General information for g14386.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 g14386 is located on chr_4: 212663..215967 (- 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 | g14386 | g14386.t1 | isoform | g14386.t1 | 212663 | 215967 |
| chr_4 | g14386 | g14386.t1 | exon | g14386.t1.exon1 | 212663 | 213585 |
| chr_4 | g14386 | g14386.t1 | cds | g14386.t1.CDS1 | 212663 | 213585 |
| chr_4 | g14386 | g14386.t1 | exon | g14386.t1.exon2 | 213746 | 214919 |
| chr_4 | g14386 | g14386.t1 | cds | g14386.t1.CDS2 | 213746 | 214919 |
| chr_4 | g14386 | g14386.t1 | exon | g14386.t1.exon3 | 215251 | 215967 |
| chr_4 | g14386 | g14386.t1 | cds | g14386.t1.CDS3 | 215251 | 215967 |
| chr_4 | g14386 | g14386.t1 | TSS | g14386.t1 | NA | NA |
| chr_4 | g14386 | g14386.t1 | TTS | g14386.t1 | NA | NA |
Sequences
>g14386.t1 Gene=g14386 Length=2814
ATGACGAAGAGCAAACAAAACGCTCCAAACAATATCAATAAACCACCACCAATAAACATC
ATTGGCGCCTCACTTTCACAAATCAACACAATTTTTAACAAACTGAAATTAACTGGTTAC
GAAGTAAAATTGACAGCACAATGCACAAAAGTTTTTAACAAAACAAATGACTCCTTCAAA
ATAATGAAGAATGCTCTGTCAGAAGAGAAGATTCAATTTTTTACACACCGACTTCGTGAT
GAACAATTGACAAAAGTGGTACTCCATGAACTTCCCAAAGCTGAAGAAAATGATGTCAAA
ACAGCAATTGAAAATATCGGTCTACAACCTGTACAAATCAAAAAAATGACAATTAAACAG
ATTAGGTACGAGTCACATGCTGTTTATTTGGTATATTTCAAGAAATTAGACAAAATAAAA
GTAAGTGAATTAAATGAAAATTACAACATTGTTGAATCAGTGAGAGTGAAATGGGATATC
TACAAAAATAAAAATAAAGGTCCCACACAATGTAGAAATTGTCAGAGATTTGGTCACGGA
AGTGATAATTGTTCAGCCACTCCTCGTTGTGTTCGATGCGCAGCAAACCACAAGTCATCA
GATTGTCCCTTTCTTTACAACGATCTCGGAGAAAAAATTCAAAATAGAATAAACTCAGTT
AACCTCAAATGTGTTCATTGTCAACAACAACATGCTGCTAGCTCCAGAGACTGTCCACTC
TTAAACACCTTACTAATGAATAAGACAAACAGCAATCTTCGAATCCTATATTGGAATACC
AATGGCATCAAAAACAAAATTTATGAGCTTTATCAATATGCAAACTCAAACTACATTCAC
ATTATTTGCTTGAATGAAACCTTCTTGAAACCTAATATCAAATTACCTAGTGATCCAAAC
TACAAAATCTACAGATTGGATAGAGATGATCAGGCAAAGGGTGGAATTGCAATATTGGTC
AGGAAGTCTATCAAACACACTCTATTACCTTTACTTAATACTTCATTGATTGAAAATCTG
GGTGTTCAAATAGCTCTCGATGACAACAAATCAATCAAAGTGTACAGTATCTATTTGCCT
GGGGGAACTAACAACACTGATATAAACTCTTACTATGCCAAGGACATCAGACTTTTAATC
AGCAATGCAAAAGACTCGATATTCTGTGGTGATCTCAACTCTAGACACAAATATTGGAAT
TGCACGAGAGCAAATAGAGCCGGCACAATCTTATACAGTGAGTATACTGCTAAAGCTTTC
AATATTGACTTTCCACAGGAACACACACATTATCCTGCTGACAATTCTAAGGCACCATCA
ACTATCGATCTAGTTCTTTCTTCTGGTCAATATGATATAAAAGTAGCAGTCTGTCCTGAA
CTCCTTAGCGACCACATAGCAAGTACGTTCTCTGTTGACACGCAAACCTCAATTGCTAAA
AAAGAACAAAGTCTTCAACTTGACTACAGCAAAGCTAAATGGCCCAGTTATAGAAGAATA
TTGTCCGAAAATATCAAACAGCTCCATTCTATACAACTAAATAGTCATACCGCCATCGAC
ACTGTGGTTGAAGCCTTCACAGACTCAATAATTGAAGCCAGAGACCTATCTGTTCCTCTT
ACAAAAAGAACTCCTTACAAATTGAACCTTCCCGATTACATAATTGAGAAGATCAAAATT
AAAAATGCACTTAAATGTCAATGGAGAAGGAACAGACTACCATTGTTAAAAAGAGAAATA
AATCAATTGGAGAAACACATAAAATTAGATATTGCTGCAGTGAAAAACGAAAATTGGGCA
TTCAAACTAAAAACATATCACCTAACAACAATGCAATTTGGAAAACGACTCTTTTGCTTA
AAAACGAGACTCGTAATATTCCTCCGCTTAAATGAGAATGCTAATAATGACAATCAAAAC
AATTTATCATTGCCCTCACTAAATGATTTATGTGATGCCATCAAGTCGCTTCCAAATAAC
