General information for g5502.t3
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 g5502 is located on chr_2: 9924828..9927314 (- 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 | g5502 | g5502.t3 | isoform | g5502.t3 | 9923357 | 9927314 |
| chr_2 | g5502 | g5502.t3 | exon | g5502.t3.exon1 | 9923357 | 9926026 |
| chr_2 | g5502 | g5502.t3 | cds | g5502.t3.CDS1 | 9923357 | 9926026 |
| chr_2 | g5502 | g5502.t3 | exon | g5502.t3.exon2 | 9926094 | 9927314 |
| chr_2 | g5502 | g5502.t3 | cds | g5502.t3.CDS2 | 9926094 | 9927314 |
| chr_2 | g5502 | g5502.t3 | TSS | g5502.t3 | NA | NA |
| chr_2 | g5502 | g5502.t3 | TTS | g5502.t3 | NA | NA |
Sequences
>g5502.t3 Gene=g5502 Length=3891
ATGCAGACTAGAGGGAGGAAGAGGAGGCAACAACAACAAGCTTCAAATGGTGAGAATAGT
GAGAATTCTGAAACTGAAAATTCACACGAGGCTACAACAACAACAAAGCCAAAAAAGGCT
AAAACGCCCAAAACAAAAACGCCCAACGCAACAACAACAACGCCTATAAAGGCAGCAACA
ACAACGCCTTCAAAGGCAACAACAACAACAAGTTCTACACAGAACAACAACATCAACAAC
AGTCAGCAAGGCAAAACCAAGCCGATTTTTATTTCGACTAATTATCAAGTCGCCATCAAC
CTGCTCAAGTCATTGAGTCTCAACAACAAGCCTGTTCTAAAAATAATTAACAGCCAGCTT
GTTTCAGTCACAGCAGCAGATCTCATCAGCAAAGAGACCATCATCAAGGCTTTGTCCGAA
AAGCAGTTCCAGTACCATTCGTTCACTGAAAAAGTGAATAGGAAGTTGACCTTTGTTCTC
AAAGGGTTTTACAAGACCACTGCTGAATCACTACTTGACGTCTTGAAGGTAGCAGGTATT
CCGGCATTGAGTGTGTCCATCATCTCCCAGTCTGATGATCGTTCAGTGTACACCGTACAG
TTCCCACAGGGAACGACAACCATCCAGCAACTCAATCAGCAATTCAAAGTCATCGACTAT
TTATTGGTTCGCTGGGAGGTCATTGACAGGTCGAAGCGTCGCCATGTCCAGTGTGGCAAC
TGCAAGAGATGGGGCCATACTTCAGCCAATTGTGGACATCCTTTCCGCTGCATCAAATGC
ACAGGCAGCCATGCCAGGGGTGAGTGTCAACGCACCACGAAGGAGAGTACAGCAGATAGC
AAGGTAGCTTGCGTTAATTGCTCAGGCGAGCATCCTGCAAACAGTCGCAAGTGTCCAGCT
TTCACAGCATACGTCGCCAGGACCAAGTCCAAAGGCAGGCCGGTCTCACAGCCATCCAAG
CCGCCTAGTAGCAGCATTGCAGATCCTTCTGCATGGCCCACTCCCAGCAGTTCTGCACCA
GCAGCACAGCTTGCACAGAACTCTTCAGCACCACAGCCGAAGATCACGCCGAGAGGACGA
GCATCATACGCAGAGGCTATTAGAAGTATTAATTCACAAGCGAGTAGTTCGGGATCTTCT
TTCAATGTCCAGTCCGTTGAGTCCGAAAATCCGTTATTGGTAGAGGCTATTAAGACTCTC
CAAGCCCAAGTGCAGAGTATGTTAATGTCTTGGAATTGTCAGTCTGTCAGTAGGAAGAAA
GCGGAATTAAGCCACTTTCTTTTAGACCATAATATTGATATTGCTCTTCTCTCTGAAACT
TGGCTCAACGATGAGGCTACGTACTCTATACCAGGTTTCAATACTTTCACTGTATGTAGG
CAACATGGTGGTGTCATGATTTTGACCAAAGACTCCATTACAGTGAATGGTGTTAATAGG
ATTGCTCTGAGCTATGCTGAGGCAATCTCGATTAACATTCCATCAGCGATAGGAACAATT
AGTGTTACTTCTATATACTGCTCTCCTGCAAGCTCTAGAAGCCAAGCTTCAGAGTTTTTC
AGAAGAGTGCTTGATTTCCCAGGTTCAGTGGTCATTGCTGGTGACTTCAATGCCAAGCAC
TCGTCTTGGAACAACAGCTCTGACACACTGAAAGGTAAAGACCTATTTGGATTATGTAGG
CATGGTAACTACACGATTCATCCTCCTGATGGCCCCACTTTATATTCAAGTAGAGGAACT
