General information for g124.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable RNA-directed DNA polymerase from transposon BS.
Parent gene
- The parent gene g124 is located on chr_3: 1181857..1184517 (+ 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 | g124 | g124.t2 | isoform | g124.t2 | 1180629 | 1184517 |
| chr_3 | g124 | g124.t2 | exon | g124.t2.exon1 | 1180629 | 1181737 |
| chr_3 | g124 | g124.t2 | cds | g124.t2.CDS1 | 1180629 | 1181737 |
| chr_3 | g124 | g124.t2 | exon | g124.t2.exon2 | 1181865 | 1184517 |
| chr_3 | g124 | g124.t2 | cds | g124.t2.CDS2 | 1181865 | 1184517 |
| chr_3 | g124 | g124.t2 | TSS | g124.t2 | NA | NA |
| chr_3 | g124 | g124.t2 | TTS | g124.t2 | NA | NA |
Sequences
>g124.t2 Gene=g124 Length=3762
ATGGAAGACGATCCCATGCGGGAAGTTTTCTCTAATGCAGATTTAAATTCTGCAAATATA
TTCTCTTCTCTGAATGATGATGTGGACGACGAACTTTGGATCGAAGAATCTGAAAAGAAA
ACACTCAACATAAACAAGAAAAGAAGAATTGGCGTTGAAAATGAAAAATGCTCAAAACCT
CAAAAAATTCAACAAAAACCACCACCAATCGTACTGCTTCACAATGACGTTACAAAAATC
AGACAGGCTCTCAATAAAATTGGAGTAACAAATTATCAGCTACGTTTAACTAGTGAAGGC
ACAAAAATTTTCTTTAATTCTATGGAAGAATTCAAATTGGTAAGAGATAAATTAATTCTT
GACAAATGTAATTTTTTCACGCACAGACTGAAAGAAGAGCAGCTCTCAAAATTTATTCTC
AAAGGACTTTTCAATATGGAAACTGAAGAATTAAAACAGCAAATCAAAATTAACAATACT
TCACCAACATCAATCAAAACGCTCAAGACAAAATCAACATCAAACGCCCATGCAATTTAC
ATGGTAAATTTTCTCAAAAAAGATAAGATAAAGCTGCAAGATCTCATTGAAAACATCAAA
ACAATTCTGCAAGTTCGTGTTACATGGGAATTTTATCAAAATAAACGCTCTGGTCCAACA
CAATGTGGAAATTGCCAACGCTTCGGTCATGGATCTGAAAATTGTCACGCTTCACCACGA
TGCGTCAGATGTTCACAGAAACATCTTTCAAAGGAATGTTTTCTCCTTGAAAATAATCTT
GGTTCAGATTCACATCCCAAAATTCCAAGTGAAAAGTTATGCTGTGTACACTGTGGTCAA
AACCACACTGCAAATTTTTCAAAATGTCCAAAGAGATTGGAGTTTATTAGATCAAGACAA
AGAAATTCAACAGTTCCCAAAAACAACCTACCAAAAAAACAATTTGGTTTTAAATTAGCT
CCCGAGCTGAATAATGTGAATTTTCCGTCGATTCCTGGCTCTTCATCTAATTTACCAGCT
TGGTCCGAACAAGCTTGGTCACAGACAGCAAATAATTTGAGAAACAACCAACTGCCCAAA
TGGGATTTTCCAACTTTTAATCCTTTAAAATTCGTTGGCAATATAAAAGTCTTTCAATGG
AACGCAAATGGCGTCAAAGAAAAATTATTCGAAATTTTCCAACATCTCAACAAATATAAT
ATTCACGTCGCATGCATATGCGAAACAAATTTAAATTATCAATCTAAATTGAAATCCGAT
CCCAATTACAGAATTCATAGACTCGATAGACAGGACCAAAGCAAAAGAGGAGGAGTTGCA
ATCCTTGTCCGAAAGGATGTAGCTTATGAATTGCTACCCTTGGTAAGCACCAAATTAATT
GAAAGCATCGGTGTAGCAATTAAACTTGAAAATGGTAGTAAAATAAATATCTTCTCATGC
TATGTACCTGGAAGTACAACGTCTCAACAAATAAATAATCTCTTTATATATGATATAAGG
