Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable RNA-directed DNA polymerase from transposon X-element.

Parent gene

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 g7104 g7104.t2 isoform g7104.t2 21198496 21200928
chr_2 g7104 g7104.t2 exon g7104.t2.exon1 21198496 21200928
chr_2 g7104 g7104.t2 cds g7104.t2.CDS1 21198496 21200928
chr_2 g7104 g7104.t2 TSS g7104.t2 NA NA
chr_2 g7104 g7104.t2 TTS g7104.t2 NA NA

Sequences

>g7104.t2 Gene=g7104 Length=2433
ATGACAACAAAAACCTACGAAATTTACAACTATATGAAACAAAAACAAATCCACATTGCT
TGTTTACAAGAAACACATTTAAAAACAAATATTAGAATTCCTGCAGATCCAGATTACAAA
ATTTACAGATACGACCGAAACAACGGTGACAAAGGCGGTGTTGCAATAGTAATACGGAAA
GACATTTCACATCAACTTCTAAATTCAAAACAAACAAAAATTATCGAAAACATTGGAGTC
AAAATTAATTTGATAAATGGTGAGAAAATTATGATCTATTCGTGTTATCTTCCAGGTGGT
TCATCGAATCAACAAATAAACGAGCACTTCATTGAAGATATCAGGAAATTGTCGAGCTCA
TCAAGTTACTTTCTAATTGGTGATTTTAATTCGAAGCATAGAAACTGGAATTGTCACATT
GCAAATAGAGCTGGTACTCTGCTTTATGATGAGTCTTGTCAGAGAGATCTATTTATAGAT
CATCCACAAGCTCATACTCATTTTCCAGGTGACGTAAATAAAAGACCATCAACACTTGAC
ATAATTTTATCAAATGGAATTCACCAAATAGAAGACATTAAACTAGCCGAATTAGTAAGC
GATCATATTTCGGTCAAGTTTCAAATTTGCACAAATGCAAGAATTGGCACTACGCAACGC
AGGAAACAACTCGACTTTGGTAGAGCAGACTGGTTGAAATATAGAGAAATTGTAAATTTC
CATATTTCACAACCTGAATATGATACACAACTCAACACTACCAATGAAATTGATTCAGCT
ATAGAAAACTTTACTAAATTGATGATACATGCAAGAAATAGGACAGTTCCACAAATAAAG
TCTAACAAATACAAATTGGTACTTCATACTGAAGTAATTGAATTGATTAAGAAGAAAAAC
AAAATTAAAAGAATCTGGCTTCGTAATAGACTTCCTCAACTCAAAACTGAAGTAAACGCG
CTTGAATATCGAATAAAAACTGCAATAAACAACATCAGGAATTCAAACTGGAATCACAAA
TTGTCGGAAATAAAGCCTAGCAATCAATCAGTATGGCGCACAGCTCGATTTCTAAAAGTT
GGAAACCGAGAGATGCCACCGCTCAGAAATAGAGCATTGGAGGCCGTATCCAATCAAGAG
AAAGCTGATATGATTGCTGATCAATTCAGAATCAATCACATAAATCCACTGGCTGACATC
AATACAAATCATGTCAATAATATTAATTGCCAAGTGAATAACTTTCTCAATACTCCAACA
AACACTGAAATACTGAATGAACTTAGCACACCGACAACTGATGAAATTATCGATATCATC
AAGCGACTTCCAAATAATAAGGCACCAGGCGAGGATCAAATCAAAAACTGTCTCATCAAA
CAATTACCATATAAAGGTTATCTATTTCTAACTACTATATTAACAGCTTGCTTCGCCCTC
GACTACTTTCCAGATGCATGGAAGAAAGCTAATGTGATCCCTATCCACAAACCAGGCAAA
GATGCAACAAATCCAGCTAGTTACAGACCAATCAGTCTCTTAAGCTCTTTAGGCAAAATA
TTGGAAAGAACTATGCTCGCTAGAATTCAAAAACACTGTAACGAATCTAATATCATTCCA
ACATTTCAACATGGTTTTAGAGCAGGCCTCTCAACCGTACATCAGTTGAAGCGAACAATA
AGTCTTATGAGGAATGCATTGGATGACAAAAAGTCTGCTGGATTCATAACACTCGACATC
GAAAAAGCCTTTGATAGAATTTATCACAACGGAGTGCTTTACAAGATGATTCAGGGTAAC
TTCAACATAAAATTGATTAAACTAATTGTCTCTTTCTTGAAAAATAGATCATTTTGCGTG
ACTGTGTGTGGAGCCAAATCTGCGACACATCCACTTATAAATGGTGTTCCTCAAGGAGCA
GTGATCAGTCCATGCTTATATAACATCTACACTGGAGATATACCATTTAGTTCAACAAAT
GATTATACTACAACACTTTTCGCTGATGACGTGGCTATAATCAAAAGCAATCGACTTGTC
AAACCAATAATCAAAGGACTTAACAAGGCATCCAAAAATTTGTCTAGCTACTTCAATAAG
TGGAAGATAAATGTCAATGGAGCAAAAACCAACGCCATGTATGTTACAAGAAGGCGTAAA
AAACAACTTCCTATTGGTCCGCTTCAAATTTTTGATGAACGAGTTGATTGGTCGAACGAG
ATCAAATATCTCGGTATTGTTATTGATAAGAAGCTAACATTCAAAGCACACATCGAATAT
GTCATCAAGCGAGCAAATAATGCAATCAGAGTGCTCTATCCTCTGTTATCAAGAAAATCG
AAACTCAATACTCATAAACAAACTCCTTATTTACAAGTTAGCTATTCGTCCAATCTTGAC
ATATGGCTTTCCAGCTATAAAAGGAATCGCTAA

