General information for g4218.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable RNA-directed DNA polymerase from transposon BS.
Parent gene
- The parent gene g4218 is located on chr_2: 324894..331269 (- 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 | g4218 | g4218.t1 | isoform | g4218.t1 | 324894 | 326535 |
| chr_2 | g4218 | g4218.t1 | exon | g4218.t1.exon1 | 324894 | 325876 |
| chr_2 | g4218 | g4218.t1 | cds | g4218.t1.CDS1 | 324894 | 325876 |
| chr_2 | g4218 | g4218.t1 | exon | g4218.t1.exon2 | 326010 | 326535 |
| chr_2 | g4218 | g4218.t1 | cds | g4218.t1.CDS2 | 326010 | 326535 |
| chr_2 | g4218 | g4218.t1 | TSS | g4218.t1 | NA | NA |
| chr_2 | g4218 | g4218.t1 | TTS | g4218.t1 | NA | NA |
Sequences
>g4218.t1 Gene=g4218 Length=1509
ATGGAAAAAAGAATCAAACATGAGATAAGCGAGATCCGTAATACAAATTGGGGACACAAA
CTACAAAACATAATACCGAGTAATCAGTCTCTATGGAAAACAGCGCGTATGCTTAAAAAT
GGAAACAAAATCATTCCTCCACTAAAGACAACAGTTGGTCTGGCAACAACTAATGTGGAA
AAAGCTAACTTAATAGCAGAAACATTAAAAAAGAACCATGCCAACCCATTATATAAAGTA
CCAAGTGTTTATGATTACACGATTAACATGACAGTTACAAATTATTTAAGCAATAACACA
AACACTGATGCATCTGACTCACTTCAGATTCCAACAATTGACGAACTGAAGGAAGCAGTC
AAAAGGCTCCCAAACAACAAAGCTCCGGGAATAGATGGCATCAAAAACTGTCTAATTAAA
AATCTCCCTGAACAAGGATTTGAGCTTCTTCTTGCCATCTTCATTGCTTGTTTGAGGCTG
GGTTACTTCCCTATGAAATGGAAACATGCTAAAGTGTTTCCAATAGACACACAACATGGC
TTTCGAGCTGGTTTCTCAACAATTCACCAGTTGCGAAGAGTCATTGACTATGCCAAGAAT
GGACTCAACAATAAGCTCTCAACAGGGTTAATCACTCTAGATGTTGAAAAAGCTTTTGAT
CGAGTGTGGCACAATGGATTAATATTTAAAATGATAAAACTTAATTTCAACCCTAACATC
ATAAAAATAATTGATTCCTTTTTGAAAAATAGAAGCTATCAAGTCACAATAAATAATGAA
CTGTCACAAACACACAAACTAGAGTTTGGAGTACCACAAGGAGCAGTGTTGAGCCCCATA
CTTTATAATATTTATACTCACGACATGCCAACAAATAACACATATGAATCCGCTTTATTC
GCTGATGATGTTGCAAAATATTCCGCAAACAATACTCTGATAAGAGTAAACAAATCGATT
GTGCAAGCCGCCAGAGAAACCTACGAATATATGCAAAAATGGAAGATTAATGTCAATGGC
TCTAAGACAAATGCAATTTACATAACTAAAAGAATCTCGAGACAAATACCTGATCATCCA
TTATCGATATTCAATTCTTCTGTTGAATGGGCCAATGAATTAAAATATCTCGGAATTGTA
ATCGATAAAAGACTCACATTTAGCAGACACATCGATTATGTAATTGCTAAAACAAACAAC
GCGATAAAAATACTATACCCACTTTTATGCAGAAAATCAAAATTAGATACAAATAATAAA
CTACTCATCTATAAACTGGCTATAAGGCCAATTTTCACCTACGGACTTCCTGCTTTGAAA
GGTATCGCCGACGCTCATTTGAAAAAACTTCAAGTCACCCAAAACAAAACATTGAAGATG
ATTCTTAACAGAAGTCACTTTGAAAACACCATCAGATTGCACAAAGACGCAGGTATTCCG
CTGGTCAAGGAATACATTGAAAAACTAACAAGAAATTTTGATGAAAAATTAACAAATTTA
CAAGAATAA
>g4218.t1 Gene=g4218 Length=502
MEKRIKHEISEIRNTNWGHKLQNIIPSNQSLWKTARMLKNGNKIIPPLKTTVGLATTNVE
KANLIAETLKKNHANPLYKVPSVYDYTINMTVTNYLSNNTNTDASDSLQIPTIDELKEAV
KRLPNNKAPGIDGIKNCLIKNLPEQGFELLLAIFIACLRLGYFPMKWKHAKVFPIDTQHG
FRAGFSTIHQLRRVIDYAKNGLNNKLSTGLITLDVEKAFDRVWHNGLIFKMIKLNFNPNI
IKIIDSFLKNRSYQVTINNELSQTHKLEFGVPQGAVLSPILYNIYTHDMPTNNTYESALF
ADDVAKYSANNTLIRVNKSIVQAARETYEYMQKWKINVNGSKTNAIYITKRISRQIPDHP
LSIFNSSVEWANELKYLGIVIDKRLTFSRHIDYVIAKTNNAIKILYPLLCRKSKLDTNNK
LLIYKLAIRPIFTYGLPALKGIADAHLKKLQVTQNKTLKMILNRSHFENTIRLHKDAGIP
LVKEYIEKLTRNFDEKLTNLQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4218.t1 | CDD | cd01650 | RT_nLTR_like | 168 | 381 | 0.000 |
| 2 | g4218.t1 | PANTHER | PTHR33332:SF29 | - | 173 | 472 | 0.000 |
| 3 | g4218.t1 | PANTHER | PTHR33332 | - | 173 | 472 | 0.000 |
| 1 | g4218.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 175 | 380 | 0.000 |
| 5 | g4218.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 1 | 381 | 13.529 |
| 4 | g4218.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 62 | 350 | 0.000 |
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. There were no conditions that were differentially expressed