AAGCTCTCAAATACAAGCAATAAATACTATCTGGTAGGAGATTTTTACTGCAAGCATAGA
TCATGGAACTGCTTTCAAGCAAATCGTGCAGGCACACTACTCTATGAAGAGTCTTGTTCA
AAAGAGCTCTTCATAGATCATCCACCAAGCCACACACATTATCCTGGTGATTTAAGTCGT
AGGCCCTCAACCATCGATCTGATTTTATCCAATGCATCACACACTATCACGAAGTTACGT
ACTGCAGAACTAATGAGCGACCATATATCCATCACCTTCAAAATTTGCACAAATGCAACA
ATCAGTGCAGCAAACGCTGGAACAAGGTTGGATTACGCAAATGCAAATTGGGATAAATAT
AAGAGAATTATCAATTATCATCTCTTGAACAATTTTAATGAACCCCAATTGGATTCTGCA
CAACAAATTGATACAACAGTTAAAAATTTATCCGAATTGATACTGCATGCAAGAAACAGA
GCAGTGCCATTGACAATCAATAAAAGCTTCTGTCTGGTAATTGATGAGAATCTAAAGGCG
AAAATAAAAGTTAAAAATCAACTTAGAAGATTGTGGATGAGAACAAGACTGCCCCATTTC
AAATCTCAAGTAAATGCTCTTGAATGCCAAATCAAACAAGAGATAAACTCTATTAGAAAT
GCAAACTGGAATCATAAATTGGCGGATATCAAGCCAAACAACCAAACAATTTGGCGAACA
GCTCGTTACCTCAAACTAGGAAAACGACAATTGCCTCCTATCAACAATAGTGGTCAATTG
GCTATTACTGATATAGAAAAAGCCAATATGATTGCAGTTCAGTTTAATGAAAACTTTTCA
AACACTCTTACCAGCAGTATCAATCAATCTCAAATTATAACTCGCACAATAAATAATTTT
ACCACGCAATTTTCAACAAACAATCAAACTGAAGAAACTCTTCTACCAACATTAGATGAA
GTGACCCAGATAATCAAGAGACTTCCTAACAAGAAAGCACCAGGTCCCGACCAAATTAAA
AATTGTCTAATCAAAAATCTTCCTACAAAAGGTTATTTATTTATTACTAGCATTCTTATT
GCTTGCTACAAAAACTGCTATTTCCCTGATGCATGGAAAACAGCTGACATAACTCCTATC
GCCAAGCCAAACAAAAATCCATCACACGCCTCAAGCTATCGACCTATCAGCCTACTTAAT
ACTTTGGGAAAAATCCTTGAGCACACAATTCTTTCACGACTCAATAAGCACTGCATTGAG
AAAAGTATAATTCCTTCTATACAACACGGTTTTAGAGCGGGCTTTTCTACCGTGCATCAA
TTAAAAAGAGTTATATCGCATATGAAGAAGGAAATTGAACACAAAAGATCCACAGCCTTG
ATAACTCTCGACGTTGAAAAAGCATTCGACAGAGTATGCCACAAAGGACTATTGTTCAAG
CTCATATCTGGTAATTTTCCTCCCTTATTAATTAAATTAATAAGTTCGTTTTTGTCAAAT
AGATCATTCAGAGTAGTAATCAATGGCAAGAGGTCTGAACCTTACCAACTACTAGCGGGT
GTACCTCAGGGCGCTGTCATGAGTCCTACACTGTTTAATGTGTTCACTGCAGATTTCCCA
CAAGAAGACTTTTACGACACAGCACTTTTTGCGGACGACGTGGCGATTTTTAAGTCACAT
AGATGCTCCAAACCAATAACAAATGGTATTTCAAAAGCAGCTAAGTCTATCTCATCATAC
TACAAAAAATGGCGAATAGGATTAAATGCCCAGAAGACCACAGCCATGTTTGTAACTCGT
AGACGAAAGAAACAATTACCATCTCAAAGACTTCGCATATTCAATGCAAATATTGAATGG
ACAAACCAAACCAAATATCTTGGCTTGATTATAGACAAGAACTTATCATTTAAACCTCAT
ATCGACTATATAATACAACGAGCGAATAATGCGATTCGACTCCTATATCCTATGTTAGCT
CGAAATTCCAAGCTAGACATTAGAAACAAGATAATTATATATAAAATGGCGATTAGACCT
ATTTTAACCTACGGTTTCCCTGCTATTCCAGCGATAGCAAAAACTCATATAAAGAAACTA
CAGGTCCTACAAAATAAAGCCTTAAAAATGATAATGAACAAGCCTTGGTATACTAGCACA
