General information for g362.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 g362 is located on chr_3: 2959070..2965288 (- 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 | g362 | g362.t1 | TTS | g362.t1 | 2957990 | 2957990 |
| chr_3 | g362 | g362.t1 | isoform | g362.t1 | 2958376 | 2965288 |
| chr_3 | g362 | g362.t1 | exon | g362.t1.exon1 | 2958376 | 2960549 |
| chr_3 | g362 | g362.t1 | cds | g362.t1.CDS1 | 2958376 | 2960549 |
| chr_3 | g362 | g362.t1 | exon | g362.t1.exon2 | 2960894 | 2961097 |
| chr_3 | g362 | g362.t1 | cds | g362.t1.CDS2 | 2960894 | 2961097 |
| chr_3 | g362 | g362.t1 | exon | g362.t1.exon3 | 2961263 | 2962114 |
| chr_3 | g362 | g362.t1 | cds | g362.t1.CDS3 | 2961263 | 2962114 |
| chr_3 | g362 | g362.t1 | exon | g362.t1.exon4 | 2965261 | 2965288 |
| chr_3 | g362 | g362.t1 | cds | g362.t1.CDS4 | 2965261 | 2965288 |
| chr_3 | g362 | g362.t1 | TSS | g362.t1 | NA | NA |
Sequences
>g362.t1 Gene=g362 Length=3258
ATGGCATTAATAATTAAGAAATTACCAGTGACAAAAGTAGTCCCTTCATGCGGATCCAAA
ATTAAAATACCGCATGGCGCGAGCCAACAAAAATTGGATGTGTTTCTATCACCTAGTCGC
TTTAAAAAGCGTGTTTATGACGATCTCCAAGATGAAGATGAAGGCTCTTCCTGTTCGCCT
AGTCCATTAAAGGTGACAAAAACATTTAATAAGACTAATTATCAAAAAATATCCACAGAA
AAATTCCCGCCATTAATTGTTTTTGGACAAAGCATTTCTAAAATACAAGAAATTACAAAT
TCAATAGGAAGTTCAAATGTTCAGCTTAAACTCGTTAAAGAAGGAATCAAAGTGTTTGTT
AGCACCAATTCTGATTTTGTAAAAATCCAAGAGTCATTTGCAAAAAATTCATTTCATTAT
TACACTCATCAACTTCGTGAAGAACAACTCTCAAAATTCGTCATCCATGGCCTGCCTAAG
CTTGAGACTGACATAATTAAACAAGCGTTAGAAAGCGCTAAATTAAATCCAGTCACCATC
AAAGATCTAAACATCAAAAAGAAAAATTATGATGAACATTTGTTTTACCTTGTGTCATTC
TATAAGAAAGAAAATATTACACTGATTGATCTTCAAGATGTCAAAGCTATCAATCACATT
CGTATCTCTTGGCAAAACTTTCGCCATACAAGGAAAGGTCCTACACAATGTATGAATTGT
CTTCGATTCGGCCACGGCACTGCAAATTGTCATTTAATATCTCGATGTATCAGGTGTGCT
GGCGATCATAAGTCTAAGGAGTGTCCTCTTATACAAGTCCCTGATGGTGAAACGCTCTCA
AAAATAGCTACAACAAAACTCAAGTGCGCATTATGTGGAGCCTGGACAAAACCTCCCTAC
CAATCGGCTATTCCATTAGCCAGGCATCCCAATGCTCAACAAAATTCAAACGTTTTATAT
TCACATGATGAACTGTTCAAAATTTTTATGGATATTACAACACAACTCTCTGGTGCTAGA
ACAAAGCAAGAGCAAATTCAAATTATGATGTCGGTTGCCATCAAATATGCAGTGCCTTAC