CTTTCAGTAGTCGACTTTGTCATTTCAAAGGCATTACCTGGGGTAAATGGGCCAAAAGTA
ATTAATGAACTTTCATCAGACCACTTACCTTTAACCTTTTCCATACCTGTAGCTTCTTCC
CAGGTATCACAGCACACCTTTTTCCACTGGCCCAAAGCCAATTGGAAGAAGTTTAGAGCA
CAACTCAACTGCAAGGTCCCAGAACTTGCAAGTCTTGACTTGTCCTCTTGCGATGCAATT
GATTGTGCTATTGATGCAGTAACTGTGGCTATTAATGACGCAGCTTCTTCATCTATTCCG
CGTAAGGCACCATATCGATTTAGATTTCCTTTCTCGGATCATTTGCATCGTCTTACTCGC
GAAAGAAATCGCTATCGCCAACAATTCAGGGCTACACAAAGACCTGAATTTAGGAGTTTG
GTCAATCAGTTGAATCGGCTAATTAAAGACGAAACAACGAAATTGAGCCAAGCTTCTTTT
GATTCCAAGCTGAGTCAGCTGTACACACAAGACTGTTCAGCATTTCGATTCATCAAAGCA
ATCAAGAACAAGCGGAATGGCTTTTCCCCCTTGTTAAATCCAGCTACTAACCAATTGGTC
TATACTGATTCTGCTAAGGCTTCTGTACTTTCAGATTCTTTTTTGACTAATCATTGTATT
ACCACCAGTTGGCTGTCTAATAAAGACGCACTGGTAAGTAATGTAGTTAATACATTCAGA
AGGAGCCAAATTGCTGTTTCTGAAAGTATCACTGATCATGAGTCTCTTACTCTGATCATT
AAATCTTTGAGAGTACGGAAGGCTGAAGGCTTAGATGGCATTGCCACTAGGTTTCTCAAA
AACCTACCAAAATCTCTACTTAAGGTAGTAACTATGATTTTTAATCAAAGTTACAAGTTG
GGCTACTTCCCAAGTGCCTGGAAGCGAGCTAAAGTTATCGCTATCCCGAAAAAGGACAAG
CCAACGGACAAACCTAGTAACTTTCGTCCAATTTCATTGCTATCTACTCTAGGAAAGCTT
TATGAGAAGGTTATTCTGGATAAAGTTTCTCGTTTTGAAGAGGCCAATGAACTCATCAAA
CCCCAGCAATTTGGGTTTCGTAGTAGGCATTCGACTACTCACCAAGTTCTGAGAATTATT
GAAGAAGCCACAATAGGCTTCAACAACAAGAAAAGCACGGGCATTGTACTTCTCGATCTC
GAGAAGGCTTTTGATACCGTGTGGCACGAGGGCCTCATTTATAAGCTTATAAAGCTCAAA
TTCCCTCCCGAACAGATCAGAGTCATTGACTCTTTTCTAACTGGAAGACAGGCGTCAGTA
TATGTCAATGGACACGCTTCGCCATTCTTCACGCTTCCAGCTGGAGTACCACAGGGCTCT
ACCTTGTCTCCATTTCTGTTCAATGTGTTTATCAATGACATTCCACGTTTGAAGCACTGC
AAGCTTGCACAGTTCGCAGATGATACCGCGCTATATACTGTTAACTCCTGGAAGAATCTT
GGCCTTATTAAAACCAGACTTTTAGGAGATTTAAGCACATTGGCGTCTTTCTATCGTGAT
TGGAAGGTCAAGATGAATGATAGTAAAACTGAGTTTTCTATCTTCACTAGATCATACAAC
ATGCGCAGGAAGGCAGAAGCTGATACAATTTCATTCGGTACCAACACTTATAAGTGGCAA
AAAGAGGTCCGATATCTAGGTGTTACACTAGATACTCGTTTGAGCTTCCAAGCCCATATA
AAGAGTGTGCTAGCAAAGGCTAGCGGCGTTGGACGCAGCATTTACTGCATTTTCAAGAAG
CATAACACTGTTCCTATCCGTACTAAAATCAATCTCTACAAAGTTTGCATAAGGCCATTA
CTGACTTATGCTGCGCCAGTTTTTGCAAACTGCCCAGTTACCTACTCGCGTAAGCTCCAA
ATTACGCAAAACAAATTCTTGAGAATGTGTCTCAACGCAAGCTATTATACTAGGACTGCG
GACCTTCATGAAGAGGGCCAAGTACCTCTTATCTCAGACTTCATTAAAAAGTTAACTACT
AACTTCTACGACAGGGCTAATAACCATACCAACTCTCTTATTTGCGCATTAGGTAACTAT
TCATCCAGACTGAGAGGTCGCAGAATCAGGCATAAACTGCCTCGTCCTTAA
>g5502.t3 Gene=g5502 Length=1296
MQTRGRKRRQQQQASNGENSENSETENSHEATTTTKPKKAKTPKTKTPNATTTTPIKAAT
TTPSKATTTTSSTQNNNINNSQQGKTKPIFISTNYQVAINLLKSLSLNNKPVLKIINSQL
VSVTAADLISKETIIKALSEKQFQYHSFTEKVNRKLTFVLKGFYKTTAESLLDVLKVAGI
PALSVSIISQSDDRSVYTVQFPQGTTTIQQLNQQFKVIDYLLVRWEVIDRSKRRHVQCGN
