General information for g14509.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RNA-directed DNA polymerase from mobile element jockey.
Parent gene
- The parent gene g14509 is located on chr_4: 930990..934369 (- 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_4 | g14509 | g14509.t1 | isoform | g14509.t1 | 929945 | 934369 |
| chr_4 | g14509 | g14509.t1 | exon | g14509.t1.exon1 | 929945 | 932241 |
| chr_4 | g14509 | g14509.t1 | cds | g14509.t1.CDS1 | 929945 | 932241 |
| chr_4 | g14509 | g14509.t1 | exon | g14509.t1.exon2 | 932955 | 933391 |
| chr_4 | g14509 | g14509.t1 | cds | g14509.t1.CDS2 | 932955 | 933391 |
| chr_4 | g14509 | g14509.t1 | exon | g14509.t1.exon3 | 933474 | 934369 |
| chr_4 | g14509 | g14509.t1 | cds | g14509.t1.CDS3 | 933474 | 933478 |
| chr_4 | g14509 | g14509.t1 | TSS | g14509.t1 | NA | NA |
| chr_4 | g14509 | g14509.t1 | TTS | g14509.t1 | NA | NA |
Sequences
>g14509.t1 Gene=g14509 Length=3630
ATGGGAAATAAAAAGAATCTCCCGCATGGTTCGGGTCAACAAAATTTAAATAATTTCCTG
CTCACTCCAACTCGTTTCAAACGAGGTTTTGATCAACTTCCAGACAATGTTGAAGATTCC
GATTGTGCTCCATCTCCACTTAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCAT
TGTGTTTACCTAGTGACATTTTTAAAAAGTGATAAAATTTCAATAATTGATCTGCAAGAG
ATCCAAGCTATAAATCAAATTCGCGTTACCTGGCAATCATATCGCTATTCTCGAAATGGA
CCCACACAATGTTCAAACTGTTTACGATTTGGACATGGAACAGCAAATTGTCATTTGGCA
CCAAGGTGCATTAGATGTGCAGGCGATCACAAATCAAAAGAGTGCCCACTTATCCAAGTG
AAAGATGGCAATCCACTTACTAAAATCACAACATCCAAACTGAAATGCGCTCTTTGTGGA
GGTAATCATACGGCAAATTTTTCTAAATGCACAAAACGCATAGAATTTGTAAAGTCTAGA
TCCACCTGGACTAAACAAACCATTAAACGAAATCCAATCGTTAATTTTCAACCAGCGCCA
CAGCTTGAGGGATTCCAATTCCCATCATTGCCAAATTCCCAGGGTCCAGCCTGGACAAAG
TCCACCTATGCTTCGGCTTTTCCAGAAGCTAAGCATGCCAATGCTCGCAGATACTCTCAA
ACACAATCAAATCCCAATGATTTGTACTCACATGAAGAGTTATTCAGCATCTTCTTAGAT
ATCACTTCTCAACTAGCAAAAGCCAAATCAAAACAAGAACAAATTCAAATTATGATCATA
AGAAACAAAATCCATGAACTATACCACTACTTACACGCAAACTTTATTCATGTCGCTTGT
ATCAATGAAACACACCTCAAAGAGAATCACAAACTTCAATCCGATCCTGATTACTTAATT
TATCGCTTAGACAGAAGCAACTACGATAAAGGAGGAGTAGCTATATTAGTTTACAAATCC
GTAATACATCAACTTTTACCTGCACTCAAAACCAAATATATTGAAAACATCGGAATATCC
ATTAAGGTATCTAATAATGAATTTATTAACATCTATTCGATTTATGTTCCAGGAAAAGGA
GACAGTTCTGAAGTCAATTCACATTTTATAAGTGATATTCGTATGCTTACAACTCTTAGA
