General information for g8673.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 5’-3’ exoribonuclease 2-like protein.
Parent gene
- The parent gene g8673 is located on chr_2: 32188481..32190037 (+ 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_2 | g8673 | g8673.t3 | TSS | g8673.t3 | 32185667 | 32185667 |
| chr_2 | g8673 | g8673.t3 | isoform | g8673.t3 | 32185768 | 32187698 |
| chr_2 | g8673 | g8673.t3 | exon | g8673.t3.exon1 | 32185768 | 32185842 |
| chr_2 | g8673 | g8673.t3 | cds | g8673.t3.CDS1 | 32185768 | 32185842 |
| chr_2 | g8673 | g8673.t3 | exon | g8673.t3.exon2 | 32185918 | 32186334 |
| chr_2 | g8673 | g8673.t3 | cds | g8673.t3.CDS2 | 32185918 | 32186334 |
| chr_2 | g8673 | g8673.t3 | exon | g8673.t3.exon3 | 32186399 | 32187698 |
| chr_2 | g8673 | g8673.t3 | cds | g8673.t3.CDS3 | 32186399 | 32187697 |
| chr_2 | g8673 | g8673.t3 | TTS | g8673.t3 | NA | NA |
Sequences
>g8673.t3 Gene=g8673 Length=1792
ATGGGAGTTCCAGCATTCTTTAGATGGTTATCAAGAAAGTATCCTAGTGTGATTATTGAA
TGTACAGAAAATAAGCGTGTTGATGAAGAAACAGGAAAGAATGTATACGAAGATTCATCA
TTACCCAATCCAAATGATATAGAATTTGACAATCTTTATCTCGATATGAACGGAATTATT
CATCCTTGCACACATCCAGAAGATAAACCGCCTCCAAAAAATGAAAATGAGATGATGATT
GCCATTTTTGAATGCATTGATCGACTTTTCTCAATTGTAAGACCAAGAAAATTACTTTAT
ATGGCAATTGATGGCGTTGCACCTCGAGCTAAAATGAATCAGCAACGTTCAAGACGTTTT
CGAGCTTCAAAAGAAGCTGCCGAAAAAGCAGCTGAAATTGCTCGAATAAGAGAAGAATTG
AAAGAAAAAGGAGCTATTCTTCCACCTGAAAAACCAAAAGAACATCATTTTGATTCAAAT
TGTATCACTCCTGGAACACCATTTATGGAGAGGCTAAGTAGATGTTTGCAGTACTACATT
CATGATCGTTTAAATAATGATCCAGGATGGCGAAATATTAAAGTAATTTTGTCTGATGCA
AATGTTCCAGGTGAAGGTGAACACAAAATTATGGATTATATTCGTAAACAAAGAGCTCAA
CCTGATCACGATCCAAATACACAGCATGTACTTTGTGGGGCTGATGCTGATTTAATTATG
CTTGGGCTTGCAACTCATGAACCTAATTTTACTATCATTCGTGAAGAGTTTCTTCCCAAT
AAGCCTCGTCCCTGTGACATTTGTTCTCAAATGGGCCATGAAATGAAAGATTGTTCCGGT
TTAGATATGGAATATCATCAACAGCCTGAAATACAATTTGGAAAGGAAACACAATTTATT
TTTGTGCGTTTAAATGTGCTCAAAGAATATCTAGCTAAAGAACTTCAAATGCCTAATTTA
CCATTTAAATATGATTTTGAGAGAGTTATAGACGATTGGGTTTTCATGTGTTTCTTTGTT
GGAAATGATTTCCTTCCTCATTTGCCGAGTTTAGAAATTCGAGAGAATGCAATTGATCGA
TTAATTCATTTATATAAAAAGTGTGTATATAAAACTGGCGGTTATTTGACTGATTCGGGT
GATGTAGCACTGGAACGAGTTGAAATGATTATGCGTGATTTGGGTGCAGTTGAAGATGAA
ATTTTTAGAGAACGTCAGCAGAATGAGGAACGTATGAAGGCTAGAAATAAACGAATGAAA