ACTCAAATACATCAAATGTGTAACATCAAACCGATTGACGAATATTTGAAGGATCTCAAT
ATTAAATTCAACAATAGACTTCCTAGTTCTCATATCTCATAA
>g124.t2 Gene=g124 Length=1253
MEDDPMREVFSNADLNSANIFSSLNDDVDDELWIEESEKKTLNINKKRRIGVENEKCSKP
QKIQQKPPPIVLLHNDVTKIRQALNKIGVTNYQLRLTSEGTKIFFNSMEEFKLVRDKLIL
DKCNFFTHRLKEEQLSKFILKGLFNMETEELKQQIKINNTSPTSIKTLKTKSTSNAHAIY
MVNFLKKDKIKLQDLIENIKTILQVRVTWEFYQNKRSGPTQCGNCQRFGHGSENCHASPR
CVRCSQKHLSKECFLLENNLGSDSHPKIPSEKLCCVHCGQNHTANFSKCPKRLEFIRSRQ
RNSTVPKNNLPKKQFGFKLAPELNNVNFPSIPGSSSNLPAWSEQAWSQTANNLRNNQLPK
WDFPTFNPLKFVGNIKVFQWNANGVKEKLFEIFQHLNKYNIHVACICETNLNYQSKLKSD
PNYRIHRLDRQDQSKRGGVAILVRKDVAYELLPLVSTKLIESIGVAIKLENGSKINIFSC
YVPGSTTSQQINNLFIYDIRKLSNTSNKYYLVGDFYCKHRSWNCFQANRAGTLLYEESCS
KELFIDHPPSHTHYPGDLSRRPSTIDLILSNASHTITKLRTAELMSDHISITFKICTNAT
ISAANAGTRLDYANANWDKYKRIINYHLLNNFNEPQLDSAQQIDTTVKNLSELILHARNR
AVPLTINKSFCLVIDENLKAKIKVKNQLRRLWMRTRLPHFKSQVNALECQIKQEINSIRN
ANWNHKLADIKPNNQTIWRTARYLKLGKRQLPPINNSGQLAITDIEKANMIAVQFNENFS
NTLTSSINQSQIITRTINNFTTQFSTNNQTEETLLPTLDEVTQIIKRLPNKKAPGPDQIK
NCLIKNLPTKGYLFITSILIACYKNCYFPDAWKTADITPIAKPNKNPSHASSYRPISLLN
TLGKILEHTILSRLNKHCIEKSIIPSIQHGFRAGFSTVHQLKRVISHMKKEIEHKRSTAL
ITLDVEKAFDRVCHKGLLFKLISGNFPPLLIKLISSFLSNRSFRVVINGKRSEPYQLLAG
VPQGAVMSPTLFNVFTADFPQEDFYDTALFADDVAIFKSHRCSKPITNGISKAAKSISSY
YKKWRIGLNAQKTTAMFVTRRRKKQLPSQRLRIFNANIEWTNQTKYLGLIIDKNLSFKPH
IDYIIQRANNAIRLLYPMLARNSKLDIRNKIIIYKMAIRPILTYGFPAIPAIAKTHIKKL
QVLQNKALKMIMNKPWYTSTTQIHQMCNIKPIDEYLKDLNIKFNNRLPSSHIS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g124.t2 | CDD | cd01650 | RT_nLTR_like | 877 | 1131 | 0.000 |
| 7 | g124.t2 | Gene3D | G3DSA:3.60.10.10 | - | 374 | 596 | 0.000 |
| 3 | g124.t2 | PANTHER | PTHR33332:SF23 | - | 817 | 1214 | 0.000 |
| 4 | g124.t2 | PANTHER | PTHR33332 | - | 817 | 1214 | 0.000 |
| 2 | g124.t2 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 475 | 591 | 0.000 |
| 1 | g124.t2 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 884 | 1131 | 0.000 |
| 8 | g124.t2 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 861 | 1131 | 22.077 |
| 6 | g124.t2 | SUPERFAMILY | SSF56219 | DNase I-like | 375 | 596 | 0.000 |
| 5 | g124.t2 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 814 | 1101 | 0.000 |
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. There were no conditions that were differentially expressed