>g7104.t2 Gene=g7104 Length=810
MTTKTYEIYNYMKQKQIHIACLQETHLKTNIRIPADPDYKIYRYDRNNGDKGGVAIVIRK
DISHQLLNSKQTKIIENIGVKINLINGEKIMIYSCYLPGGSSNQQINEHFIEDIRKLSSS
SSYFLIGDFNSKHRNWNCHIANRAGTLLYDESCQRDLFIDHPQAHTHFPGDVNKRPSTLD
IILSNGIHQIEDIKLAELVSDHISVKFQICTNARIGTTQRRKQLDFGRADWLKYREIVNF
HISQPEYDTQLNTTNEIDSAIENFTKLMIHARNRTVPQIKSNKYKLVLHTEVIELIKKKN
KIKRIWLRNRLPQLKTEVNALEYRIKTAINNIRNSNWNHKLSEIKPSNQSVWRTARFLKV
GNREMPPLRNRALEAVSNQEKADMIADQFRINHINPLADINTNHVNNINCQVNNFLNTPT
NTEILNELSTPTTDEIIDIIKRLPNNKAPGEDQIKNCLIKQLPYKGYLFLTTILTACFAL
DYFPDAWKKANVIPIHKPGKDATNPASYRPISLLSSLGKILERTMLARIQKHCNESNIIP
TFQHGFRAGLSTVHQLKRTISLMRNALDDKKSAGFITLDIEKAFDRIYHNGVLYKMIQGN
FNIKLIKLIVSFLKNRSFCVTVCGAKSATHPLINGVPQGAVISPCLYNIYTGDIPFSSTN
DYTTTLFADDVAIIKSNRLVKPIIKGLNKASKNLSSYFNKWKINVNGAKTNAMYVTRRRK
KQLPIGPLQIFDERVDWSNEIKYLGIVIDKKLTFKAHIEYVIKRANNAIRVLYPLLSRKS
KLNTHKQTPYLQVSYSSNLDIWLSSYKRNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g7104.t2 CDD cd01650 RT_nLTR_like 489 748 3.64113E-45
7 g7104.t2 Gene3D G3DSA:3.60.10.10 - 1 210 2.4E-34
3 g7104.t2 PANTHER PTHR33332:SF29 - 370 792 3.8E-54
4 g7104.t2 PANTHER PTHR33332 - 370 792 3.8E-54
2 g7104.t2 Pfam PF14529 Endonuclease-reverse transcriptase 90 205 1.3E-11
1 g7104.t2 Pfam PF00078 Reverse transcriptase (RNA-dependent DNA polymerase) 495 747 9.8E-46
10 g7104.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 463 -
11 g7104.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 464 483 -
9 g7104.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 484 810 -
8 g7104.t2 ProSiteProfiles PS50878 Reverse transcriptase (RT) catalytic domain profile. 476 748 24.168
6 g7104.t2 SUPERFAMILY SSF56219 DNase I-like 3 210 4.19E-30
5 g7104.t2 SUPERFAMILY SSF56672 DNA/RNA polymerases 409 717 5.23E-16

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