Gene loci information

Transcript annotation

  • This transcript has been annotated as Ribonuclease H2 subunit A.

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 g8268 g8268.t1 TSS g8268.t1 29415446 29415446
chr_2 g8268 g8268.t1 isoform g8268.t1 29415497 29416572
chr_2 g8268 g8268.t1 exon g8268.t1.exon1 29415497 29415629
chr_2 g8268 g8268.t1 cds g8268.t1.CDS1 29415497 29415629
chr_2 g8268 g8268.t1 exon g8268.t1.exon2 29415689 29415712
chr_2 g8268 g8268.t1 cds g8268.t1.CDS2 29415689 29415712
chr_2 g8268 g8268.t1 exon g8268.t1.exon3 29415773 29416572
chr_2 g8268 g8268.t1 cds g8268.t1.CDS3 29415773 29416572
chr_2 g8268 g8268.t1 TTS g8268.t1 29416615 29416615

Sequences

>g8268.t1 Gene=g8268 Length=957
ATGGACTCATTAAATACAATAAAATGTTTAGAATCTCTTAAAAATTATATTAAAAGACAG
GATAATTCAAAGAGTTTTGTGTACTTTTCGTCAATTCCAGACATTTGCAAAACAGAAAAA
TGTATTTTAGGAGTTGATGAAGCCGGAAGAGGACCTGTTTTAGGGCCTATGGTCTACGGA
ATCGCTTTTTGTCCTAAATCCAATGAATCAATCCTTAAAGATTTGGGATGTGCAGATTCT
AAGCAACTTAATGAACAACAAAGAGATGATATCTTTGTCAATACTAATCAAAAAGATTAT
TCTACTGAATCAATTGGTTGGGCTACTAATGTCATTTCTCCTAATGAAATAAGTACCAGT
ATGTTAAGACGAACAAAAAGAAGTTTAAATGAAGTTTCTATGGATAGCGCAATATCATTA
ATTAAAACAGCTATTGAAAATGGAGTGAATGTTGCAGAAATCTTTGTCGATACAGTTGGC
CCTCCAGAAAAATATCAAGCAAAATTAAAAGCTATTTTTCCATCATGTAAAGTTACGGTC
GCTAAGAAAGCTGATTCAACTTATCCAATTGTATCTCTGGCTTCAATTTGTGCTAAAGTC
TCACGTGATCATGCACTTAAAGTATGGGAATTTAGAGAAAACGTAGAAGTGCCTGAAGAT
GGCTTTGGTTCAGGATACCCAGGAGACCCTGTAACAAAAAGATTTTTACGTAATTTTGAG
CCTCTTTTTGGGTATTCACGTATTGTTAGATTCAGTTGGTCGACTGCTTCAAATCAATTG
GAAGAGAATAATGCTGTAACAATCGAATTTGAGGAAGAAGAGGAGGGAAGCGAGAAGAAA
GTAAAATTAGCCAGTAAAAAGATGACTGCATTTTTCAAATCTGAAGTTCCTGTAAAAAAA
TTCAAGCGACACAATTTTTTTAAAGAAAGATTTTTAGAGGATGTAATTGATTTTTAA

>g8268.t1 Gene=g8268 Length=318
MDSLNTIKCLESLKNYIKRQDNSKSFVYFSSIPDICKTEKCILGVDEAGRGPVLGPMVYG
IAFCPKSNESILKDLGCADSKQLNEQQRDDIFVNTNQKDYSTESIGWATNVISPNEISTS
MLRRTKRSLNEVSMDSAISLIKTAIENGVNVAEIFVDTVGPPEKYQAKLKAIFPSCKVTV
AKKADSTYPIVSLASICAKVSRDHALKVWEFRENVEVPEDGFGSGYPGDPVTKRFLRNFE
PLFGYSRIVRFSWSTASNQLEENNAVTIEFEEEEEGSEKKVKLASKKMTAFFKSEVPVKK
FKRHNFFKERFLEDVIDF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8268.t1 CDD cd07181 RNase_HII_eukaryota_like 43 265 0
6 g8268.t1 Gene3D G3DSA:3.30.420.10 - 12 217 0
5 g8268.t1 Gene3D G3DSA:1.10.10.460 Ribonuclease hii. Domain 2 218 264 0
2 g8268.t1 PANTHER PTHR10954 RIBONUCLEASE H2 SUBUNIT A 19 297 0
3 g8268.t1 PANTHER PTHR10954:SF7 RIBONUCLEASE H2 SUBUNIT A 19 297 0
1 g8268.t1 Pfam PF01351 Ribonuclease HII 43 255 0
4 g8268.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 41 261 0
7 g8268.t1 TIGRFAM TIGR00729 TIGR00729: ribonuclease HII 42 259 0

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:0016070 RNA metabolic process BP
GO:0003723 RNA binding MF
GO:0004523 RNA-DNA hybrid ribonuclease activity MF
GO:0003676 nucleic acid binding 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