Gene loci information

Transcript annotation

  • This transcript has been annotated as Piwi-like protein Siwi.

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 g8254 g8254.t1 TTS g8254.t1 29353431 29353431
chr_2 g8254 g8254.t1 isoform g8254.t1 29353614 29356599
chr_2 g8254 g8254.t1 exon g8254.t1.exon1 29353614 29354285
chr_2 g8254 g8254.t1 cds g8254.t1.CDS1 29353614 29354285
chr_2 g8254 g8254.t1 exon g8254.t1.exon2 29354350 29354468
chr_2 g8254 g8254.t1 cds g8254.t1.CDS2 29354350 29354468
chr_2 g8254 g8254.t1 exon g8254.t1.exon3 29354524 29355450
chr_2 g8254 g8254.t1 cds g8254.t1.CDS3 29354524 29355450
chr_2 g8254 g8254.t1 exon g8254.t1.exon4 29355516 29355727
chr_2 g8254 g8254.t1 cds g8254.t1.CDS4 29355516 29355727
chr_2 g8254 g8254.t1 exon g8254.t1.exon5 29355788 29356599
chr_2 g8254 g8254.t1 cds g8254.t1.CDS5 29355788 29356599
chr_2 g8254 g8254.t1 TSS g8254.t1 29357045 29357045

Sequences

>g8254.t1 Gene=g8254 Length=2742
ATGAGTAATTATGATCAGTATAGAGGACGTCGAGGTGGTCACAGTGGAAATTCTGATAGA
AATTATGAGCGAGAGAGAAGCAATCATTATCCAGATTATAGTAGAAACAGAGATAATAGT
AGCAATAGAGACTCTAATAGAAGAAATGAAGACAGAGGAAACGAATTTGGTCGTGGTTAT
GATTCAAGCCGTAAAAGATTTCATGATGATGGTCCAAGTACATCAGGTACTTATCGTGGA
AATTTTTCAAAACGTGGCAGAGGTGGAAGAGGAGGCAGAGGCAGTGGAAACAAAAAAGAT
CCACGTCCAGAATTCCCAAGTGAAATCGATTCTCGTCCTAAAAATTTCACAGAAAAAGTC
GCTTCTTATAATCAGGGAGATGAAAGTGTTACACTCGTTACCAATTATTTTGAATTTAAT
TTGAGAAAATTCAGATCAAAAATTATTGTCACTATGTGCTTTGTTGATTTTAATCCTATG
GTTGCGAATAAATGGGAGAAGAGTTATTTGATTGCTCAACATAAGGCACGACTGGGAACA
TATGTTTACGATAATTCTGCTTCTATTTATCTTGCACAGCCTCTTGAAAAAGGTGATAGG
ATTAGTCTTGAAAGTAGAGGAAGAAATAATCAAACATATAGCATTATTTTGACAGCAAAA
AACAATATATCACCAACTGATTCTATGTTTTTGACCGTTATTAATTTGATTATAAGACAA
GCTATGATTGCATGTAATTTTGACCTTATCGGACGAAATTACTTTGATCCTTCCACAGCA
TCTAACATGGAACAATATAGATTACAAATCTGGGATGGATTTAAAACATCAGTTCGTCAA
CATGAAGAAAAGTTATTGATGTGTTGTGACTTGGCTCATAAAGTTATACGTAATGAAAAT
ATTTATACAATGATTCAAGACGTGATCAATGACACAAGAAGAAGAGGAGATTATCAAAAA
ACCGTCAAACAAAAGTTATTAGGAATGGTTGTTTTAACAAACTATAATAACAAAACTTAT
AAAGTTTCTGACATCGATTTCGAAAAAAATCCATTGTCAACTTTTACTATGAAAGGAAGA
TCTAAAAGTTATATTGATTACTATAAAGAATTTTACAAAATTACAATTAGAGATCCGAAA
CAACCGTTACTGGTACATAAGCCAAAAGCAAAAGAACGTCGTGGTGGAGCAAAAGACATA
ATTTACCTTGTACCTGAACTATGTCAAGCAACTGGTCTAGATGAAAGTGTAAGAAAAAAT
TTTCAATTGATGCGCGATATGGCAAACAAAACACGCAAAACACCAAGAGAACGCGCTGAG
TTACTGCAAAATTTTGTTAAAAAATTGCAAACAAATGAAAAGAGTCTTCAAGTTTTTAGA
GAAAACAATTGCTCTTTGAATACAGATCTCGAAGAAGTTCCTGCAAGACGCATGGAACAA
AACAATATTATATTTGGAGAAGGACAAAATATTAATTTAAATGAGCAATCAGATTTAAGA
GATTTGGTGGATTGGACAAAATGTCTACACGATAAAAACTTGTTTGAACCTAAATCAATT
AATGATTGGGTTATAATCTTTTCTGATTCTATTAATCGTGATCAATCAATCAGTTCTTTT
GCAAAAAGATTTATAAACACAGGAAAGAATTTGGGAATGATTTTTAATAACAGACACAGA
GAAGTTAAACTTCGAAGTGAAAGATTATACGATTTTATTGAATCATTGAAAGAAAATCTA
ATAAATGCCAAGAAAAATGAGACATCTTTTATAATGATTATTTTGACTAAAATGCAAGCC
CGTATATATTCGGATATAAAAAGAACCGTTCTTTGCAGTCAAGATCTTCAACCTATACCA
ATTCAAGTAGTTCTTAATACCACAATAACAAAGCCTAATATTGAATCTGTGACACAAAAA
ATTGCAATTCAGGTCAATTGCAAGTTAGGAGGAATTCCCTGGTTTGTGAATATTCCAATG
AAAAGTGTAATGATTATTGGATTTGACCTTTCAAAAGATTCAAAAGAGAAGAAACATTCA
TTTGGCGCATTTGTAGCACACTCTATTGAGAAAAATAAAGCTTCAGATGCATGTAGCGGT
GATTTTTTCTCAATTGTGGATCGTCATGAAAATGGACAGGATGTTTCACAACGTTTTAGC
ATTAATATAATGGTAGCAGTTAATACATTCATCGAAAAATACGGTAAACCACCAAGAAAA
ATTATTATTTACCGTAATGGAGTTGGTGATGGTGATATTGAACGTGTAATACAACATGAA
GTTAACGACACAAAAGAGAAACTTTTGAAAACTTACAAAAATTATGATATGAAACTTGAA
TTTGGTTTCATTATTATCAACAAAAAGATAAACACTCGTTTCTTTAGAAAGCCAAGAAAC
AGTCGCGAAGATTATAACAATCCACTTCCAGGAACTGTCGTTGATCAGGTTGTGACACTT
CCTTATAGATATGATTTTTATCTTATATCTCAAAGCGTTAATCAAGGTACTGTTTCTCCT
ACTTCATACAATGTAATTGAAGATTCACTAGAACTGAATCCTTCAATAATTCAGAAATTG
ACCTACAGATTGTGTCACATGTATTACAACTGGAGCGGTACAACCAAAGTTCCATCAGTT
GTACAATATGCTAAAAAATTAGCATTTTTATCTGCTCAATACTTGCATAATATTCCTTTA
AATGAAAACATTAAAAGCGATCAATACTTATACTTTTTGTAA

