General information for g4481.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable RNA-directed DNA polymerase from transposon X-element.
Parent gene
- The parent gene g4481 is located on chr_2: 2773965..2775461 (- 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 | g4481 | g4481.t1 | isoform | g4481.t1 | 2773965 | 2775461 |
| chr_2 | g4481 | g4481.t1 | exon | g4481.t1.exon1 | 2773965 | 2775461 |
| chr_2 | g4481 | g4481.t1 | cds | g4481.t1.CDS1 | 2773965 | 2775461 |
| chr_2 | g4481 | g4481.t1 | TSS | g4481.t1 | NA | NA |
| chr_2 | g4481 | g4481.t1 | TTS | g4481.t1 | NA | NA |
Sequences
>g4481.t1 Gene=g4481 Length=1497
ATGCAATTCAAAGATGATTCTTTCTTCTGTGGCGACTACAACTCTAAACATAGATTTTGG
AACTGTTTTGTTGCTAATCGTGCTGGCACACTCTTATATAATGAACTCAGCTCTAACAAT
TTAAATTTGTTTTATCCTGATGAACACACCTATTTTCCTCTTGATCCAACTCGTAAACCA
TCAACAATAGACTTAGTGTTATCCAATAATCACTATAACATCAGTCCTACAATCGTCTCT
GAATTGATCAGCGATCATGCAGCTATCACCTTCGAAATCATCACACAATCACAAACTCAT
GAACAAATCCATAGAAAACAACTTGATTTTAGTCGAGCTAACTGGTCAGCATATCGTAAA
ATCCTTAATATCGACTTTCCTATCATATTGCAAACAAACATCAACACTATAAATGACATC
GACGCCAGAGTTGATTCCTTCACATCCTCAATTCTTGAAGCCAGAAACACTACTATTCCT
TGCTTAGTTAAAAACCCATACAAATTAAACCTTCCTGATGAATTAATCAATCTGATTAAG
CTGAAAAATTCTTTGAAATGTAATTGGCGTAGAAATAGAGATCCAACTCTAAAAACTGTG
ATAAATCACTATGAAAGACAAATTAAATACTCCATTTCGATGATAAGAAATGAAAACTGG
GCTAAAAAATTAAGCAACATCTCACCGAGTAACCAGTCAATTTGGAAAACAGCTCGCCTC
CTCAAATGTGGCAACAAAAATATTCCACCTATTGAGACTGAAAATGGTTTTGCGATTTCA
AACGTCGACAAAGCTAACAAATTAGCAGAGACATTTAGCCAAAACCATGAAAATCCTCTT
CATCGAGTCCGATCGATGACGGATTACACGGTGAAGCATTCTGTCAATACATTTATCAAT
CAAAACATAACACTAGACACTAGCGACAGTCTGCCCCTTCCAACCCTCGACGAAGTAAAG
GAAGCTGTCAAATCATTGCCTAATAATAAGGCTCCAGGTAACGATGATATTAAAAATTGT
CTTTTAAAACAGCTCCCTCCCATGGGATTTGAGATTCTCCTCACAATTTTCATCGCTTGC
TTCAAACTTGGATACTTTCCTAAAAAGTGGAAGCATGCTAGAATTACGCCAATCTGTAAA
CCACAAAAAGATCCTAAAAAATCAACTAGCTATCGCCCAATTAGTCTGCTAAGTTCAATT
AGTAAAGTGCTTGAAAAGCTTATCTTGGCTAAAATCAATAAACACTGTAATGACAACAAT
ATAATCCCTCCAACTCAACATGGCTTCAGAACTGGATACTCAACACTCCACCAGCTGAAA
AGAGTTATAGGACATGCAAGTTTTGGATTGCAAAACAAAATGTCAACTGGATTGATAACG
CTCGATGTCGAGAAAGCTTTCGACCGTGTATGGTACCAAGCATTAATATACAAGATGATT
AATCTTAAATTCCACCCAACAATTATAAAGATAATAAATAGTTTCTTAAATGCATAG
>g4481.t1 Gene=g4481 Length=498
MQFKDDSFFCGDYNSKHRFWNCFVANRAGTLLYNELSSNNLNLFYPDEHTYFPLDPTRKP
STIDLVLSNNHYNISPTIVSELISDHAAITFEIITQSQTHEQIHRKQLDFSRANWSAYRK
ILNIDFPIILQTNINTINDIDARVDSFTSSILEARNTTIPCLVKNPYKLNLPDELINLIK
LKNSLKCNWRRNRDPTLKTVINHYERQIKYSISMIRNENWAKKLSNISPSNQSIWKTARL
LKCGNKNIPPIETENGFAISNVDKANKLAETFSQNHENPLHRVRSMTDYTVKHSVNTFIN
QNITLDTSDSLPLPTLDEVKEAVKSLPNNKAPGNDDIKNCLLKQLPPMGFEILLTIFIAC
FKLGYFPKKWKHARITPICKPQKDPKKSTSYRPISLLSSISKVLEKLILAKINKHCNDNN
IIPPTQHGFRTGYSTLHQLKRVIGHASFGLQNKMSTGLITLDVEKAFDRVWYQALIYKMI
NLKFHPTIIKIINSFLNA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4481.t1 | CDD | cd01650 | RT_nLTR_like | 372 | 479 | 1.84466E-28 |
| 7 | g4481.t1 | Gene3D | G3DSA:3.60.10.10 | - | 2 | 94 | 5.3E-12 |
| 3 | g4481.t1 | PANTHER | PTHR19446:SF438 | RNA-DIRECTED DNA POLYMERASE FROM TRANSPOSON X-ELEMENT-LIKE PROTEIN-RELATED | 147 | 497 | 3.6E-31 |
| 4 | g4481.t1 | PANTHER | PTHR19446 | REVERSE TRANSCRIPTASES | 147 | 497 | 3.6E-31 |
| 2 | g4481.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 7 | 89 | 4.0E-9 |
| 1 | g4481.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 385 | 496 | 2.8E-23 |
| 10 | g4481.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 347 | - |
| 11 | g4481.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 348 | 366 | - |
| 9 | g4481.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 367 | 498 | - |
| 8 | g4481.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 359 | 498 | 10.126 |
| 6 | g4481.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 6 | 93 | 5.76E-13 |
| 5 | g4481.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 295 | 497 | 1.11E-10 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
