General information for g9005.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 g9005 is located on chr_2: 34496360..34499225 (- 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 | g9005 | g9005.t1 | isoform | g9005.t1 | 34496360 | 34499225 |
| chr_2 | g9005 | g9005.t1 | exon | g9005.t1.exon1 | 34496360 | 34497214 |
| chr_2 | g9005 | g9005.t1 | cds | g9005.t1.CDS1 | 34496360 | 34497214 |
| chr_2 | g9005 | g9005.t1 | exon | g9005.t1.exon2 | 34497719 | 34498739 |
| chr_2 | g9005 | g9005.t1 | cds | g9005.t1.CDS2 | 34497719 | 34498739 |
| chr_2 | g9005 | g9005.t1 | exon | g9005.t1.exon3 | 34499218 | 34499225 |
| chr_2 | g9005 | g9005.t1 | cds | g9005.t1.CDS3 | 34499218 | 34499225 |
| chr_2 | g9005 | g9005.t1 | TSS | g9005.t1 | NA | NA |
| chr_2 | g9005 | g9005.t1 | TTS | g9005.t1 | NA | NA |
Sequences
>g9005.t1 Gene=g9005 Length=1884
ATGTACAGTTTCGGCGATTTATTGCTCGCCTCTGCTACTAGAGCAGACTGTTTTCAATTT
TTCACCAAATTAAGTGAGATACCAGGACCTCATTTAGTTGCAGGTGATTTTAATGCTAAA
AATAATGCTTGGAATAATTCCAAAACAGATTTAAAAGGTACTGATATTTTCAATATTTTT
TCTAAGAAAAACTTTATTTTTCATGCTCCTGACTCAGTTACTCATATACCCTATAGAGAG
AATCCATCTTGCATTGATTTTGCTATCTCTAGAAATATCCCTCAAATTACCAATCTTCGT
GTTATTAACGATCTTTCATCTGATCATCTTCCTATAGTTTTCTCTATATTTGATCCATTG
ATCTCTTCCAACACATCGAATAACTACAATTTTGCTAAAACCAATTGGAGGAAATTATCC
AATTTTATCAATTGTAATAGTTCTATTATTTCCCATTCTTTCATTACTAGTAAAGATATT
GATACTTGTATCAACGATATTGAACTAATGATAAATGAAGCTATGCGACGATTCGTTCCT
AGAAAGAGTAATATTGTAACTAATTATACTTACTCTCCTCAAATTCAATTACTTATTAAG
ACTAGGAATTTTTTTAGGAATAAATTTAGGAGAACAGGCCTTGCTCACTTCAGATCGTCT
TTCTATCAACTCAATAGAATTATTCACAGACTAGTCAGACAGCATAAATTAGAGATTTTT
AATGACAAATTAGCTTTGCTTAATAGGAAAGATAATTCTATATTTAAATTAACAAAAGCA
TTGAAGAGGAAAAAATTAGAAGTTCCTCCTTTGTTAAACAGTAGTAAAAATCTTGTTTAT
TCTGATGAAGATAAAGCGAATTTATTTGCTGATACATTCAAAAACAGTCATGCAATTCCT
TCCAAAAATGATTTAACAGTTAAATCATCAATTGAGCTTATTATGCAGTCGAATCTGCCG
TCTTTCAATGTAATAACTGAAGATCAAATTATTGAATCCTTAAGCTTTTTGAATACTAGA
AAGCGACAGGTCAGCAGTAGTAAGTTTAAAGCATATGTTTCAAAGCCTTATCATGTCAGT
GCTGGTGTTCCTCAAGGCAGTTTACTTGCCCCTCATTTATTTAATTTATTCATCAACGAT
ATTCCAATTCCTAAAAATGCTAAATTGTCATTATTTGCAGATGACACTGCCTTAGCAGTT
GAAGTTAATTGGAAGAATCTCAAATTAGCGAAAAAGCAAGTTCTAAGTTCCTTGGATTTG
TTAGTTAAGTTTTTCGACAAATGGAACATTAAAATTAATGAATCAAAAACTAAATTTATC
ATGTTTAGTAAGTCAAGAGTAATGCTAAATAGAACTGAAATTGATCAAATTAACTTTGGT
AATTCTATCTCCAAATGGGAGAAATCAGTTAAATATCTTGGAATTAATCTTGATCAGAAA
CTCTTATTTAAAGATCATATTAATAAATCTCTATTTATTGCCAAATCTATCGCCTTCTCT
ACCTTGTACTGTTTTTTTAAGAAAAATAATGTTGTCAAGGAGCATGAAAAGATTCATTTG
TACAAGGCGGTCATAAGACCTATTTTGACCTATGGTTGTCAAGTATTTAATAATTGTGCC
AAGAGTCACTTCAACAAGCTTCAAATTTTCCAAAACAAATTGTTAAGACTCTGTCTTAAT
ATTAATTGGGATGATTTTATCAACAATGAAAAACTTCATGAATTAGCTAATATTCCAACG
ATCAGAGAATATGTTAATAAATTAACTTCTCGCTTCTATGACGATTGTCATTCACATGAT
AATACTCTTATTTTGAATTTAGGTAATTATGATCACTCTTTAATTGCGGGTGGTTTGAAG
CACAACCTACCATTAGCAGTTTAA
>g9005.t1 Gene=g9005 Length=627
MYSFGDLLLASATRADCFQFFTKLSEIPGPHLVAGDFNAKNNAWNNSKTDLKGTDIFNIF
SKKNFIFHAPDSVTHIPYRENPSCIDFAISRNIPQITNLRVINDLSSDHLPIVFSIFDPL
ISSNTSNNYNFAKTNWRKLSNFINCNSSIISHSFITSKDIDTCINDIELMINEAMRRFVP
RKSNIVTNYTYSPQIQLLIKTRNFFRNKFRRTGLAHFRSSFYQLNRIIHRLVRQHKLEIF
NDKLALLNRKDNSIFKLTKALKRKKLEVPPLLNSSKNLVYSDEDKANLFADTFKNSHAIP
SKNDLTVKSSIELIMQSNLPSFNVITEDQIIESLSFLNTRKRQVSSSKFKAYVSKPYHVS
AGVPQGSLLAPHLFNLFINDIPIPKNAKLSLFADDTALAVEVNWKNLKLAKKQVLSSLDL
LVKFFDKWNIKINESKTKFIMFSKSRVMLNRTEIDQINFGNSISKWEKSVKYLGINLDQK
LLFKDHINKSLFIAKSIAFSTLYCFFKKNNVVKEHEKIHLYKAVIRPILTYGCQVFNNCA
KSHFNKLQIFQNKLLRLCLNINWDDFINNEKLHELANIPTIREYVNKLTSRFYDDCHSHD
NTLILNLGNYDHSLIAGGLKHNLPLAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9005.t1 | Gene3D | G3DSA:3.60.10.10 | - | 11 | 116 | 0.0000000 |
| 3 | g9005.t1 | PANTHER | PTHR33332 | - | 332 | 559 | 0.0000000 |
| 2 | g9005.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 19 | 113 | 0.0000000 |
| 1 | g9005.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 337 | 477 | 0.0000000 |
| 7 | g9005.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 228 | 477 | 15.2710000 |
| 5 | g9005.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 19 | 116 | 0.0000000 |
| 4 | g9005.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 362 | 489 | 0.0000029 |
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.
