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.t3 isoform g14529.t3 1001048 1004748
chr_4 g14529 g14529.t3 exon g14529.t3.exon1 1001048 1001700
chr_4 g14529 g14529.t3 cds g14529.t3.CDS1 1001048 1001700
chr_4 g14529 g14529.t3 exon g14529.t3.exon2 1001770 1002243
chr_4 g14529 g14529.t3 cds g14529.t3.CDS2 1001770 1002243
chr_4 g14529 g14529.t3 exon g14529.t3.exon3 1002302 1004634
chr_4 g14529 g14529.t3 cds g14529.t3.CDS3 1002302 1004634
chr_4 g14529 g14529.t3 exon g14529.t3.exon4 1004693 1004748
chr_4 g14529 g14529.t3 cds g14529.t3.CDS4 1004693 1004748
chr_4 g14529 g14529.t3 TSS g14529.t3 NA NA
chr_4 g14529 g14529.t3 TTS g14529.t3 NA NA

Sequences

>g14529.t3 Gene=g14529 Length=3516
ATGACAAAAGACATTAAATTTGACAATGTGCAGAAAGCACAAAATGACAAAAAAGTGAAA
ACCACAAATGAAGCTCTTCTTCTCAATAACACTTATGCTTGTCTTAAAAACAACGATGAT
GGTCAATACGTCGAAACATTAATGACAAAAGGTAATAAACAAAGCAACTCAAAACAACAA
AAACCGCCTCCAATTAACCTATTTGGAGTAAGTTTGCAACAATTGGACCAAATGTTCACC
ACTATGGACAAATCAAATTACGAACTTAAATTGACTGCTGATGGCATTAAACTGTTTTCA
AAAGAAATCGAAACATACAAAACAATTAGAAATATACTAATCGAGCACAATATACAATTT
TACACTCACCAATTACGTGAGGAACAAATGACAAAAATGGTACTGCATGGATTACCTGAA
TCAGATAGAGATACCAATACAGTTACACAAGCGTTGAAAGAGATACAATTAAATCCAGTC
ATGGTAAAGAAGATGCAAATTAAGAATGCAAGATATGTCGGTCATGCCGTCGATCTTGTT
TACTTCAAGAAAATTGATAATATTAGACTGAGTGATCTAATAGAGAATCATCGAATTGTG
TGCTGCATAAGAGTAAAATGGGAGCTGTATAAAAATCCTTCAAAAGGACCAACGTGTGCA
CAAAATCATAAATCAGGTGACTGTCCTCTAATTAAAAATGACAAAGGTGAAACAATTCTG
AAAAGAATAAAAGACACCGCGCTTAGGTGCGCTCTCTGTGGAATGAACCATGCTGCAAGC
TCAAAAGAATGCAGCAAAAGAAGAGAGTTTATCAACGCTAAAAAGTTCAACAAACCTGAA
ATAAAGAAAATAAACACAGAGAGAAGATCATTCCAACCAGCACCAGAATTGAATGATTTC
AATTTTCCAAGACTTCCTCAGAAAAAATTCGATCGCACTACCAAATCAGCACCTCCCCCG
CTCCGTGAAGTCCCGCCTAAGATACCGAATGTCGAGCAAACGGAAAACATTTTTAGCACT
GAAAGAAGAAGTGAATTGCTCAAAATTTTTACAGAAATGACCACTCAATTAGCACAAGCA
AAAACAAAATCAGAACAAGTCATGATACTCATGGACATTGCCCTCAATAATAGCATTCAA
ACAAAAATCCACGAACTTTACTTATATGCAAACAACAACTTTATTGATGTCATCTGTCTC
AGTGAGACATTCCTAAAATATCACATGAAACTAGCCCGCGATCCAGAATTCCTGATTTAT
CGACTGGACCGAGTTGATCAAGAAAAAGGTGGTGTTGCAATTCTTGTCCGAAAGAATTTG
AAACACAAAATCTTACCAATACCTAACACCAAAATTATTGAATCCATCGGTATATCAGTT
TTGCTCTCTAATGGCACAAATGCCAACATTTTTAGCGTCTACCTCCCAGGTGGCACTAAG
