General information for g3629.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 BS.
Parent gene
- The parent gene g3629 is located on chr_3: 26915715..26917974 (- 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_3 | g3629 | g3629.t1 | isoform | g3629.t1 | 26915715 | 26917974 |
| chr_3 | g3629 | g3629.t1 | exon | g3629.t1.exon1 | 26915715 | 26916754 |
| chr_3 | g3629 | g3629.t1 | cds | g3629.t1.CDS1 | 26915715 | 26916754 |
| chr_3 | g3629 | g3629.t1 | exon | g3629.t1.exon2 | 26916903 | 26917974 |
| chr_3 | g3629 | g3629.t1 | cds | g3629.t1.CDS2 | 26916903 | 26917974 |
| chr_3 | g3629 | g3629.t1 | TSS | g3629.t1 | NA | NA |
| chr_3 | g3629 | g3629.t1 | TTS | g3629.t1 | NA | NA |
Sequences
>g3629.t1 Gene=g3629 Length=2112
ATGGCAAGAGGAAAGAAGAGAAAAGGATCCAAATCACCGCAAAATGGTGTTTCTAATTTT
GATGCAAAGAAAAATAAAAATCATAACCTACAAAAAAATGTTTCCAGATCCGCATCATTA
ATGAGCTTACCAAGCTCAAATGGAAGTGTTAAATCGTCAAACAAACCAATGGTCAATGAA
GAGCAATCAATTGGCGTTCGTATCAAGCCAATTTTTGTCCAAGGAAATTTAGTGACAGTG
AGAAATATCATTTCGAATATTGTCCTTAAAATTAAGCCAACGTTGAAATGCGCAGGAAAA
GCAGTGCAGATTAATTGCAGTAACAGTGCTGATAAAAATACTATCATTACCAAGCTGAGA
AGTCAACAGATACAATTTCACACATTTACTGAAATTGTTGAAAAAAAGCAAATAATTGTT
CTCAAAGGTTTCTACTCTGATTCAATTGAAAATATTAAAGATATTCTGAACCAAGCTGGT
CTCACTGTGTCTTCTATTAGAGCTATAGTTAAGAATGATGATTCGGCTATTTATGCCATA
CAATTTGCTCAGTCAATATCATTAAAGTCACTGAATCACAACCATCGTGTCATTGATTCA
GTTGTTGTGCGATGGGAGCCACTTGACCGTTCCAAAAAGAGACCAACGCAGTGTTATCGA
TGTCAACAATTTGGTCATGCATCAGTTAATTGTGGATATCAAGTCAGATGTGTCAAGTGC
TTGGAGTCACATGAGCCAGGAGCCTGCAAAAGAACCTCGAGAGAAGGTACAGCCAAATGT
GTGAATTGCGATGGTGATCATGCGGCAAACTATAAAGGATGTCAAGCATTTAAGAAGTAT
CAGGAAAAACTTGAAGCTAATGCGAAACCAAAAAAGAAGGGAACCTCATCAAGATTTTCA
GCGCAAACAAGAATAAATGCAATTCGTGATCAGGTGAGTGATGATGACTTTCCGCAGTTA
AACATGAGTGATAATCCGCGCCCTACATTATTTAATAATTCATCAAGTAGACCATCTTAT
AGTGTAGTTACTAAGAAAGATAATCCACTCTTTGCTAAATTTGAAGAAGCTTTTGCTATT
TGGAATGCTCATTCAATCGGCAATAAAATTTGTGAACTTACTTCATTTATTGATAATCAT
CATTTAGATATTGTTCTTGTTTCTGAAACTTGGACTAATGATAATTCAAAGATTCACATT
AGTAATTTTGCTCAATATAGAATCAATCGCGATCATGGTGGTGTTTTGATTTTGATACGG
TCTAACATTAGCCACAAATTTCATTCTTCTATTTCTTTATCTTATGCAGAGGCAATTTCG
ATCTGTGTTTGTAGTTTTACTAGTTCTGTTATTTACTGTTCACCTTCTGCAACAAGAAAA
CAAACACTTGATTTCTTCGTCAAAGTCTCATCGTTGCCAGGTCCTCATTTGATTGGAGGA
