General information for g6605.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-directed DNA polymerase from mobile element jockey.
Parent gene
- The parent gene g6605 is located on chr_2: 17787350..17788027 (- 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 | g6605 | g6605.t1 | isoform | g6605.t1 | 17787350 | 17788027 |
| chr_2 | g6605 | g6605.t1 | exon | g6605.t1.exon1 | 17787350 | 17788027 |
| chr_2 | g6605 | g6605.t1 | cds | g6605.t1.CDS1 | 17787350 | 17788027 |
| chr_2 | g6605 | g6605.t1 | TSS | g6605.t1 | NA | NA |
| chr_2 | g6605 | g6605.t1 | TTS | g6605.t1 | NA | NA |
Sequences
>g6605.t1 Gene=g6605 Length=678
ATGGCCATACCTAAGAAAGATAAAGATTTTAGTAACCCCAATAATTACAGACCCATCTCA
TTACTTTCTACAGTTGGAAAACTATTTGAAAGAATCATTCTAAATTTTCTTATACACCAT
GAAGATGTGAACAATTTATTTATTAACCAACAGTTTGGTTTTCGTTCCAAGCACTCAACT
ACTCTCCAAATCATAAGAATAGTCGAGACAGCTTCTATTGGTTTCAATCATAATCAGAGT
ACAGGAATGGTACTACTAGACATTCAAAAAGCCTTTGATTCTGTTTGGTTAAACGGCCTT
GTGTTCAAATTGATTAAGCTCAATTTTCCACCGGGACTCATTAAAGTTATAGACTCGTTC
TTATTCAATCGTACAGCACAAGTTGATATTAATCAGTGTCTTTCAGATACATTTTCTATT
CCTGCAGGTGTCCCTCAAGGATCTGCTCTTTCACCGTTCTTATTCAATATTTACATTAAT
GACTTGCCTAAACTCAAAAAAGGTGAGATTGCTGCCTTTGCTGACGATTTAGCTATTTTT
TGCTCTATTAAATCAAGAAATCCAAATTCATTCAAAAAAGCAATCATGCATGACCTCAAC
ATTCTCTCAAAATTCTATAGCGACTGGAAAATTAATTTAAATATGGACAAAACCGAGTTC
ATAATTTTCACTACCTAG
>g6605.t1 Gene=g6605 Length=225
MAIPKKDKDFSNPNNYRPISLLSTVGKLFERIILNFLIHHEDVNNLFINQQFGFRSKHST
TLQIIRIVETASIGFNHNQSTGMVLLDIQKAFDSVWLNGLVFKLIKLNFPPGLIKVIDSF
LFNRTAQVDINQCLSDTFSIPAGVPQGSALSPFLFNIYINDLPKLKKGEIAAFADDLAIF
CSIKSRNPNSFKKAIMHDLNILSKFYSDWKINLNMDKTEFIIFTT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6605.t1 | CDD | cd01650 | RT_nLTR_like | 3 | 225 | 0.000 |
| 2 | g6605.t1 | PANTHER | PTHR33332:SF29 | - | 3 | 224 | 0.000 |
| 3 | g6605.t1 | PANTHER | PTHR33332 | - | 3 | 224 | 0.000 |
| 1 | g6605.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 3 | 223 | 0.000 |
| 5 | g6605.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 1 | 225 | 22.118 |
| 4 | g6605.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 9 | 224 | 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