATTATGCCA
AGTGAATTTTTCCATAAAAGTGACTATCTTAATCAAATTTTTATTCACAAGAGAGTAATT
TATTTGTCATACATTGCAAAGAAATTGATAGAAAAAGGCACTCTCGGTGGAAATATCAAA
ATTTCCAATTTAAAGAATGATTCTTCAAATCCAGTGTTGGTTTTAGATGCTGAGGAGTTT
AATATTTCAATTACAGCAACACCACCAGAGAATTTTTTCAAACTGAATCGATTTATACCA
ATAACTAATAATATTAAACTAAAAAGTGTTGAAGAATCGACAACACCAACGCCACATTAT
AATTTCGAAGTACTTTATGCATCTACCATTCAAAGAAATCAAAAAATTCTTGAGGATCAA
ATAGCAAAATATTCAAATATTAAAAATGCAATTAAACTCATAAAAATTTGGTTGCATCAA
CGTGAATTTGATGCTGGATTTCATGGAATAAATGGATTCATTGTATCATGTTATCTCATT
TATTTGATGAAAATTAAGAAAATATTTCACACAATGAGTTGTTATCAAATATTGCGAGTC
TTTTGGAATCATTTTGGTCATTCTCAATTAGATGTAACTGGTATTACAATATGTAACGAG
AAAAATTTGCCTAATCAGCCATCATTGGAAGATTTCCGTAAATTTTACGAGGTCGTTATG
ATTGATTCATCAGGTTATTGCAACATTCTTTCACACCTATCAATCGATCTTTATAAAAGA
ATTCGCATAGAATGTCTGAATGCCATCGAAATATTAGATGATAAATTAATCAACAATTTT
CAGCAACTATTTCTCACTCCAATTCCTTTCTATATTCAATATGACCACTTTGTATCAATC
AAATGTGATAACAATCTGCTAGAACAACTCATTAATAAACGTGGAACTGTTGATGATAAA
ATTAATTATCACAATTTGACTTATGCACATGCAAGAAAATTAATAATGAATGTGCTAAGA
AGAGGCTTAGGAGAACGAGCTTTATCTATTGTTCCGGTGTCAATTAATGATGAGGAAAAC
TTTAATGTAGGAATAATTTTAAATCTTGAACATGCAGTAAATATAGTTGATAAAGGTCCA
CAATCAAATCAGCCAGAAGCTGAAGATTTTAGAAAATTTTGGGGAAATAAATCAGAAATT
CGTCGTTTTAAAGACGGTTCTATTACAGAATCAGTTCTTTGGTGCACTGCGGACGTTCCA
ATTGGAGAAAAACGCTTAATTTGTAAGAAAATTGTGTTATTCTTATTGAAACAACATTTT
AATATAAGCATTGACAAAATCAATTATATTGCTGGTCAATTTGATATCACGATTCGAACA
ATCTTTAATGAACTAATGGAAACTAATGAAGAACGTTCGTTGGCTGCAATTCATGCATTT
GATGAACTCAGCAAAGAATTAAGAAACTTGAACGATCTTCCATTAGAAATTGTTAGTGTT
CTTGGAGTTGATTCAACTTTTCGTTATACTGATGTCACACCACCATTGGCCAATGCTTTG
GCGACCAAAAATGGCTTCGTTAGCAAAGAATTGAAGGGAATGTTTCTAGCACAAAAAGTT
TTAAATGGAGTAATTCAATTAACGGCAAGTGGAAAATGGCCAGATGAAATTGACGCCATG
CAACGAATTAAAGCAGCCTTCTATAATGAAATTGCAAAAAAGACACAAGTACAATATCCA
ACAACAATTATTCATGTCATGTCGGATTGCATTGAAGTTCTAAAGAATAAGTTTGTATTT
AGACTAAAAATTGTGCATCCGAAGGAAATTGCATTGGCTAAAGAGGAAATATCGCCAACA
AACAACCTTACAAAGTTGTATAGAGAAAATGAAGAAAGTTTAAAATTAGAGTACGAAAGC
AAAGTGCTTCCAAAGTTAACGAGTTTTCTTCACGGTCTTCATCATCGTTTTGCTAGTTAT
GGACCAACAGTTGCAATAGCTAAACGATGGCTTTACTCGCAGTTGATTGACTCATTTCTT
TGGCCCGATGAATGCACTGAACTTATTATTGCTGAAATGTTTTTAAAAAATTTTCCAATG
AAACCAACTTTTCAACCACAAACTGGTTTTATAAGATTTCTTTATTATCTCGTGAATTTT
TCACCTGAAAACGACATGATTGTTGTGAACTTCAATGAAGAAATGGATGTCGATCAAATC
AATGAACTCGAAACAAATTTCCATAAAAATCGGAAAAATTTTCCGCCACTTTTCATCGTT
ACATCGAGTGATTTGCCTCACCAATTTGGAATGTATAGCTCACGTGCACCATCAATAGAA
ATTTTGAAACGTGTAAAAATGCTTGCAGAATTTTCCATAAAAATTCTATCTCAAGACTAT
GCAAAGTTAAACGAAAGCATTGTAGAAGATTTATTTACACCATCATTTGAAGGATATAAT
TTACTGATCAATTTAAATGAGAAGTTTGTAAGAAAGTCGGACATAGTCAAATATAAATTT
GCAAATTTTAAGGCAATTCAGTATGAAAAGAAAACTCCAGTTGGTGCAGGTATCGATTTT