GATTTCAATGCCAAGCACACTGCATGGAACAATGTTAATTCAGATAATAAGGGAAAAGAT
ATATTTAAGCTTTTCTCTAGCAAGAGTTTTTCGTTTCACGCTCCTGATGACTTTACTCAT
ATTTCTTATCATGGAACTCAGTCATGTTTGGATTTTGGCATTTCAAGGCATATATATGGT
ATATCTCAATTTAAAGTAGTTAATGAACTTTCTTCTGACCATCTTCCCATTCTTTTTGAT
ATCGCTTGTGCCGATTCTACAAATTCTAATGATTTCAATTTTTGCTTTTCAAAAATTAAT
TGGAAGAAAGTGTTTAGAATAGTCAGTAATGAGTGTACTAAAATTAGTTATTCATTAATT
GAAAATAAGGATATTGATTTATGTGTTAGAAAAATTGAGCTTTTGGTAAAAGCAGTTATA
GACTCCTCAGTGCCTAAAATTAAAAAGCGTTGTTCTAATTATGTTTACTCTGCAGAGATT
AGTTTTTTAATTAGCCAAAGGAATAACTTTAGAAACAAATATAAAAGATCTTTACTTCCT
CATTATCGTTCTTGTTATTATCAACTTAACAGATTAATTAAAAAACTGACTTCACAGCAT
AAACTTAGTCTTTTTAGAGAGAAAATATCAGAAATCAATAGAAAGGATGGTTCATTTATT
CCAAATTTGTAA
>g3629.t1 Gene=g3629 Length=703
MARGKKRKGSKSPQNGVSNFDAKKNKNHNLQKNVSRSASLMSLPSSNGSVKSSNKPMVNE
EQSIGVRIKPIFVQGNLVTVRNIISNIVLKIKPTLKCAGKAVQINCSNSADKNTIITKLR
SQQIQFHTFTEIVEKKQIIVLKGFYSDSIENIKDILNQAGLTVSSIRAIVKNDDSAIYAI
QFAQSISLKSLNHNHRVIDSVVVRWEPLDRSKKRPTQCYRCQQFGHASVNCGYQVRCVKC
LESHEPGACKRTSREGTAKCVNCDGDHAANYKGCQAFKKYQEKLEANAKPKKKGTSSRFS
AQTRINAIRDQVSDDDFPQLNMSDNPRPTLFNNSSSRPSYSVVTKKDNPLFAKFEEAFAI
WNAHSIGNKICELTSFIDNHHLDIVLVSETWTNDNSKIHISNFAQYRINRDHGGVLILIR
SNISHKFHSSISLSYAEAISICVCSFTSSVIYCSPSATRKQTLDFFVKVSSLPGPHLIGG
DFNAKHTAWNNVNSDNKGKDIFKLFSSKSFSFHAPDDFTHISYHGTQSCLDFGISRHIYG
ISQFKVVNELSSDHLPILFDIACADSTNSNDFNFCFSKINWKKVFRIVSNECTKISYSLI
ENKDIDLCVRKIELLVKAVIDSSVPKIKKRCSNYVYSAEISFLISQRNNFRNKYKRSLLP
HYRSCYYQLNRLIKKLTSQHKLSLFREKISEINRKDGSFIPNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3629.t1 | Gene3D | G3DSA:3.60.10.10 | - | 356 | 563 | 1.3E-32 |
| 4 | g3629.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 58 | - |
| 3 | g3629.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 31 | 58 | - |
| 1 | g3629.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 450 | 558 | 7.5E-15 |
| 6 | g3629.t1 | ProSiteProfiles | PS50158 | Zinc finger CCHC-type profile. | 218 | 231 | 8.581 |
| 2 | g3629.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 358 | 561 | 5.1E-29 |
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:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid binding | MF |
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