General information for g2732.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable RNA-directed DNA polymerase from transposon X-element.
Parent gene
- The parent gene g2732 is located on chr_3: 19920480..19922468 (- 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 | g2732 | g2732.t1 | TTS | g2732.t1 | 19919692 | 19919692 |
| chr_3 | g2732 | g2732.t1 | isoform | g2732.t1 | 19920480 | 19922468 |
| chr_3 | g2732 | g2732.t1 | exon | g2732.t1.exon1 | 19920480 | 19922468 |
| chr_3 | g2732 | g2732.t1 | cds | g2732.t1.CDS1 | 19920480 | 19922468 |
| chr_3 | g2732 | g2732.t1 | TSS | g2732.t1 | NA | NA |
Sequences
>g2732.t1 Gene=g2732 Length=1989
ATGCATTCCGTTTTTCGTGAACACGGTGGTGTATCTATTCTTATAAAAAACACCATTCCT
GTACTCAAGATAGATAAGATAGTTTTCTCATTTGCTGAAGCAATAATCGCTAGCATAGAA
AGTCATATAGGTTTAGTTCAAGTAGTCTCAATTTATATCTCGCCAGCTGCTAACAGAGCT
CAATCAGCTATTTTCTTCGAACGAATATTTAAATATCCAGGTCAACTCATTATAGCCGGT
GATGTAAACGCAAAACACCAATCGTGGAATAATATTAACAACACTCTTAAAGGAATTGAT
CTTTTTAATATCGCGTCTAGGAATAACTGTATCATTCATCCTCCAGACTCCCCAACACTT
TATTCTTGTAGAGGCTCAATCTCAACGGTAGATATATTAATTACTAAAGCTATCTGTGGC
ATTTCTAGTCCTCTAACATATAATGATCTTTCGTCTGATCACATGCCTATCGTCTTTTCT
TTTTCACAAATCATATCTTTAGATGAATGTCTTATTTTCAATTGGAAGAAAGCCAATTGG
AAAAAATTTAAAGAAATTGTCAATACATCTTCAGTAGTACTATCAAATCAATCCATCAAT
TCTATAAATGATATAGACAATATCATTAAAAATCTTACAGAAAGCATCATCCATGCTTCT
GAAGCTTCAATTCCTAAGAAAAAACCTTACAGATTTAGATATCCTTTTTCTTCTCGCCTC
GATCTTCTCTGTAAAGAACGAACACGGTTGAGAAATAGGTATAAGGTTACTCTTCACCAT
GAATACAAATCACTAATTAATCAATTAAGCAGATTAATAAAACTAGAAACTTCAAAAATT
AACAAAGAATCCTACGAATCTCGTTTAGCGTCACTTAAAACAGATGACAACTCGGCATTT
AACTTTGTTAAAGCACTCAGAAAGTCCAAAAATATTTTACCACCTCTTGTAGATAACGGA
AATTTATCTTACTCGAACGTCGATAAGGCTAACGTACTAGCCAAAAGCTTTCTTACTAAT
TATTTAAATACATCCAATCAAATTTCTCCTCATGAGCAATCAGTGAATGATACAGTTAAC
CACTTCAGATCACAGCGACATAATTGTAATTTTAACATAACTCCTGAAAACATCATTGTA
ATTATTCAAGATTTAAAACTAAGAAAAGCAGCTGGCTTTGATAAAATTAAAACTCAATTC
TTAAAAAATTTACCACTTTCTACAATTCAGCTTTTTTCAAAAATCTTCAACAACTGTCTA
AAATTTGGTTATTTTCCTCAACAATGGAAACATGCCAAAATTATAGCCATACCTAAGAAA
GATAAAGATTCTAGTAATCCCAATAATTACAGACCCATCTCATTACTTTCTACAGTTGGA
AAACTATTTGAAAGAATCATTCTAAATTTTCTCATACACCATGAAGATGTGAACAATTTA
TTTATTAACCAACAGTTTGGTTTTCGTTCCAAGCACTCAACTACTCTCCAAATCATAAGA
ATAGTCGAGACAGCTACTATTGGTTTCAATCATAATCAGAGTACAGGAATGGTACTACTA
GACATTCAAAAAGCCTTTGATTCTGTTTGGTTAAACGGCCTTGTGTTCAAATTGATTAAG
CTCAATTTTCCACTGGGACTCATTAAAGTTATAGACTCGTTCTTATTCAATCGTACAGCA
CAAGTTGATGTAAATCAGTGTCTTTCAGATACATTTTCTATTCCTGCAGGTGTCCCTCAA
GGATCTGCTCTTTCACCGTTCTTATTCAATATTTACATTAATGACTTGCCTAAACTCATA
AAAGGTGAGATTGCTGCCTTTGCTGACGATTTAGCTATTTTTTGCTCTATTAAATCAAAA
AATCCAAATTCATTCAAAAAAGCAATCACGCATGACCTCAACATTCTCTCAAAATTCTGT
AGCGACTGGAAAATTAATTTAAATATGGACAAAACCGAGTTCATAATGAAGTTCAATAAT
TTTCACTAG
>g2732.t1 Gene=g2732 Length=662
MHSVFREHGGVSILIKNTIPVLKIDKIVFSFAEAIIASIESHIGLVQVVSIYISPAANRA
QSAIFFERIFKYPGQLIIAGDVNAKHQSWNNINNTLKGIDLFNIASRNNCIIHPPDSPTL
YSCRGSISTVDILITKAICGISSPLTYNDLSSDHMPIVFSFSQIISLDECLIFNWKKANW
KKFKEIVNTSSVVLSNQSINSINDIDNIIKNLTESIIHASEASIPKKKPYRFRYPFSSRL
DLLCKERTRLRNRYKVTLHHEYKSLINQLSRLIKLETSKINKESYESRLASLKTDDNSAF
NFVKALRKSKNILPPLVDNGNLSYSNVDKANVLAKSFLTNYLNTSNQISPHEQSVNDTVN
HFRSQRHNCNFNITPENIIVIIQDLKLRKAAGFDKIKTQFLKNLPLSTIQLFSKIFNNCL
KFGYFPQQWKHAKIIAIPKKDKDSSNPNNYRPISLLSTVGKLFERIILNFLIHHEDVNNL
FINQQFGFRSKHSTTLQIIRIVETATIGFNHNQSTGMVLLDIQKAFDSVWLNGLVFKLIK
LNFPLGLIKVIDSFLFNRTAQVDVNQCLSDTFSIPAGVPQGSALSPFLFNIYINDLPKLI
KGEIAAFADDLAIFCSIKSKNPNSFKKAITHDLNILSKFCSDWKINLNMDKTEFIMKFNN
FH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2732.t1 | CDD | cd01650 | RT_nLTR_like | 431 | 660 | 3.68013E-49 |
| 8 | g2732.t1 | Coils | Coil | Coil | 275 | 295 | - |
| 7 | g2732.t1 | Gene3D | G3DSA:3.60.10.10 | - | 2 | 161 | 1.9E-20 |
| 3 | g2732.t1 | PANTHER | PTHR33332:SF29 | - | 320 | 658 | 1.1E-53 |
| 4 | g2732.t1 | PANTHER | PTHR33332 | - | 320 | 658 | 1.1E-53 |
| 2 | g2732.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 47 | 158 | 2.9E-15 |
| 1 | g2732.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 437 | 656 | 2.7E-47 |
| 9 | g2732.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 418 | 662 | 22.999 |
| 6 | g2732.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 6 | 162 | 4.97E-19 |
| 5 | g2732.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 336 | 656 | 1.93E-20 |
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.
