General information for g12066.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative exonuclease GOR.
Parent gene
- The parent gene g12066 is located on chr_1: 20730520..20731808 (+ 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_1 | g12066 | g12066.t1 | TSS | g12066.t1 | 20720062 | 20720062 |
| chr_1 | g12066 | g12066.t1 | isoform | g12066.t1 | 20720549 | 20731808 |
| chr_1 | g12066 | g12066.t1 | exon | g12066.t1.exon1 | 20720549 | 20720648 |
| chr_1 | g12066 | g12066.t1 | cds | g12066.t1.CDS1 | 20720549 | 20720648 |
| chr_1 | g12066 | g12066.t1 | exon | g12066.t1.exon2 | 20728719 | 20728820 |
| chr_1 | g12066 | g12066.t1 | cds | g12066.t1.CDS2 | 20728719 | 20728820 |
| chr_1 | g12066 | g12066.t1 | exon | g12066.t1.exon3 | 20728878 | 20728991 |
| chr_1 | g12066 | g12066.t1 | cds | g12066.t1.CDS3 | 20728878 | 20728991 |
| chr_1 | g12066 | g12066.t1 | exon | g12066.t1.exon4 | 20730274 | 20731808 |
| chr_1 | g12066 | g12066.t1 | cds | g12066.t1.CDS4 | 20730274 | 20731808 |
| chr_1 | g12066 | g12066.t1 | TTS | g12066.t1 | 20732287 | 20732287 |
Sequences
>g12066.t1 Gene=g12066 Length=1851
ATGTTGGATACGATTATAATTGGATTACTTATTTTGTCGGCATTGGTGTATGGATTTTGG
CAATACTTTGCCGAGTCTGATGCCCGTGAAAAGAAGCAAAATGAGGCACATAAGAAAATT
GATGAATATGCACCAAAGAGCAACAAGTCATCGATTACAAAAAAAGCAACAGAAGGAAAC
AACAATAATAACAGCAACAACGACAAGGCAAATTATTCCCACAATTGGCTTTTGACCACA
TTGAAGGGACATACAGGCAACGTTATGGACATGGATTTTTCATCAAATGGGAAATATCTT
GCTACATGTGCTGACGATCCCACATCAATGGTGCAAATTGATGGCGAATCGGATGTCACG
AATGAGACGTCGACAAGTAGCGAAGATTCTCCAAAACAAAAACGTACACAGCGTAATCGA
AAGGCAAATCATTTTGCCAAACAGCGAGCAACTCGCAATAATCAAAACGCCAAAGTGCTG
TCAAATCATGGTCAGACACAGGCACTATCAGTGAAGAATCATGGCGTTTATGAAAAGTGT
GAGCAACAGCAGAGATATCGTGCACTTGAGCCACCACTTAGACAACATACAAAATTAAAT
TTAACTGAAGCACAATTGGTGCATTATTTGCGTAATTATTTGCTCGATGAGATGCTCATG
CGTCTTCTTGGTTTTCCAATCGAGCATGATTTAGCACCAAATCTTGCTATAATCTACAAA
TATCCACCATATGAGTTTATTTCGCAACATCGTTCAGCTATGGCTAATGCAAATAACTCA
TCAACTTATTATAGTGGCAGTCCTATTTTTGTCAATCAACATGATGGTTTGACTTCATCA
TCATCGACAAAAGAGAACTTTAATGATAGTGATAGTGGTCAAGGCTCTGGTTCATCATCA
CCTTCCGATGACTTCGAATTGAATCAAGCACCGACTATCAAACCATTGCCAAAGCAGTAT
ATGTCAATGGTGAGTTCACAGAAAGAGTGCACACGCTGTGGCAAAGGATTCTTCGTGACC
AATGATGGCGAATACGTGACAACCGAACCGTGTTTGTTCCATTGGGGAAAAGTCAATCAA
TTCTTTGATGGACATCAGATGCGACGCATTTATTCATGCTGTAATCGCGATCATAATTCG
CACTTTAATAACGGTTGTACAGCAAATAGAGTTCATGTATGGACAGGAGTGAGTGCTGGT
CTCAATGGGCCTTATGATGGATTCGTAAAAACAAAGCGACGACCTGGACCAAGACCAGAA
AATACAGGTGTTTTCGCACTTGATTGCGAAATGTGCTTTACAGGCTGCGGTCTAGAGCTT
ACAAAAGTGACAATAATAAGATCTGATGGAAATTTGCAGTATGAGAGTTTTGTGCGACCC
GATCGGGAAATTGTAGATTTTAATACACGTTTCTCGGGCATTACAGAGAAAGATCTGAAT
ATAGGTATTCACGGCAACTACAATCGTCATGCATCAACTGCCTCAAATTCGAGCTCAAGT
TCAACAAGCTCAAACGGCTATCATAGAACCGTTAAAACTCTGCAAGAAGTACAAAAAGAT
CTTCTCAAGTTCATCTTCGAAGATACAATACTGATCGGGCATTCGATCGAAAATGATCTC