AACAGCATGATAAATGACCAATTTATCAATGATATCCGAATCTTGATGTCCTCGTCAAAG
AATTCCTTTTTCTGCGGAGACCTAAATGCTAAACACCGCTACTGGAACTGCAACATAGCA
AATCGAGCAAGAACACTCCTATACAATGAGTTCTGTAATAAGAATTTTAATATCTACTTC
CCACAAGGTAACACATATATACCAAGCGACATAAATAGACAACCATCAACCATTGACCTG
GTGCTCACAAACAGCAACTACGACATCGAGCCCAAAATAAGCAACGAATTAGTTAGCGAC
CATACAGCTATTACTTTTGACATAAACACTCATTCACCAGCTCAGTTAACAGAAAATAAG
CGTCAACTAGATTATAGTAAAGCAAATTGGCACAATTACAGACGCATGTTGATCAAATCA
CTTAACATTCAAAATAACCATGAAACAATAGCAACAGTCGATGACATTGACACTCAAATC
GAAAAAATTACAACAGAAATTACAAAAGCCAGAGATGCATCCATACCTAAGGTTATCTGC
AACCAATATAAATTAAACCTACCAGATTCACTGATCGGTTTAATTAAACGGAAAAATGCA
CTCAAGTGTGCCTGGAGAAGAAATAGAGTGCCTTCACTCAAAACAGAAATTAATTGTATG
GAGAAAAAGATAAAGTATGAAATTAGCCTAATCCGAAACAAAAACTGGGAGCACAAACTG
AAAAGTATAAAGCCAAGTAATCAGGCACTATGGAAAACCACTCGTATGTTGAAGAGTGGA
AACAAAATTATTCCTCCATTGATGACAGCAGATGGACGGGTTATAAGAAGTGTTGATAAA
GCTAATGTTATAGCAGACACTTTCAAAGAAAATCACAAGAACCCACTATTTAAATCACCA
ACTGTTTATGATTACTCAATCAAAACAACAGTCGCAAACTATCTTAACAATAACACAAAT
GTTGATACACTAGACTCACTTTCGCTCCCCACAATTGAGGAACTAAAAGAAGCAGTCAAC
AGGCTTCCCAACAACAAAGCACCGGGAAAAGACGATATCAAAAACAGCCTGATTAAAAAT
CTTCCCAATATCGGATATGAGCTACTCCTCTCCATTTTCATTGCTTGCTTAAGACTGGGA
TACTTTCCTATGAGCTGGAAACATGTCAAAGTGTTTCCCATAGGTAAGCCAAACAAGGAT
CCCACATTGCCATCAAGTTACAGACCAATAAGTTTACTAAGCACAATTCGTAAACTTCTT
GAAAGATTAATTTTGACTAGAGTGAACAATCATTGCGAAATAAACAAAATATTACCTGAC
ACACAACATGGATTTCGCTCAGATTTTTCAACTATTCACCAATTGAAAAGGGTGATTGAA
CATGCAAAACAAGGATTAAACAATAAAGAATCAACTGGACTAGTACTGCTCGACGTTGAA
AAGGCGTTCGATCGCGTGTGGCATGATGGATTAATTTATAAAATGATAAGACTAAAATTT
AACACAAACATTATAAAAATAATAAACTCCTTCTTGAGAGATAGAAGTTTTCAAGTCGCG
ATCAACAACGAATGGTCACAATCACATAAAATAGAGTTCGGCGTACCACAAGGAGCGGTA
TTGAGTCCCGTTCTTTACAACGTTTATACTTACGACCTGCCTACAAATGAATCTTATGAA
TCCGCTCTCTTTGCTGATGATGTTGCTAAATTTTCCTCCAGTTCCACTCTATTAAGAGTT
AACAAATCGATCACTCAAGCAGCTAAAGAAACCTACGAATACATGAACAGGTGGAAAATA
AGCATAAATGGTTCCAAAACAAATGCTATTTTTATAACAAAGAGAATTTCAAAACAATTA
CCAGATAGTCCTTTGATGATTTTTAATTCTGCTGTAGATTGGAAAGACGAGTCGAAATAT
CTCGGTGTGGTTATTGATAAACGACTCACGTTTAGAAAACATGTTGACTATGTAATAGCT
AAAACGAACAATGCAATTAGAACACTTTATCCACTCTTATGCCAAATTTTACTTATGGCA
TGCCGGCACTTGATGGACTTGCTGATTCACATTTAA

>g14529.t3 Gene=g14529 Length=1171
