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_4 g14529 g14529.t1 isoform g14529.t1 1002399 1004915
chr_4 g14529 g14529.t1 exon g14529.t1.exon1 1002399 1004915
chr_4 g14529 g14529.t1 cds g14529.t1.CDS1 1002399 1004915
chr_4 g14529 g14529.t1 TSS g14529.t1 NA NA
chr_4 g14529 g14529.t1 TTS g14529.t1 NA NA

Sequences

>g14529.t1 Gene=g14529 Length=2517
ATGAAACTAGCCCGCGATCCAGAATTCCTGATTTATCGACTGGACCGAGTTGATCAAGAA
AAAGGTGGTGTTGCAATTCTTGTCCGAAAGAATTTGAAACACAAAATCTTACCAATACCT
AACACCAAAATTATTGAATCCATCGGTATATCAGTTTTGCTCTCTAATGGCACAAATGCC
AACATTTTTAGCGTCTACCTCCCAGGTGGCACTAAGAACAGCATGATAAATGACCAATTT
ATCAATGATATCCGAATCTTGATGTCCTCGTCAAAGAATTCCTTTTTCTGCGGAGACCTA
AATGCTAAACACCGCTACTGGAACTGCAACATAGCAAATCGAGCAAGAACACTCCTATAC
AATGAGTTCTGTAATAAGAATTTTAATATCTACTTCCCACAAGGTAACACATATATACCA
AGCGACATAAATAGACAACCATCAACCATTGACCTGGTGCTCACAAACAGCAACTACGAC
ATCGAGCCCAAAATAAGCAACGAATTAGTTAGCGACCATACAGCTATTACTTTTGACATA
AACACTCATTCACCAGCTCAGTTAACAGAAAATAAGCGTCAACTAGATTATAGTAAAGCA
AATTGGCACAATTACAGACGCATGTTGATCAAATCACTTAACATTCAAAATAACCATGAA
ACAATAGCAACAGTCGATGACATTGACACTCAAATCGAAAAAATTACAACAGAAATTACA
AAAGCCAGAGATGCATCCATACCTAAGGTTATCTGCAACCAATATAAATTAAACCTACCA
GATTCACTGATCGGTTTAATTAAACGGAAAAATGCACTCAAGTGTGCCTGGAGAAGAAAT
AGAGTGCCTTCACTCAAAACAGAAATTAATTGTATGGAGAAAAAGATAAAGTATGAAATT
AGCCTAATCCGAAACAAAAACTGGGAGCACAAACTGAAAAGTATAAAGCCAAGTAATCAG
GCACTATGGAAAACCACTCGTATGTTGAAGAGTGGAAACAAAATTATTCCTCCATTGATG
ACAGCAGATGGACGGGTTATAAGAAGTGTTGATAAAGCTAATGTTATAGCAGACACTTTC
AAAGAAAATCACAAGAACCCACTATTTAAATCACCAACTGTTTATGATTACTCAATCAAA
ACAACAGTCGCAAACTATCTTAACAATAACACAAATGTTGATACACTAGACTCACTTTCG
CTCCCCACAATTGAGGAACTAAAAGAAGCAGTCAACAGGCTTCCCAACAACAAAGCACCG
GGAAAAGACGATATCAAAAACAGCCTGATTAAAAATCTTCCCAATATCGGATATGAGCTA
CTCCTCTCCATTTTCATTGCTTGCTTAAGACTGGGATACTTTCCTATGAGCTGGAAACAT
GTCAAAGTGTTTCCCATAGGTAAGCCAAACAAGGATCCCACATTGCCATCAAGTTACAGA
CCAATAAGTTTACTAAGCACAATTCGTAAACTTCTTGAAAGATTAATTTTGACTAGAGTG
AACAATCATTGCGAAATAAACAAAATATTACCTGACACACAACATGGATTTCGCTCAGAT
TTTTCAACTATTCACCAATTGAAAAGGGTGATTGAACATGCAAAACAAGGATTAAACAAT
AAAGAATCAACTGGACTAGTACTGCTCGACGTTGAAAAGGCGTTCGATCGCGTGTGGCAT
GATGGATTAATTTATAAAATGATAAGACTAAAATTTAACACAAACATTATAAAAATAATA
AACTCCTTCTTGAGAGATAGAAGTTTTCAAGTCGCGATCAACAACGAATGGTCACAATCA
CATAAAATAGAGTTCGGCGTACCACAAGGAGCGGTATTGAGTCCCGTTCTTTACAACGTT
TATACTTACGACCTGCCTACAAATGAATCTTATGAATCCGCTCTCTTTGCTGATGATGTT
GCTAAATTTTCCTCCAGTTCCACTCTATTAAGAGTTAACAAATCGATCACTCAAGCAGCT
AAAGAAACCTACGAATACATGAACAGGTGGAAAATAAGCATAAATGGTTCCAAAACAAAT
GCTATTTTTATAACAAAGAGAATTTCAAAACAATTACCAGATAGTCCTTTGATGATTTTT
AATTCTGCTGTAGATTGGAAAGACGAGTCGAAATATCTCGGTGTGGTTATTGATAAACGA
CTCACGTTTAGAAAACATGTTGACTATGTAATAGCTAAAACGAACAATGCAATTAGAACA
CTTTATCCACTCTTATGTAGAAATTCAAAACTTGATACGGAAAACAAACTACTTATCTAT
AAATTGGCTATTAGGCCAAATTTTACTTATGGCATGCCGGCACTTGATGGACTTGCTGAT
TCACATTTAAAAAGACTACAAACCACTCAAAACAAAATGTTGAAGATGATACTTAATAGA
AATCATTTTGAAAACACCGCAAAATTGCACAGAGAAGCAAATATCCCGATGGTCAAGGAA
TGTATTAATAAGCTCACAATTAATTTTAACACTAAAACAAATTTATCACAATATTAA