CKRWGHTSANCGHPFRCIKCTGSHARGECQRTTKESTADSKVACVNCSGEHPANSRKCPA
FTAYVARTKSKGRPVSQPSKPPSSSIADPSAWPTPSSSAPAAQLAQNSSAPQPKITPRGR
ASYAEAIRSINSQASSSGSSFNVQSVESENPLLVEAIKTLQAQVQSMLMSWNCQSVSRKK
AELSHFLLDHNIDIALLSETWLNDEATYSIPGFNTFTVCRQHGGVMILTKDSITVNGVNR
IALSYAEAISINIPSAIGTISVTSIYCSPASSRSQASEFFRRVLDFPGSVVIAGDFNAKH
SSWNNSSDTLKGKDLFGLCRHGNYTIHPPDGPTLYSSRGTLSVVDFVISKALPGVNGPKV
INELSSDHLPLTFSIPVASSQVSQHTFFHWPKANWKKFRAQLNCKVPELASLDLSSCDAI
DCAIDAVTVAINDAASSSIPRKAPYRFRFPFSDHLHRLTRERNRYRQQFRATQRPEFRSL
VNQLNRLIKDETTKLSQASFDSKLSQLYTQDCSAFRFIKAIKNKRNGFSPLLNPATNQLV
YTDSAKASVLSDSFLTNHCITTSWLSNKDALVSNVVNTFRRSQIAVSESITDHESLTLII
KSLRVRKAEGLDGIATRFLKNLPKSLLKVVTMIFNQSYKLGYFPSAWKRAKVIAIPKKDK
PTDKPSNFRPISLLSTLGKLYEKVILDKVSRFEEANELIKPQQFGFRSRHSTTHQVLRII
EEATIGFNNKKSTGIVLLDLEKAFDTVWHEGLIYKLIKLKFPPEQIRVIDSFLTGRQASV
YVNGHASPFFTLPAGVPQGSTLSPFLFNVFINDIPRLKHCKLAQFADDTALYTVNSWKNL
GLIKTRLLGDLSTLASFYRDWKVKMNDSKTEFSIFTRSYNMRRKAEADTISFGTNTYKWQ
KEVRYLGVTLDTRLSFQAHIKSVLAKASGVGRSIYCIFKKHNTVPIRTKINLYKVCIRPL
LTYAAPVFANCPVTYSRKLQITQNKFLRMCLNASYYTRTADLHEEGQVPLISDFIKKLTT
NFYDRANNHTNSLICALGNYSSRLRGRRIRHKLPRP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5502.t3 | CDD | cd01650 | RT_nLTR_like | 889 | 1150 | 4.67967E-53 |
| 12 | g5502.t3 | Gene3D | G3DSA:3.60.10.10 | - | 407 | 617 | 6.6E-37 |
| 7 | g5502.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 81 | - |
| 8 | g5502.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 30 | - |
| 9 | g5502.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 44 | 81 | - |
| 11 | g5502.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 309 | 360 | - |
| 10 | g5502.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 312 | 355 | - |
| 3 | g5502.t3 | PANTHER | PTHR33332:SF29 | - | 800 | 1237 | 1.0E-63 |
| 4 | g5502.t3 | PANTHER | PTHR33332 | - | 800 | 1237 | 1.0E-63 |
| 2 | g5502.t3 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 501 | 611 | 1.9E-15 |
| 1 | g5502.t3 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 895 | 1150 | 7.6E-52 |
| 13 | g5502.t3 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 876 | 1150 | 28.329 |
| 6 | g5502.t3 | SUPERFAMILY | SSF56219 | DNase I-like | 408 | 616 | 8.77E-32 |
| 5 | g5502.t3 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 810 | 1117 | 8.9E-22 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5502/g5502.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5502.t3.fa.iupred3.txt does not exist
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