GTAGCATCATTTTTGAAAGAACTTCGTGAAGCATTCAATGATATTGCTCTATTTTTTTAC
AATCCAATTTCGGGTAACAAAATTGCAATGCTATGGAAACCATCAATCAAGGAAAGCAAA
AAGTTTGCAGCATCACATGTCAATATGTGCAAGCTAGTAAATGAGAAATTACATGTTAAC
ATAGATGCTATTCTCAATGACATAAATATTATAGGAGCAGGAATTATTGATTCAATTGAA
ATTTGTTAA
>g3020.t1 Gene=g3020 Length=1102
MAKVKQSAGLFVRNPNFVKNDSESDIDDDEFNDSGVSDDHAIEEKPTKKRKNKSKDGKKA
KKIKSDEKLTAEEINELKETEELYHSSLFRMQIDETLKEVQLSNDQQEFVKKWLTTFKKF
LNKLPSVEISGFAKNLKVIDGTKKPQFNYKPPEDAILFGSHAIETNIEAKSSVDVLLIMP
SEFFHKSDYLNQIFIHKRVIYLSYIAKKLIEKGTLGGNIKISNLKNDSSNPVLVLDAEEF
NISITATPPENFFKLNRFIPITNNIKLKSVEESTTPTPHYNFEVLYASTIQRNQKILEDQ
IAKYSNIKNAIKLIKIWLHQREFDAGFHGINGFIVSCYLIYLMKIKKIFHTMSCYQILRV
FWNHFGHSQLDVTGITICNEKNLPNQPSLEDFRKFYEVVMIDSSGYCNILSHLSIDLYKR
IRIECLNAIEILDDKLINNFQQLFLTPIPFYIQYDHFVSIKCDNNLLEQLINKRGTVDDK
INYHNLTYAHARKLIMNVLRRGLGERALSIVPVSINDEENFNVGIILNLEHAVNIVDKGP
QSNQPEAEDFRKFWGNKSEIRRFKDGSITESVLWCTADVPIGEKRLICKKIVLFLLKQHF
NISIDKINYIAGQFDITIRTIFNELMETNEERSLAAIHAFDELSKELRNLNDLPLEIVSV
LGVDSTFRYTDVTPPLANALATKNGFVSKELKGMFLAQKVLNGVIQLTASGKWPDEIDAM
QRIKAAFYNEIAKKTQVQYPTTIIHVMSDCIEVLKNKFVFRLKIVHPKEIALAKEEISPT
NNLTKLYRENEESLKLEYESKVLPKLTSFLHGLHHRFASYGPTVAIAKRWLYSQLIDSFL
WPDECTELIIAEMFLKNFPMKPTFQPQTGFIRFLYYLVNFSPENDMIVVNFNEEMDVDQI
NELETNFHKNRKNFPPLFIVTSSDLPHQFGMYSSRAPSIEILKRVKMLAEFSIKILSQDY
AKLNESIVEDLFTPSFEGYNLLINLNEKFVRKSDIVKYKFANFKAIQYEKKTPVGAGIDF
VASFLKELREAFNDIALFFYNPISGNKIAMLWKPSIKESKKFAASHVNMCKLVNEKLHVN
IDAILNDINIIGAGIIDSIEIC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3020.t1 | Gene3D | G3DSA:3.30.460.10 | Beta Polymerase | 102 | 259 | 4.8E-24 |
| 11 | g3020.t1 | Gene3D | G3DSA:1.10.1410.10 | - | 284 | 449 | 5.3E-22 |
| 10 | g3020.t1 | Gene3D | G3DSA:3.30.70.3030 | - | 977 | 1101 | 1.2E-7 |
| 9 | g3020.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 65 | - |
| 8 | g3020.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 35 | 50 | - |
| 7 | g3020.t1 | PANTHER | PTHR17972 | NUCLEOLAR RNA-ASSOCIATED PROTEIN | 70 | 1101 | 3.0E-247 |
| 3 | g3020.t1 | Pfam | PF03813 | Nrap protein domain 1 | 173 | 300 | 1.7E-27 |
| 6 | g3020.t1 | Pfam | PF17403 | Nrap protein PAP/OAS-like domain | 307 | 446 | 8.3E-30 |
| 2 | g3020.t1 | Pfam | PF17404 | Nrap protein domain 3 | 451 | 602 | 6.9E-37 |
| 5 | g3020.t1 | Pfam | PF17405 | Nrap protein nucleotidyltransferase domain 4 | 620 | 815 | 2.4E-42 |
| 4 | g3020.t1 | Pfam | PF17406 | Nrap protein PAP/OAS1-like domain 5 | 817 | 974 | 7.5E-32 |
| 1 | g3020.t1 | Pfam | PF17407 | Nrap protein domain 6 | 977 | 1099 | 2.8E-24 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K14544 (U3 small nucleolar RNA-associated protein 22)
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.