AATGGGCGAGGTGATACTAATCAAGTCAATTCGCACTTCATAAACGATATCAGGAAACTC
ACCAACGGCAGAACGAGCTTCTTTGTATGTGGTGATTTCAATGCTAAGCATCAGTATTGG
AATTGCACTAGAGCAAACAATGCTGGTAAATTATTATACCATGAGTTGTGCCAGAACAAT
TTCTTTATTGAATATCCACATGAACACACTTATATACCATCTTACTCTAGCAATTCACCC
TCAACAATAGACTTAATAGTTACAAATAAAATTCACAAAATCAATGATCTCAAAACTATA
GATCTAACAAGCGACCATCGCGCAGTGACATTCACAATTGATGCATCAGTCGAATTGGAT
TTCCGACCCAAGACATTCCTTGATTTCTCCAAAGCCAATTGGAATAAATTTCAAGACCTC
ATACACAATAATCTCGATACTTCCTATCAAATGACAGAAAAACAACATATTGATGATTAT
ATAAATCAATTTACAAAAACTATCCTAGACGCTCAGCATAAAGCAGTTCCACATAAGACC
TGTTCCAACTACAAGCTAAACCTTCCAGATGACCTTATCGAAAAGATTAAAATTAAAAAT
ACAATGAAGAGAAGATGGCAAAGATCTCGTGACGTCACTTTAAAAGCTCAGGTCAGATTC
CTGGAAAGATTGATCAAAGTGAGAGTCAACTTAGTCAGAAATGAGAACTGGTCACATAAA
CTTAGTACTATAAAACCAAATCACACCAATGTTTGGAAATTAACAAAATTTTTAAAGAAG
CGCGATTCAAATATTCCTCCAATTAAAACTGCAGATGGTATTCTAAATACTCCCGAAGAA
AAAGCCAACAAGTTAGCGGAAGTTTTCGAATCAAATCATCTAAACCCACTTGAAAGAAGT
TCTCCGGACTTCACTTCCCTAATTAAAAATAAGGTCTCCGGCCTTAGGCAACCACTGCCA
GCAAACGAATTGCCAACTTTCACTGATGCCGATGAAATATTTTCAATCATTCAAAATCTG
AAAAATCCCAAATGTCCTGGTGCTGATCAAATCTCAAATCGACTCATTAAGAAACTACCA
CGTCGCGGTATTATTCATTTAGTCAACATTCTAAATGCTTGTCTTCAATTAAATTACTTT
CCCAACAAGTGGAAATTTGCAAAAATTATCCCAATTCCAAAACCAGGAAAAGTAAAATCA
AATCCTACATCGTACAGACCTATTTCGCTCCTCAGTTCGCTGAGTAAAATACTTGAAAAA
GTTATTCTTGTTCGTCTGCAACATCACATTGAAGTCAATAACATCATTCCTAAGGAACAA
TTTGGCTTTAGAAGTAACTCTTCCACTACTCATCAACTCTACAAAATCATCAACAATGCT
CATGAGGGATTAAAGTTCAAAAAGTCTACAGGTCTGCTTTCACTAGATGTCGAGAAAGCA
TTCGATCGTATCTGGCATGATGGACTTATTGCAAAGATGATTGATTTCGATTTTCCAACT
AATTTGATCTTAATCACAAAATCGTTCTTGTCCGAGAGAACGTTTAAAGTGATTTGTAAT
GGCTCATATTCAACTATCCGCTCAATTCGAGCCGGGGTACCACAAGGTGCAGTCCTGAGT
CCAACGCTCTACAACATTTACACGGCGGATATCCCATTAAATAGTTTTTACGAGACAACC
ATGTTTGCAGACGACACTTCATTTTACAAAACTGCGTTACATCACTCGACAATTTCATCA
AAACTTAAAGTCGCATCAAGAAGTATTGAGACGTATATGACCAAATGGAAAATTTCTATA
AACAAGGACAAAACTGCTGCAATTTACATCACAAATCGTAGGAAAAATGAAATTCCAACG
GGTCCAATTGAAGTTTTTGGAACCTTTATCAATTGGCAAGATTCAATCAAACTTCTAGGA
GTGCACCTTGACAAACGCTTAACTTTTAAGTATCATATTGAAAATGTGACTAGAAAAGCA
AATATCGCAATTCGTACTCTTTACCCTCTTATAAATCGTAAATCAAAACTACACATCACA