CTTGAGCGTCAACAAAGACCAAATTTTGAAATGATTCATAAGACACAATTTGCACCAACT
GCTGTTGGAAGAGGCATTACACCGAATGCAATTGTAAATGCTAAAGAAGATATTTTGCGC
ATCAGTAAAATGGCAATGGAATCTACTGCATCAAATAATGATGCTTTAGAGTCAATGCTT
AAGCCTGTTGGTGAGAGTGATTCACCAAATAATCAAAATCGTAGAGGGATCAAAAGAAAA
GCAGAAGATGAGTCAGTAAAAGAAGAAGATGAAGAAGAGGATGATCAAGCACATGACGAA
GTTCGATTATGGGAAGATGGGTTTAAAGATCGGTATTATGAGTCTAAATTCGATGTTATG
CCAGATAACATTCAATTTCGTTATTCTGTTGCACTTCAATACGTAAAAGGTTTGTGCTGG
GTGCTGCAATATTATTATCAAGGTTGTGCAAGTTGGGAATGGTATTTTCCATTTCATTAT
GCTCCATTTGCTTCTGATTTTGTAAATATCAAGGGGTTAAGCAAGAAATTTG
>g8673.t3 Gene=g8673 Length=597
MGVPAFFRWLSRKYPSVIIECTENKRVDEETGKNVYEDSSLPNPNDIEFDNLYLDMNGII
HPCTHPEDKPPPKNENEMMIAIFECIDRLFSIVRPRKLLYMAIDGVAPRAKMNQQRSRRF
RASKEAAEKAAEIARIREELKEKGAILPPEKPKEHHFDSNCITPGTPFMERLSRCLQYYI
HDRLNNDPGWRNIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHVLCGADADLIM
LGLATHEPNFTIIREEFLPNKPRPCDICSQMGHEMKDCSGLDMEYHQQPEIQFGKETQFI
FVRLNVLKEYLAKELQMPNLPFKYDFERVIDDWVFMCFFVGNDFLPHLPSLEIRENAIDR
LIHLYKKCVYKTGGYLTDSGDVALERVEMIMRDLGAVEDEIFRERQQNEERMKARNKRMK
LERQQRPNFEMIHKTQFAPTAVGRGITPNAIVNAKEDILRISKMAMESTASNNDALESML
KPVGESDSPNNQNRRGIKRKAEDESVKEEDEEEDDQAHDEVRLWEDGFKDRYYESKFDVM
PDNIQFRYSVALQYVKGLCWVLQYYYQGCASWEWYFPFHYAPFASDFVNIKGLSKKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g8673.t3 | CDD | cd18673 | PIN_XRN1-2-like | 52 | 311 | 1.45897E-149 |
| 9 | g8673.t3 | Coils | Coil | Coil | 123 | 143 | - |
| 8 | g8673.t3 | Coils | Coil | Coil | 404 | 424 | - |
| 6 | g8673.t3 | Gene3D | G3DSA:3.40.50.12390 | - | 1 | 141 | 6.0E-43 |
| 7 | g8673.t3 | Gene3D | G3DSA:3.40.50.12390 | - | 156 | 356 | 1.6E-51 |
| 5 | g8673.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 481 | 519 | - |
| 3 | g8673.t3 | PANTHER | PTHR12341:SF41 | 5’-3’ EXORIBONUCLEASE 2 | 1 | 594 | 1.3E-236 |
| 4 | g8673.t3 | PANTHER | PTHR12341 | 5’->3’ EXORIBONUCLEASE | 1 | 594 | 1.3E-236 |
| 2 | g8673.t3 | Pfam | PF03159 | XRN 5’-3’ exonuclease N-terminus | 1 | 256 | 6.6E-103 |
| 1 | g8673.t3 | Pfam | PF17846 | Xrn1 helical domain | 323 | 597 | 3.8E-95 |
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:0004527 | exonuclease activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12619 (5’-3’ exoribonuclease 2 [EC:3.1.13.-])
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.
