Gene loci information

Transcript annotation

  • This transcript has been annotated as RNA cytidine acetyltransferase.

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_3 g2446 g2446.t1 TTS g2446.t1 18014441 18014441
chr_3 g2446 g2446.t1 isoform g2446.t1 18014506 18017723
chr_3 g2446 g2446.t1 exon g2446.t1.exon1 18014506 18017175
chr_3 g2446 g2446.t1 cds g2446.t1.CDS1 18014506 18017175
chr_3 g2446 g2446.t1 exon g2446.t1.exon2 18017238 18017397
chr_3 g2446 g2446.t1 cds g2446.t1.CDS2 18017238 18017397
chr_3 g2446 g2446.t1 exon g2446.t1.exon3 18017464 18017558
chr_3 g2446 g2446.t1 cds g2446.t1.CDS3 18017464 18017558
chr_3 g2446 g2446.t1 exon g2446.t1.exon4 18017616 18017723
chr_3 g2446 g2446.t1 cds g2446.t1.CDS4 18017616 18017723
chr_3 g2446 g2446.t1 TSS g2446.t1 18017792 18017792

Sequences

>g2446.t1 Gene=g2446 Length=3033
ATGGTGAAGAAAAAGATTGATAATCGTATTCGAGTGATGATTGAGAATGGAGTAAAGTTG
AAGCATCGAACAATGTTTGTTGTAGTTGGTGATAAAGCAAGAGATCAGGTGCCTATTCTT
TATGATATGCTCGTAAAATCATCTGTTAAAGCGAGACCTACTGTATTATGGTGTTATAAG
AATAAAGATGAAGCTATTTCAAATCATGGTCGTAAAAAAGCAAAAAAGATTCAATCTGGA
AAAATTAATATTGAGGAAGCAGATCTCTTTGATGTATTTCGTTGTTCAACTACAATTCAT
GGAAAATATTACAAGGATTCTCATCAAATTTTGGGTCGCACATATGGAGTTTGTGTATTA
CAGGATTTCGAGGCGCTTACACCAAATCTTCTTGCAAGAACAGTTGAAACTGTTGAAGGA
GGTGGTTTAATTATTTTGCTGTTAAAGACAATTTCATCTCTAAAACAACTTTATACGATG
AATATGGATATTCACAAAAGATATAGAACTGAATCACATCAAGAAATAAAATGTCGTTTC
AACGAAAGATTAATCTTATCATTAGCTGATTGTGATCGCTGTTTGCTAGTTAATGATAGT
CTTACTGTTCTTCCTTTAAGCCAAATAACAGCAAACGTTGAGCCTATCAACGTTGGTGAA
ATTGTTAAATCACAAAATGATATACAGCTTGAGGAATTAAAAGAATCATTGCGAGATACT
CCTCCTGCTGGTCCATTAATAAATTTATGCAAGACTTTTGATCAAGCAAAAGCAGTTGCT
CAATTCATTGATTCATTGGCAGAAAAACAATTGAAACCTCCAACATCGTTGACAGCTGCG
AGAGGAAGAGGAAAATCCGCTGCAATGGGACTTGCAGTCGCTGGTGCTATCTCATTTGGT
TATAGTCAAATTTATGTTACATCTCCATCACCTGAGAATTTAATCACATTTTTTGAATTC
ATCATGAAAGGTTTTGATGTTTTAGCTTATCAAGAGCATCTCGATTACACTATCATAAGA
TCAACAAATCCAGATTTCAATAAAGCAATTGTTCGTATAAATTTAACAAGAAATAATCGG