>g8254.t1 Gene=g8254 Length=913
MSNYDQYRGRRGGHSGNSDRNYERERSNHYPDYSRNRDNSSNRDSNRRNEDRGNEFGRGY
DSSRKRFHDDGPSTSGTYRGNFSKRGRGGRGGRGSGNKKDPRPEFPSEIDSRPKNFTEKV
ASYNQGDESVTLVTNYFEFNLRKFRSKIIVTMCFVDFNPMVANKWEKSYLIAQHKARLGT
YVYDNSASIYLAQPLEKGDRISLESRGRNNQTYSIILTAKNNISPTDSMFLTVINLIIRQ
AMIACNFDLIGRNYFDPSTASNMEQYRLQIWDGFKTSVRQHEEKLLMCCDLAHKVIRNEN
IYTMIQDVINDTRRRGDYQKTVKQKLLGMVVLTNYNNKTYKVSDIDFEKNPLSTFTMKGR
SKSYIDYYKEFYKITIRDPKQPLLVHKPKAKERRGGAKDIIYLVPELCQATGLDESVRKN
FQLMRDMANKTRKTPRERAELLQNFVKKLQTNEKSLQVFRENNCSLNTDLEEVPARRMEQ
NNIIFGEGQNINLNEQSDLRDLVDWTKCLHDKNLFEPKSINDWVIIFSDSINRDQSISSF
AKRFINTGKNLGMIFNNRHREVKLRSERLYDFIESLKENLINAKKNETSFIMIILTKMQA
RIYSDIKRTVLCSQDLQPIPIQVVLNTTITKPNIESVTQKIAIQVNCKLGGIPWFVNIPM
KSVMIIGFDLSKDSKEKKHSFGAFVAHSIEKNKASDACSGDFFSIVDRHENGQDVSQRFS
INIMVAVNTFIEKYGKPPRKIIIYRNGVGDGDIERVIQHEVNDTKEKLLKTYKNYDMKLE
FGFIIINKKINTRFFRKPRNSREDYNNPLPGTVVDQVVTLPYRYDFYLISQSVNQGTVSP
TSYNVIEDSLELNPSIIQKLTYRLCHMYYNWSGTTKVPSVVQYAKKLAFLSAQYLHNIPL
NENIKSDQYLYFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g8254.t1 CDD cd02845 PAZ_piwi_like 309 413 1.22278E-41
12 g8254.t1 CDD cd04658 Piwi_piwi-like_Euk 422 893 6.54467E-128
8 g8254.t1 Gene3D G3DSA:2.170.260.10 paz domain 298 420 2.1E-38
10 g8254.t1 Gene3D G3DSA:3.40.50.2300 - 511 648 2.1E-20
9 g8254.t1 Gene3D G3DSA:3.30.420.10 - 657 909 2.3E-59
17 g8254.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 115 -
16 g8254.t1 MobiDBLite mobidb-lite consensus disorder prediction 12 72 -
15 g8254.t1 MobiDBLite mobidb-lite consensus disorder prediction 93 115 -
4 g8254.t1 PANTHER PTHR22891 EUKARYOTIC TRANSLATION INITIATION FACTOR 2C 57 904 3.5E-193
5 g8254.t1 PANTHER PTHR22891:SF164 PIWI-LIKE PROTEIN 1 57 904 3.5E-193
3 g8254.t1 Pfam PF08699 Argonaute linker 1 domain 250 296 1.8E-4
2 g8254.t1 Pfam PF02170 PAZ domain 305 432 8.6E-31
1 g8254.t1 Pfam PF02171 Piwi domain 590 895 1.2E-72
19 g8254.t1 ProSiteProfiles PS50821 PAZ domain profile. 293 412 23.209
18 g8254.t1 ProSiteProfiles PS50822 Piwi domain profile. 617 896 40.487
13 g8254.t1 SMART SM00949 PAZ_2_a_3 299 436 1.9E-53
14 g8254.t1 SMART SM00950 Piwi_a_2 590 896 2.0E-91
7 g8254.t1 SUPERFAMILY SSF101690 PAZ domain 131 458 2.2E-61
6 g8254.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 431 913 8.6E-83

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF
GO:0003676 nucleic acid binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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.

Raw TPM values