AAAGCACCAGGTCCTGATCAAATTAAAAACTGTCTCATTAAACAATTGCCACTAAATGGA
ATTAAATTGTTACTTGTTATCCTAACTGCCTGCATCTCACTGAATTATTTCCCAAGATCA
TGGAAACATGCGACTGTTTTTCCGATCCCAAAGCCACAAAAGGATCACACAAATCCAGCA
AACTATCGTCCTATCAGTCTTCTTTCCTCACTTGGTAAACTACTGGAGAAACTAATTTTG
TCTCACATAAATCGACACTGCATGAAATACAACATATTTCCAGAAACACAACACGGATTC
AGACAAAATTATTCAACACTACATCAATTGAGACGTGTAATTAGTCATGCAAAACAAGGT
CTTGATAATAAACTGTCGACTGGACTCATCACAATGGACATTGAGAAGGCATTTGATCGA
GTATGGACTAAAGGTCTTCTTTATAAGATGATCAAATTGAAATTCCACTCCAGCCTCATT
AAGCTTGTTGATTCCTTCCTGAAAGATAGAAGTTACTGTGTAACAGTAAATGGAAAACTT
TCAGATACTCACAACTTTTTCTATGGAGTTCCCCAAGGAGCAATATTAAGTCCTATTTTA
TACAATATTTACACTCATGACTCACCGCATAATAATTCATACCAAACAGCACTCTATGCA
GACGACACAGCAAAATATAAAACTGCTAGAAAGTTCTCTATCATCAATAAATCACTCATC
ACTGCCACTGACGAATTAGCAATATATCTACAAAAATGGAAAATTAGTATTAACGGTGCA
AAAACAAACTCACTATTTATTTCCAAAAGAATCTCTGAAGATATTCGGCACTAA
>g14386.t1 Gene=g14386 Length=937
MTKSKQNAPNNINKPPPINIIGASLSQINTIFNKLKLTGYEVKLTAQCTKVFNKTNDSFK
IMKNALSEEKIQFFTHRLRDEQLTKVVLHELPKAEENDVKTAIENIGLQPVQIKKMTIKQ
IRYESHAVYLVYFKKLDKIKVSELNENYNIVESVRVKWDIYKNKNKGPTQCRNCQRFGHG
SDNCSATPRCVRCAANHKSSDCPFLYNDLGEKIQNRINSVNLKCVHCQQQHAASSRDCPL
LNTLLMNKTNSNLRILYWNTNGIKNKIYELYQYANSNYIHIICLNETFLKPNIKLPSDPN
YKIYRLDRDDQAKGGIAILVRKSIKHTLLPLLNTSLIENLGVQIALDDNKSIKVYSIYLP
GGTNNTDINSYYAKDIRLLISNAKDSIFCGDLNSRHKYWNCTRANRAGTILYSEYTAKAF
NIDFPQEHTHYPADNSKAPSTIDLVLSSGQYDIKVAVCPELLSDHIASTFSVDTQTSIAK
KEQSLQLDYSKAKWPSYRRILSENIKQLHSIQLNSHTAIDTVVEAFTDSIIEARDLSVPL
TKRTPYKLNLPDYIIEKIKIKNALKCQWRRNRLPLLKREINQLEKHIKLDIAAVKNENWA
FKLKTYHLTTMQFGKRLFCLKTRLVIFLRLNENANNDNQNNLSLPSLNDLCDAIKSLPNN
KAPGPDQIKNCLIKQLPLNGIKLLLVILTACISLNYFPRSWKHATVFPIPKPQKDHTNPA
NYRPISLLSSLGKLLEKLILSHINRHCMKYNIFPETQHGFRQNYSTLHQLRRVISHAKQG
LDNKLSTGLITMDIEKAFDRVWTKGLLYKMIKLKFHSSLIKLVDSFLKDRSYCVTVNGKL
SDTHNFFYGVPQGAILSPILYNIYTHDSPHNNSYQTALYADDTAKYKTARKFSIINKSLI
TATDELAIYLQKWKISINGAKTNSLFISKRISEDIRH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g14386.t1 | CDD | cd01650 | RT_nLTR_like | 703 | 930 | 1.07758E-29 |
| 7 | g14386.t1 | Gene3D | G3DSA:3.60.10.10 | - | 252 | 474 | 7.0E-34 |
| 3 | g14386.t1 | PANTHER | PTHR33332:SF29 | - | 671 | 930 | 2.4E-43 |
| 4 | g14386.t1 | PANTHER | PTHR33332 | - | 671 | 930 | 2.4E-43 |
| 2 | g14386.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 353 | 467 | 4.4E-12 |
| 1 | g14386.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 709 | 925 | 1.7E-40 |
| 10 | g14386.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 675 | - |
| 11 | g14386.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 676 | 697 | - |
| 9 | g14386.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 698 | 937 | - |
| 8 | g14386.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 690 | 937 | 18.428 |
| 6 | g14386.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 252 | 474 | 9.81E-34 |
| 5 | g14386.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 646 | 884 | 1.0E-18 |
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.