CAAACTATTCAATACATTTCACCTAATGATTCTCATCTATTAAATGCTGCTGATTTATTG
GTCATCGATGAAGCTGCTGCGATCCCCTTACCGCTTGTAAAATCAATGCTCGGACCATAC
CTTGTTTTCATGGCATCAACAATAAATGGATATGAAGGAACTGGAAGATCACTAAGTTTG
AAATTATTGTCACAAATTCAGAAGGAAAACAATGCACCGCCTCCTATCAAATTAGAAGAA
TCAATTCGTTATAATCCAAATGATAGTGTTGAAAAATGGTTAACAACATTGCTTTGTTTG
GATGCACAAGTTGTTCCTGCGCTTAATTCGGGTTGTCCAACGCCAGACATGTGTGAACTT
TATTATATCGACAGAGATGCTCTCTTCTCTTATCATCGAGCTGCAGAAGCATTTTTACAA
CGAGTTGTTGCAATATTTGTTTCATCGCATTACAAAAATACACCAAATGATTTACAAATG
CTTAGTGATGCACCGGCACATCATTTGTTTTGCCTACTTGGTCCAATCACGAAAAAAGAT
CAATTGCCTGAAATTCTTGTAATCATTCAAGTTTGTCTTGAAGGAAAAATCTCACAAAGA
CGCTTAAATGATGCAACTGGATCGAAAGCAGCTGGTGATTTGATTCCTTGGAATGTATCT
GAACAATTCAATGATAGAGAGTTTACTAAATTAGCAGGTGCAAGAATTGTTCGCATTGCA
ACTCATCCAAATTATCAAAGAATGGGCTATGGTAAAAAAGCATTGAAATTGCTCAAGAAT
TACTATGAAGGTAAATTTACATCTCTGAATGAAACTACAGCAAATGATGAAGAAAATGAT
GGAATTGAAGAAATTAATGACGAAGATGCTGATATATTGACAGAAGTTATCAAACCAAGA
AAAAAAATTCCAACTCTTTTGAAACGTTTACAAGAGAGAAAACCGGAAATGCTTGATTAT
ATTGGAACATCTTATGGAATGACTCAAGAACTTTTAAAATTCTGGAAAAGTCAAAAGTTT
ATTCCAGTTTATTTAAGTCAAAAAGAAAATGACTTGACTGGCGAAAATTCTTGTATCATG
ATATCTTCATTAAATGATGAGCGAGTTAAAACAAAAAATTGGCTTCAAGAATATTATATT
GATTTTCGTCGTAGACTTTTGAGACTGTTGCCAAAAGCTTTTCGCAAATATACAACTGGA
TTAGGACTCTCACTTCTAGATAACAAAAGCGTGGTTGTCCCAATTAAAGAACTCGATCAA
CTTGAATTAAATTCATTTTTCACACCACATGATGTGCAACGACTTGAGTCGTATGTTCGC
AATCAAATTGAGTATAGATTGATATTAGATTTAACTTCTGATTTATCATCGTTATACTTT
CAAATGAGACTGCCTAACACACCGCTTGATGCTCTGCAAAAAGCAATATTGCTTGGAATA
GGCACTCAAAATAAAAACTTGGATGATCTTCAAAATGAATTTAATATGCCAAGTAGTCAG
ATTCTTGCTAAATTTTCTGACACAATAAGGAAACTTACTAAAAATCTTTTGCAAATTATG
GAGAAAACAATTGAAAGTGAGATGCTTGATGAAGGACAATTGAACGAAGGAAAAGAATTT
AAACCATTAGAGCAAACAATTGAAGAAGAACTCGATGAAGAAGCTAAAAAACTTGAGAAA
AAGCAGAAAAAAGAATTGATTAAATTGAAGAAGGAATCATTAGCTCAGTATGCTATTAAA
GGGACAAATGAAGATTGGTCAAAAGCATTAAAAAGTGGCAACAACAAATCAATTATTTCT
GTTAAAAGTGGAGAAAAACGTAGTTTTGAAAACGAAGATGATGAAATAGCCTCAAATGAG
CAAAAAGAAAAAGAAGGTTGGAATAAAAATAAAAAGAAGAAATTCCAATACAATCAAACT
AATAAGAAGAAAGACAAATTTTTTAAAAAATGA