>g14529.t1 Gene=g14529 Length=838
MKLARDPEFLIYRLDRVDQEKGGVAILVRKNLKHKILPIPNTKIIESIGISVLLSNGTNA
NIFSVYLPGGTKNSMINDQFINDIRILMSSSKNSFFCGDLNAKHRYWNCNIANRARTLLY
NEFCNKNFNIYFPQGNTYIPSDINRQPSTIDLVLTNSNYDIEPKISNELVSDHTAITFDI
NTHSPAQLTENKRQLDYSKANWHNYRRMLIKSLNIQNNHETIATVDDIDTQIEKITTEIT
KARDASIPKVICNQYKLNLPDSLIGLIKRKNALKCAWRRNRVPSLKTEINCMEKKIKYEI
SLIRNKNWEHKLKSIKPSNQALWKTTRMLKSGNKIIPPLMTADGRVIRSVDKANVIADTF
KENHKNPLFKSPTVYDYSIKTTVANYLNNNTNVDTLDSLSLPTIEELKEAVNRLPNNKAP
GKDDIKNSLIKNLPNIGYELLLSIFIACLRLGYFPMSWKHVKVFPIGKPNKDPTLPSSYR
PISLLSTIRKLLERLILTRVNNHCEINKILPDTQHGFRSDFSTIHQLKRVIEHAKQGLNN
KESTGLVLLDVEKAFDRVWHDGLIYKMIRLKFNTNIIKIINSFLRDRSFQVAINNEWSQS
HKIEFGVPQGAVLSPVLYNVYTYDLPTNESYESALFADDVAKFSSSSTLLRVNKSITQAA
KETYEYMNRWKISINGSKTNAIFITKRISKQLPDSPLMIFNSAVDWKDESKYLGVVIDKR
LTFRKHVDYVIAKTNNAIRTLYPLLCRNSKLDTENKLLIYKLAIRPNFTYGMPALDGLAD
SHLKRLQTTQNKMLKMILNRNHFENTAKLHREANIPMVKECINKLTINFNTKTNLSQY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14529.t1 CDD cd01650 RT_nLTR_like 460 717 2.75773E-40
7 g14529.t1 Gene3D G3DSA:3.60.10.10 - 2 182 8.5E-22
3 g14529.t1 PANTHER PTHR33332:SF29 - 378 816 2.2E-60
4 g14529.t1 PANTHER PTHR33332 - 378 816 2.2E-60
2 g14529.t1 Pfam PF14529 Endonuclease-reverse transcriptase 61 176 6.1E-13
1 g14529.t1 Pfam PF00078 Reverse transcriptase (RNA-dependent DNA polymerase) 469 717 5.3E-46
10 g14529.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 435 -
11 g14529.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 436 453 -
9 g14529.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 454 838 -
8 g14529.t1 ProSiteProfiles PS50878 Reverse transcriptase (RT) catalytic domain profile. 447 717 22.794
6 g14529.t1 SUPERFAMILY SSF56219 DNase I-like 8 182 1.57E-22
5 g14529.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 354 685 3.83E-17

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