Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein argonaute-3.

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_3 g807 g807.t1 isoform g807.t1 6142945 6146323
chr_3 g807 g807.t1 exon g807.t1.exon1 6142945 6143099
chr_3 g807 g807.t1 cds g807.t1.CDS1 6142945 6143099
chr_3 g807 g807.t1 exon g807.t1.exon2 6143497 6144353
chr_3 g807 g807.t1 cds g807.t1.CDS2 6143497 6144353
chr_3 g807 g807.t1 exon g807.t1.exon3 6144413 6145777
chr_3 g807 g807.t1 cds g807.t1.CDS3 6144413 6145777
chr_3 g807 g807.t1 exon g807.t1.exon4 6145833 6146323
chr_3 g807 g807.t1 cds g807.t1.CDS4 6145833 6146323
chr_3 g807 g807.t1 TSS g807.t1 NA NA
chr_3 g807 g807.t1 TTS g807.t1 NA NA

Sequences

>g807.t1 Gene=g807 Length=2868
ATGTCATCTGGACGCGGACGTGGATTTTCTGTATTCAGTGCCAAATCATCTGAAGATGGT
GACGATCAAAAATCAGATGAAAGTTCATCTGTTGTTAAACAGACTAGTAGTGGCCGAGGC
AGAGCTTTATCATTTCAACCTGCGTCAACAGATTCCGATGGTGCTTCAACGATTTCCCAA
ATTCCATTTACTGGCAGAGGAGCTGGTCGCGGTTTGGGTCGTGGATTTGTTGGCATCAGT
ACTAAATCTAAATCATCTGGATCTGAACCTACGGAATCTAAAAAGGAGAGTACAAGCGAG
GATCAATTTAAAGATATATCTCCAAAAAAATTGTCATCATCGGGACGAGGTGGAGAAGGA
AGTGGATCTGGTCGAGGTCTCAGTAGTTCAGGAAGAGGTTTGACATCAGGATTTTATAGT
GAAGAAAGAAGTGGTGAACATGAAATAACTGCTGGATTACAAACAATGAATATTCAAGCT
GAACAACAGCCACCAACAGTTTTGCCACAAAGATCGACAACAGCTTTGGCTGCTGAAGCA
AGCGCTCAAAGAGTAGAGCCGGAGGTAGATCTTCCAACAGTTATGAAACATGGAAGAGCG
GGCAAAGCATTTGATTCAATAACAAATTGCATAACAATAAAATGTAATAAAGATTCTGGC
GTATTTGAATATGAAGTTCGTTTTCAACCAGAGATCGATAACATGAGATTAAGAGGAAAA
TATTTGGCTCAATTGAAGGATGTAATTGGAAGTATTAAAACATTTGACGGAGTTACATTA
TATTTGCCAAAAAAATTGGAAGAAAACAATATCGAAATAACAACATCATTGGAAGGTGGT
GAAGAAGTTAAAATTAAATTTATCTTTCGACGTCAGAAGCGCTTGGCTGAATGTGTTCAT
TTATATAATGTTCTTTTTGAGCGAATTATGGGTATTCTCAATTATCAACGTGTTGGTCGT
AAGTCTTTTGATCCAACTTCTCCGAAAATCATTACACAACATAAACTTGAAGTTTGGCCT
GGTTTCGTAAAAAGCGTTGAAGAGCATGAAGGCGGTCTTATGCTTTTGTTAGATGTTTCT
CATCGTGTTTTATCACAAAAAACAGTTTTGGAATTTTTCAAAGAATGTATCCAGAAAACT
GATAACTGGAAGGATATGGCTAAAAAAGGAGTCGTTGGCAATATAGTTTTGACACGATAT
AATAACAAAAGCTATAGAATTGATGATATTGATTTTTCTCAAAATCCATTAAGTACATTC
AAGAAAGGCGATCGTGAAATTTCTTACGCAGATTATTACAAGAATGAATACAATATCAAA
ATTCAAGATTTGAAACAACCATTGCTCATAAGTCGTAAAGAAATGCGAGTGAGTGGAGAA
AAGAAGAAATTGGATTTTGTTGTTTGCTTAGTACCAGAACTTTGCTTTTTAACTGGTTTA
TCTGATGAAATGAGAAGCAATTATAATGTTATGAAAGATCTTGCCTCATTTACAAAGTTA
ACTCCATTTCAACGTGTTGAAGCATACCGAAAATATGTCACTAATATTGCCAATAATGAA
AAAGCTAGTGCATTACTATCAGGATGGGGTTTAGAATTAGATAAGGATCCGACACGTGTA
ACAGCTCGATTGCTTGATGAAGAATTTGTGGTTTTCGGAAATAAGAAGGAATTTTCAGTA
GGTCCACAAGCTGATTTTGGACGTCATGCAACATCAAATCAAGTGCTTGAACCAATTAAA
CTTCAAAATTGGCTTATTATTTACGTAAATCGAGATGTCAAAACTGCTGATGCATTTGAG
GAAATGGTTAGAAAAGTTTCTGGTCCAACTGGAATAAATTGCGCAAATCCTCGACGTATT
GAATTAGGAAATGATCGAACTGACACTTATGTTAATGAAATTCGAAAACAACTCAATGAC
AAATATATTCAAATGGTAGTTACAATTTTTCCATCCCTTCGAGATGATCGATATGCAGCT
GTAAAGAAAATTTTATGCGCAGAATGCCCTTGTCCATCACAATGCATCAATAGTAGAACT
CTACGAAATGATGCCAAGAATCGATCAATTGTTCAAAAGATTCTCTTACAAATGAACTGC
AAATTGGGTGGTAGTCTTTGGGGAATTAAAATTCCATTGAAAGACTCAATGATTATAGGC
ATTGACACATATCATGAGGCTAGTCACAAAGGATTAACAGTTGGTGGCTTTGTTGCTTCT
TTAAATTCTTCATTCACAAAATATTTCAGCAAGCCTGCTATTCAACAAAAGCGAGAAGAA
TTAATTAATGGATTATTGAATTGCATGTCTCAAGCATTATTGCATTATAAGACTGAAAAC
AATAGTCTTCCGGAGAAAATTATAATCTATCGAGATGGTGTTGGTGATGGTCAATTGCAA
TATGTCGAAAGCTACGAAATACCACAATTTGAAGATGCTTGTCGAAAGATGGCTTCCAAT
TATAATCCAAAGCTCACATTCATTGTAGTGCAAAAGCGAATCAATCATAAATTTTTCAAA
GTTGCTCGTGATGCAGGAAAAGAGACTTTGGTCAATCCACCACCTGGATCAGTTTTAGAT
AACACAATCACTCGTCGCACATTTTGTGACTTCTTCCTTTGTTCTCAACATGTACGCGAA
GGCACAACAACTCCGACTCACTATATTGTTCTTCGAGATGACAACAATTATAATCCTGAT
ATTGTTCAACGCTTAACATACAAACTATGCTTCATGTATTACAATTGGGTTGGCACTGTT
CGCGTTCCTGCACCATGTCAATACGCTCATAAGCTTGCATACTTAGTAGGATTGGCTATT
AAGCGACAAGTCGACGACTCACTCTTAAATAAACTTTTCTACTTGTAA