AATAAGCTTCTATTATACAAATTAGCAATAAGACCTATCCTGACATACGGATATCCAGCA
TTTCATGGCATCATCGCCGCAACTCATACGCGAAAACTTCAAACGCTACAAAACAGAACT
TTGAAAAATGATCCTTGA
>g362.t1 Gene=g362 Length=1085
MALIIKKLPVTKVVPSCGSKIKIPHGASQQKLDVFLSPSRFKKRVYDDLQDEDEGSSCSP
SPLKVTKTFNKTNYQKISTEKFPPLIVFGQSISKIQEITNSIGSSNVQLKLVKEGIKVFV
STNSDFVKIQESFAKNSFHYYTHQLREEQLSKFVIHGLPKLETDIIKQALESAKLNPVTI
KDLNIKKKNYDEHLFYLVSFYKKENITLIDLQDVKAINHIRISWQNFRHTRKGPTQCMNC
LRFGHGTANCHLISRCIRCAGDHKSKECPLIQVPDGETLSKIATTKLKCALCGAWTKPPY
QSAIPLARHPNAQQNSNVLYSHDELFKIFMDITTQLSGARTKQEQIQIMMSVAIKYAVPY
NGRGDTNQVNSHFINDIRKLTNGRTSFFVCGDFNAKHQYWNCTRANNAGKLLYHELCQNN
FFIEYPHEHTYIPSYSSNSPSTIDLIVTNKIHKINDLKTIDLTSDHRAVTFTIDASVELD
FRPKTFLDFSKANWNKFQDLIHNNLDTSYQMTEKQHIDDYINQFTKTILDAQHKAVPHKT
CSNYKLNLPDDLIEKIKIKNTMKRRWQRSRDVTLKAQVRFLERLIKVRVNLVRNENWSHK
LSTIKPNHTNVWKLTKFLKKRDSNIPPIKTADGILNTPEEKANKLAEVFESNHLNPLERS
SPDFTSLIKNKVSGLRQPLPANELPTFTDADEIFSIIQNLKNPKCPGADQISNRLIKKLP
RRGIIHLVNILNACLQLNYFPNKWKFAKIIPIPKPGKVKSNPTSYRPISLLSSLSKILEK
VILVRLQHHIEVNNIIPKEQFGFRSNSSTTHQLYKIINNAHEGLKFKKSTGLLSLDVEKA
FDRIWHDGLIAKMIDFDFPTNLILITKSFLSERTFKVICNGSYSTIRSIRAGVPQGAVLS
PTLYNIYTADIPLNSFYETTMFADDTSFYKTALHHSTISSKLKVASRSIETYMTKWKISI
NKDKTAAIYITNRRKNEIPTGPIEVFGTFINWQDSIKLLGVHLDKRLTFKYHIENVTRKA
NIAIRTLYPLINRKSKLHITNKLLLYKLAIRPILTYGYPAFHGIIAATHTRKLQTLQNRT
LKNDP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g362.t1 | CDD | cd01650 | RT_nLTR_like | 747 | 1003 | 0.000 |
| 7 | g362.t1 | Gene3D | G3DSA:3.60.10.10 | - | 331 | 475 | 0.000 |
| 3 | g362.t1 | PANTHER | PTHR33332:SF29 | - | 669 | 1082 | 0.000 |
| 4 | g362.t1 | PANTHER | PTHR33332 | - | 669 | 1082 | 0.000 |
| 2 | g362.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 371 | 469 | 0.000 |
| 1 | g362.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 752 | 1003 | 0.000 |
| 8 | g362.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 733 | 1003 | 24.557 |
| 6 | g362.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 372 | 475 | 0.000 |
| 5 | g362.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 686 | 973 | 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.