>g2446.t1 Gene=g2446 Length=1010
MVKKKIDNRIRVMIENGVKLKHRTMFVVVGDKARDQVPILYDMLVKSSVKARPTVLWCYK
NKDEAISNHGRKKAKKIQSGKINIEEADLFDVFRCSTTIHGKYYKDSHQILGRTYGVCVL
QDFEALTPNLLARTVETVEGGGLIILLLKTISSLKQLYTMNMDIHKRYRTESHQEIKCRF
NERLILSLADCDRCLLVNDSLTVLPLSQITANVEPINVGEIVKSQNDIQLEELKESLRDT
PPAGPLINLCKTFDQAKAVAQFIDSLAEKQLKPPTSLTAARGRGKSAAMGLAVAGAISFG
YSQIYVTSPSPENLITFFEFIMKGFDVLAYQEHLDYTIIRSTNPDFNKAIVRINLTRNNR
QTIQYISPNDSHLLNAADLLVIDEAAAIPLPLVKSMLGPYLVFMASTINGYEGTGRSLSL
KLLSQIQKENNAPPPIKLEESIRYNPNDSVEKWLTTLLCLDAQVVPALNSGCPTPDMCEL
YYIDRDALFSYHRAAEAFLQRVVAIFVSSHYKNTPNDLQMLSDAPAHHLFCLLGPITKKD
QLPEILVIIQVCLEGKISQRRLNDATGSKAAGDLIPWNVSEQFNDREFTKLAGARIVRIA
THPNYQRMGYGKKALKLLKNYYEGKFTSLNETTANDEENDGIEEINDEDADILTEVIKPR
KKIPTLLKRLQERKPEMLDYIGTSYGMTQELLKFWKSQKFIPVYLSQKENDLTGENSCIM
ISSLNDERVKTKNWLQEYYIDFRRRLLRLLPKAFRKYTTGLGLSLLDNKSVVVPIKELDQ
LELNSFFTPHDVQRLESYVRNQIEYRLILDLTSDLSSLYFQMRLPNTPLDALQKAILLGI
GTQNKNLDDLQNEFNMPSSQILAKFSDTIRKLTKNLLQIMEKTIESEMLDEGQLNEGKEF
KPLEQTIEEELDEEAKKLEKKQKKELIKLKKESLAQYAIKGTNEDWSKALKSGNNKSIIS
VKSGEKRSFENEDDEIASNEQKEKEGWNKNKKKKFQYNQTNKKKDKFFKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g2446.t1 CDD cd04301 NAT_SF 594 621 9.92611E-4
11 g2446.t1 Coils Coil Coil 904 928 -
8 g2446.t1 Gene3D G3DSA:3.40.50.11040 - 9 235 1.5E-6
10 g2446.t1 Gene3D G3DSA:3.40.630.30 - 481 633 4.8E-41
9 g2446.t1 Gene3D G3DSA:3.40.630.30 - 661 722 1.3E-11
6 g2446.t1 Hamap MF_03211 RNA cytidine acetyltransferase [NAT10]. 2 971 24.819653
13 g2446.t1 MobiDBLite mobidb-lite consensus disorder prediction 963 1010 -
15 g2446.t1 MobiDBLite mobidb-lite consensus disorder prediction 963 992 -
14 g2446.t1 MobiDBLite mobidb-lite consensus disorder prediction 995 1010 -
5 g2446.t1 PANTHER PTHR10925 N-ACETYLTRANSFERASE 10 1 989 0.0
3 g2446.t1 Pfam PF08351 Domain of unknown function (DUF1726) 104 198 2.2E-33
1 g2446.t1 Pfam PF05127 Helicase 277 461 8.1E-60
4 g2446.t1 Pfam PF13718 GNAT acetyltransferase 2 501 725 1.2E-92
2 g2446.t1 Pfam PF13725 Possible tRNA binding domain 734 949 2.1E-62
7 g2446.t1 SUPERFAMILY SSF55729 Acyl-CoA N-acyltransferases (Nat) 591 625 1.87E-5

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:0034470 ncRNA processing BP
GO:0016072 rRNA metabolic process BP
GO:0005524 ATP binding MF
GO:0008080 N-acetyltransferase activity MF

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