GGGAGTTACTTTCTTTGCGGCGACTTTAATGCCAAACATCAACAATGGAACTGTAATAGA
GCAAATCATGCTGGAAAAGGAGACAGTTCTGAAGTCAATTCACATTTTATAAGTGATATT
CGTATGCTTACAACTGCTAGAGGGAGTTACTTTCTTTGCGGCGACTTTAATGCCAAACAT
CAACAATGGAACTGTAATAGAGCAAATCATGCTGGTACACTACTATACAATGAACTATGT
CAAAATAATTTCTTCGTTGACTTTCCTGATGATTTTACACATATTCCTTCAAACTCAACA
AATTCAGCATCAACAATTGATTTAGTGATTTCTAACAAATTACATGACGTAAACAATCTT
AAAACAATTGATCTATCCAGTGATCATCGTGCAATCACCTTCCAAATTGATACGCAAGTC
AAATTATCTTTCCAGACTAAAACTTATCTTGATTTCTCGAAAGCTAACTGGACCAAATTT
CAGAACATTGTTCACAAAAATATTGACAGCACTTATATTCAAAGTCGACTCTTTGAACCA
CAACAAATTGACGATCATATACATAAACTCACTAAAATCATCTTAGAGGCACAAGACAAA
GCAATTCCACGCAAACAATGTTCATCCTATAAGTTGAATCTTCCTGATGAATTAATAAAC
ACAATTAAAATTAAAAATTCTATTAAGAGAGCATGGCAAAGATCACGTGATGACCGTTTT
AAAGCACAAGTCAGACTAATGGAGAGAATTATCAAAGAAAGAGTCAATATCATCCGAAAC
GATAATTGGTCACATAAACTTAGTACAATACTACCAAATCACACAAACATTTGGAAAGTT
AGTAAGTTTCTCAAGAAACAAAATTCAAAAATTCCACCATTACAAACTGTTGATGGACTT
CTGATCACTTCCGAGCAAAAAGCAAACAAAATTGCTGATGTCTTTCAAACAAATCACATT
AACCCACTCAATGAAAGTTCACCGGATTTCTCTTCTCATATTAAAAGTAAGGTCTCCGAC
CTTCGGCAACCATTGCCATCCGACCGTTCAACAACGCTAACAGACGAAGCCGAGATCAAT
GCAATAATTCGAAATTTAAAAAATCCTAAGTGTCCAGGCCCTGACAAAATTTCAAATCGT
CTTATCAAAAATCTACCACGTCGAGGAATAAAATATTTATCAAAAATTTTCAATTCCTGC
TTATATCACAATTATTTTCCTACCACATGGAAATCAGCTAACGTCGTTCCTATCCCTAAA
CCTGGGAAGAAAAAGGCGGATCCAACCGCCTATAGACCTATCTCTCTGTTGAGCTCACTG
AGTAAAATTCTTGAAAGAATCATTTTGATTCGTATACAAAACCATATCGAAATAAATAAT
GTCATTCCGAATGAGCAACATGGTTTTAGAAGCAATTCTTCAACGACTCACTTGCTTTAC
AAAATTATCAATCATGCGAATACTGGTCTTAAGTCCAAAAAGTCTACAGGTCTTCTTTCC
TTAGATGTGGAGAAGGCATTTGATCGTATCTGGCATGAGGGACTTATAGCGAAGATGATC
GACTTCAAATTCCCAAACAGTTTGATCCTTATCACCAAATCGTTCTTGTCAGAAAGAACA
TTCAAGGTGATTTGCAATGGCTCACATTCAACCATTCGTTCAATTCCAGCTGGTGTTCCG
CAGGGAGCAGTCCTCAGTCCGACGCTATACAATATCTACACAGCTGATGTCCCAATCAGT
TCCTATTATGAAACGGCACTTTTTGCAGACGATACTTCGTTCTACAAAACTGCTGCAAAT
TTTGCAATCATTTCGTCACAACTCAAATTAGCATCCAGGAAGATCGCATCATACATGGAA
AAGTGGAAAATCTCTATCAACACTACCAAAACATCAGCGATTTATATAACAAATCGTAAG
AAAAAAGAAATCCCTATCGGTCCAATTGAAGTTTTCGATACAAATGTTGAATGGCAAGAT
TCAATCAAGTTATTAGGCATACATATTGACAAAAGACTTACTTTTAAACAACACATTGAT
AGTGTGATAGCCAAAGCTAATTTAGCAATTAGAATGCTCTATCCATTGATATGTCGAAAA
TCAAAACTCCATGTTGAAAACAAACTCCTCATATACAAACTTGCTATACGACCTATCCTG