AAAGCATTGAAGCTTATACACAAAACTGTCATTGATACGGCAATTGCTTTTCCACACTAT
TACGGTTTGCCTTATCGACGATCATTAAAATCACTCACAAAGACCATTCTTAAGCGTGAT
ATACAAACGGCAGAAAATGGTCATTGTAGTTTTGAAGACTCTAGAGCATGCTTAGAATTG
ATGTTATATAAGGTCAGGAAAGATTTTCGAGAAGTACTTGAGCAACATTAG
>g12066.t1 Gene=g12066 Length=616
MLDTIIIGLLILSALVYGFWQYFAESDAREKKQNEAHKKIDEYAPKSNKSSITKKATEGN
NNNNSNNDKANYSHNWLLTTLKGHTGNVMDMDFSSNGKYLATCADDPTSMVQIDGESDVT
NETSTSSEDSPKQKRTQRNRKANHFAKQRATRNNQNAKVLSNHGQTQALSVKNHGVYEKC
EQQQRYRALEPPLRQHTKLNLTEAQLVHYLRNYLLDEMLMRLLGFPIEHDLAPNLAIIYK
YPPYEFISQHRSAMANANNSSTYYSGSPIFVNQHDGLTSSSSTKENFNDSDSGQGSGSSS
PSDDFELNQAPTIKPLPKQYMSMVSSQKECTRCGKGFFVTNDGEYVTTEPCLFHWGKVNQ
FFDGHQMRRIYSCCNRDHNSHFNNGCTANRVHVWTGVSAGLNGPYDGFVKTKRRPGPRPE
NTGVFALDCEMCFTGCGLELTKVTIIRSDGNLQYESFVRPDREIVDFNTRFSGITEKDLN
IGIHGNYNRHASTASNSSSSSTSSNGYHRTVKTLQEVQKDLLKFIFEDTILIGHSIENDL
KALKLIHKTVIDTAIAFPHYYGLPYRRSLKSLTKTILKRDIQTAENGHCSFEDSRACLEL
MLYKVRKDFREVLEQH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g12066.t1 | CDD | cd06145 | REX1_like | 425 | 602 | 3.12235E-81 |
| 8 | g12066.t1 | Gene3D | G3DSA:2.130.10.10 | - | 20 | 113 | 3.1E-9 |
| 9 | g12066.t1 | Gene3D | G3DSA:3.30.420.10 | - | 420 | 616 | 2.1E-49 |
| 17 | g12066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 34 | 69 | - |
| 20 | g12066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 46 | 69 | - |
| 19 | g12066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 160 | - |
| 18 | g12066.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 280 | 304 | - |
| 2 | g12066.t1 | PANTHER | PTHR12801:SF138 | FI18136P1-RELATED | 31 | 479 | 3.2E-87 |
| 4 | g12066.t1 | PANTHER | PTHR12801 | RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED | 31 | 479 | 3.2E-87 |
| 1 | g12066.t1 | PANTHER | PTHR12801:SF138 | FI18136P1-RELATED | 509 | 607 | 3.2E-87 |
| 3 | g12066.t1 | PANTHER | PTHR12801 | RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED | 509 | 607 | 3.2E-87 |
| 11 | g12066.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 12 | g12066.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 24 | - |
| 10 | g12066.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 25 | 616 | - |
| 16 | g12066.t1 | SMART | SM00320 | WD40_4 | 74 | 114 | 0.0024 |
| 15 | g12066.t1 | SMART | SM00479 | exoiiiendus | 423 | 610 | 1.2E-31 |
| 6 | g12066.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 75 | 108 | 2.29E-5 |
| 5 | g12066.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 424 | 605 | 1.77E-27 |
| 7 | g12066.t1 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 18 | - |
| 14 | g12066.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 24 | - |
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:0005515 | protein binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14570 (RNA exonuclease [EC:3.1.-.-])
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.