MTKDIKFDNVQKAQNDKKVKTTNEALLLNNTYACLKNNDDGQYVETLMTKGNKQSNSKQQ
KPPPINLFGVSLQQLDQMFTTMDKSNYELKLTADGIKLFSKEIETYKTIRNILIEHNIQF
YTHQLREEQMTKMVLHGLPESDRDTNTVTQALKEIQLNPVMVKKMQIKNARYVGHAVDLV
YFKKIDNIRLSDLIENHRIVCCIRVKWELYKNPSKGPTCAQNHKSGDCPLIKNDKGETIL
KRIKDTALRCALCGMNHAASSKECSKRREFINAKKFNKPEIKKINTERRSFQPAPELNDF
NFPRLPQKKFDRTTKSAPPPLREVPPKIPNVEQTENIFSTERRSELLKIFTEMTTQLAQA
KTKSEQVMILMDIALNNSIQTKIHELYLYANNNFIDVICLSETFLKYHMKLARDPEFLIY
RLDRVDQEKGGVAILVRKNLKHKILPIPNTKIIESIGISVLLSNGTNANIFSVYLPGGTK
NSMINDQFINDIRILMSSSKNSFFCGDLNAKHRYWNCNIANRARTLLYNEFCNKNFNIYF
PQGNTYIPSDINRQPSTIDLVLTNSNYDIEPKISNELVSDHTAITFDINTHSPAQLTENK
RQLDYSKANWHNYRRMLIKSLNIQNNHETIATVDDIDTQIEKITTEITKARDASIPKVIC
NQYKLNLPDSLIGLIKRKNALKCAWRRNRVPSLKTEINCMEKKIKYEISLIRNKNWEHKL
KSIKPSNQALWKTTRMLKSGNKIIPPLMTADGRVIRSVDKANVIADTFKENHKNPLFKSP
TVYDYSIKTTVANYLNNNTNVDTLDSLSLPTIEELKEAVNRLPNNKAPGKDDIKNSLIKN
LPNIGYELLLSIFIACLRLGYFPMSWKHVKVFPIGKPNKDPTLPSSYRPISLLSTIRKLL
ERLILTRVNNHCEINKILPDTQHGFRSDFSTIHQLKRVIEHAKQGLNNKESTGLVLLDVE
KAFDRVWHDGLIYKMIRLKFNTNIIKIINSFLRDRSFQVAINNEWSQSHKIEFGVPQGAV
LSPVLYNVYTYDLPTNESYESALFADDVAKFSSSSTLLRVNKSITQAAKETYEYMNRWKI
SINGSKTNAIFITKRISKQLPDSPLMIFNSAVDWKDESKYLGVVIDKRLTFRKHVDYVIA
KTNNAIRTLYPLLCQILLMACRHLMDLLIHI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14529.t3 CDD cd01650 RT_nLTR_like 868 1125 1.54099E-40
7 g14529.t3 Gene3D G3DSA:3.60.10.10 - 375 590 1.1E-28
3 g14529.t3 PANTHER PTHR33332:SF29 - 786 1149 2.5E-53
4 g14529.t3 PANTHER PTHR33332 - 786 1149 2.5E-53
2 g14529.t3 Pfam PF14529 Endonuclease-reverse transcriptase 469 584 9.7E-13
1 g14529.t3 Pfam PF00078 Reverse transcriptase (RNA-dependent DNA polymerase) 877 1125 9.6E-46
10 g14529.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 843 -
11 g14529.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 844 861 -
9 g14529.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 862 1171 -
8 g14529.t3 ProSiteProfiles PS50878 Reverse transcriptase (RT) catalytic domain profile. 855 1125 22.794
6 g14529.t3 SUPERFAMILY SSF56219 DNase I-like 378 590 7.59E-28
5 g14529.t3 SUPERFAMILY SSF56672 DNA/RNA polymerases 762 1093 9.78E-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