ACTTATGGATACCCAGCATTCCATGGTTTCATCGCCGATACACACACACGCAAACTACAA
ACGCTACAAAATCGTTCACTGAAGATGATTCTTGATCGACCTTGGTGGGAAAGCACTCAA
CAAATTCACGAAGATACAAATCTACCTCGGATCAACAGCTACTTATACAAAATCACAACA
AAATTTAGAAACAAGCTGACCCAGTCTTAG
>g14509.t1 Gene=g14509 Length=912
MIIRNKIHELYHYLHANFIHVACINETHLKENHKLQSDPDYLIYRLDRSNYDKGGVAILV
YKSVIHQLLPALKTKYIENIGISIKVSNNEFINIYSIYVPGKGDSSEVNSHFISDIRMLT
TLRGSYFLCGDFNAKHQQWNCNRANHAGKGDSSEVNSHFISDIRMLTTARGSYFLCGDFN
AKHQQWNCNRANHAGTLLYNELCQNNFFVDFPDDFTHIPSNSTNSASTIDLVISNKLHDV
NNLKTIDLSSDHRAITFQIDTQVKLSFQTKTYLDFSKANWTKFQNIVHKNIDSTYIQSRL
FEPQQIDDHIHKLTKIILEAQDKAIPRKQCSSYKLNLPDELINTIKIKNSIKRAWQRSRD
DRFKAQVRLMERIIKERVNIIRNDNWSHKLSTILPNHTNIWKVSKFLKKQNSKIPPLQTV
DGLLITSEQKANKIADVFQTNHINPLNESSPDFSSHIKSKVSDLRQPLPSDRSTTLTDEA
EINAIIRNLKNPKCPGPDKISNRLIKNLPRRGIKYLSKIFNSCLYHNYFPTTWKSANVVP
IPKPGKKKADPTAYRPISLLSSLSKILERIILIRIQNHIEINNVIPNEQHGFRSNSSTTH
LLYKIINHANTGLKSKKSTGLLSLDVEKAFDRIWHEGLIAKMIDFKFPNSLILITKSFLS
ERTFKVICNGSHSTIRSIPAGVPQGAVLSPTLYNIYTADVPISSYYETALFADDTSFYKT
AANFAIISSQLKLASRKIASYMEKWKISINTTKTSAIYITNRKKKEIPIGPIEVFDTNVE
WQDSIKLLGIHIDKRLTFKQHIDSVIAKANLAIRMLYPLICRKSKLHVENKLLIYKLAIR
PILTYGYPAFHGFIADTHTRKLQTLQNRSLKMILDRPWWESTQQIHEDTNLPRINSYLYK
ITTKFRNKLTQS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g14509.t1 | CDD | cd01650 | RT_nLTR_like | 536 | 792 | 0.0000000 |
| 8 | g14509.t1 | Gene3D | G3DSA:3.60.10.10 | - | 2 | 150 | 0.0000000 |
| 9 | g14509.t1 | Gene3D | G3DSA:3.60.10.10 | - | 151 | 262 | 0.0000000 |
| 4 | g14509.t1 | PANTHER | PTHR33332 | - | 479 | 876 | 0.0000000 |
| 2 | g14509.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 92 | 148 | 0.0000004 |
| 3 | g14509.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 158 | 255 | 0.0000000 |
| 1 | g14509.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 541 | 792 | 0.0000000 |
| 10 | g14509.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 522 | 792 | 23.2250000 |
| 7 | g14509.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 4 | 149 | 0.0000000 |
| 6 | g14509.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 166 | 262 | 0.0000000 |
| 5 | g14509.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 453 | 761 | 0.0000000 |
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.