>g807.t1 Gene=g807 Length=955
MSSGRGRGFSVFSAKSSEDGDDQKSDESSSVVKQTSSGRGRALSFQPASTDSDGASTISQ
IPFTGRGAGRGLGRGFVGISTKSKSSGSEPTESKKESTSEDQFKDISPKKLSSSGRGGEG
SGSGRGLSSSGRGLTSGFYSEERSGEHEITAGLQTMNIQAEQQPPTVLPQRSTTALAAEA
SAQRVEPEVDLPTVMKHGRAGKAFDSITNCITIKCNKDSGVFEYEVRFQPEIDNMRLRGK
YLAQLKDVIGSIKTFDGVTLYLPKKLEENNIEITTSLEGGEEVKIKFIFRRQKRLAECVH
LYNVLFERIMGILNYQRVGRKSFDPTSPKIITQHKLEVWPGFVKSVEEHEGGLMLLLDVS
HRVLSQKTVLEFFKECIQKTDNWKDMAKKGVVGNIVLTRYNNKSYRIDDIDFSQNPLSTF
KKGDREISYADYYKNEYNIKIQDLKQPLLISRKEMRVSGEKKKLDFVVCLVPELCFLTGL
SDEMRSNYNVMKDLASFTKLTPFQRVEAYRKYVTNIANNEKASALLSGWGLELDKDPTRV
TARLLDEEFVVFGNKKEFSVGPQADFGRHATSNQVLEPIKLQNWLIIYVNRDVKTADAFE
EMVRKVSGPTGINCANPRRIELGNDRTDTYVNEIRKQLNDKYIQMVVTIFPSLRDDRYAA
VKKILCAECPCPSQCINSRTLRNDAKNRSIVQKILLQMNCKLGGSLWGIKIPLKDSMIIG
IDTYHEASHKGLTVGGFVASLNSSFTKYFSKPAIQQKREELINGLLNCMSQALLHYKTEN
NSLPEKIIIYRDGVGDGQLQYVESYEIPQFEDACRKMASNYNPKLTFIVVQKRINHKFFK
VARDAGKETLVNPPPGSVLDNTITRRTFCDFFLCSQHVREGTTTPTHYIVLRDDNNYNPD
IVQRLTYKLCFMYYNWVGTVRVPAPCQYAHKLAYLVGLAIKRQVDDSLLNKLFYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g807.t1 CDD cd02845 PAZ_piwi_like 354 481 1.04937E-47
11 g807.t1 CDD cd04658 Piwi_piwi-like_Euk 489 937 0.0
7 g807.t1 Gene3D G3DSA:2.170.260.10 paz domain 366 487 2.3E-39
9 g807.t1 Gene3D G3DSA:3.40.50.2300 - 572 701 6.4E-35
8 g807.t1 Gene3D G3DSA:3.30.420.10 - 710 951 2.4E-80
17 g807.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 133 -
16 g807.t1 MobiDBLite mobidb-lite consensus disorder prediction 29 63 -
15 g807.t1 MobiDBLite mobidb-lite consensus disorder prediction 88 107 -
14 g807.t1 MobiDBLite mobidb-lite consensus disorder prediction 114 133 -
3 g807.t1 PANTHER PTHR22891 EUKARYOTIC TRANSLATION INITIATION FACTOR 2C 143 955 1.9E-294
4 g807.t1 PANTHER PTHR22891:SF111 PIWI-LIKE PROTEIN 2 143 955 1.9E-294
2 g807.t1 Pfam PF02170 PAZ domain 371 499 8.8E-33
1 g807.t1 Pfam PF02171 Piwi domain 646 938 9.7E-89
19 g807.t1 ProSiteProfiles PS50821 PAZ domain profile. 367 479 23.23
18 g807.t1 ProSiteProfiles PS50822 Piwi domain profile. 645 941 46.506
12 g807.t1 SMART SM00949 PAZ_2_a_3 367 503 2.4E-58
13 g807.t1 SMART SM00950 Piwi_a_2 645 941 1.1E-112
6 g807.t1 SUPERFAMILY SSF101690 PAZ domain 220 520 4.4E-70
5 g807.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 497 955 1.26E-120

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