Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein argonaute-2.

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 g34 g34.t1 TTS g34.t1 355359 355359
chr_3 g34 g34.t1 isoform g34.t1 355663 359260
chr_3 g34 g34.t1 exon g34.t1.exon1 355663 355941
chr_3 g34 g34.t1 cds g34.t1.CDS1 355663 355941
chr_3 g34 g34.t1 exon g34.t1.exon2 355997 357680
chr_3 g34 g34.t1 cds g34.t1.CDS2 355997 357680
chr_3 g34 g34.t1 exon g34.t1.exon3 357746 358952
chr_3 g34 g34.t1 cds g34.t1.CDS3 357746 358952
chr_3 g34 g34.t1 exon g34.t1.exon4 359254 359260
chr_3 g34 g34.t1 cds g34.t1.CDS4 359254 359260
chr_3 g34 g34.t1 TSS g34.t1 359374 359374

Sequences

>g34.t1 Gene=g34 Length=3177
ATGGGAAAGAAAAAAAATAAGAATCTGTCGGACGAACCCGATAATACACAGCAACAGCAA
ACTGTTGCTACATCTCAACAAACCCAAGCTTCTCAAGTTCCTCAGCAGCAAAAACAGCAG
TCTCAACAACCAAAACAACAAAAGAAGTCACAATCTGATGATTCTCAAACTGCATCGACT
TCTCAACAAAGTCATCAAAAGAAATCACAGCCTCAGCAACAATCAGTTCAATCACAACCT
TCTCAAGAAGGTCAGCAACAGAAACAATCGAAAAAGAAACAACAATCTGGTGATGCACAA
GTTTCTCAAGAGGGCCAACAGCAGCAAAGATATCAATGGAAGGATAAAAAACCAAAAGGT
GATGGCCAAAAACAACAACAACCAGAACATTCAAAAAATATTCAACAGTCACAACCACCA
CAAAGTACTTTGGGACCAAAACAAGGACAACAGTCTCAACAGCAGCGCGGACAACCACAA
AGTGCTTGGGGACCAAAGCAAGGACCACAGTCTCAACGACCTGCAAGTCAATCACAGCAG
CAAAGAGAAAAGCAACAAACTGGTCCAAGATCATCAACAAGCGGTGTTTCTGTATCATCA
CTTTCATCTAGCATGAAAAAATTGAGTATTGTTCCATATAATGCAAAAATTCCAATTGAA
ACAAGTCCAGACGGAAGAGTTTATGAAGGAAAAAAAGGTAGAAAATGCAAAGTTCAAGTC
AATTATGGAACAATTTCTTTTGATCCAAAGAAATTTCCACAAAAAGCCTATCATTATGAC
ATTAGCTTTGATCCAAATGCACCTAAAAAAATGTTGCCTTTCGCACTTCGAGCTTTTATG
ACAAATTATTTTAGAAACTATTTGTACGGAACTGATGAGCGAAGCAACTTGTATACAAGT
CAAAAATTGGCAATTAATGGCACAGATATTGAAGTTTACACTAATGAAGCTAAAGCTGTA
ATGGGAGATCGTACCAGAGATTTCAAAGTTACAATCAAATTTGCACGAGAAGTAGATCTT
GGTATTTTGTTGAATTATCAGAATCCTCAAAATGAAACACTTGATCAGCCTGCAACTGCT
GTTCAAGTACTTGACATTATTCTAAGATCAGCATTCAATAATTTATTAGCTGAAAATCGA
GCAGTGCGTGCTGGTAGACAAGTCTTTTTTGTTCCTCCTAAGCAAATGCCTCTAGGTGAT
GGAATGGAATTATGGTATGGACTTTTCCAATCAGCAATATTGGGTCGCAGTAGATTGTAT
TTAAATGTGGATGTTTTACATAAAGCATTTCCAAGCCAAATGCTTGTTCTTGACTATCTT
GCATCAATTTGTCGTGATGGTAGAGTTCCACAAAGATTAGATGAAAGAAGTGGAGAATTC
AGACAACTTAAAGAATTTCTCTCAATGCTTTCAATCCAATATAGAACAAAAGATAATGAA
CCATTTAAAACATACGGTGTTAATGGGCTTATTGGAAGTTCAAGACAAGAAAGATTTGAA
CAAGATGGCAGATCAATGTCGGTTGAAGAATATTATCGAAACTTTAAAAATATCAATTTG
AGATTTCCCGATTTGCCATGTTTATGGGTTGGAAGTCGACAAAGAAGAATTGCTCTTCCT
ATGGAATTTTGCTACATTCCACCAGGTCAAGCGACAAACAAGAAATGTTCAAGTCGAACT
GTCGCTGAAATTATCAGGTATTCTGCTACAACTACTGATGACAGAAAGAGAAAAATATTG
GATCTACTTCGACAAATCAACTATGCAAATGATCCAACAGTTTCTGGTTTTGGTATTCGT
GTTGATCCTAATTTTCAAGATATTGATGCAAGAGTCATTTCACCTCCTCAATTGGAGTAT
AAAGGTGAAAAACTTGTTACACCAAGAAATGGTGTGTGGCGTGAAGAGACTTATGCCCGG
ACAAATAATCAAGAAATCAATTGGGCTATTGTCAATTGTGATGATAGAACAAACAATGTT
GCTCTTGAAAATCTAAAGAATAATATTGTTTCAGAAGCCAGAAGACAAAACATAAATTTG
CGTGACATTCGTTCAAACGATTTTATTCGAATCAATGCTTATCAAAGTAGAAATCTGAAA
CAAGATTTAGAAAATATTTTTGAAAAGTGTAAGAATAATGCATGCCAACTTGTTATTGTT
ATCATTATTGATCAAAAAGATTGTTATGCTCGTGTAAAGCAAGCTGCAGAACTAAGAGTT
GGAATTTTAACACAATGCATTAAAGCAAATACAATTTTTAGAATGGGAAAAGGCAACCCA
ATGATGACAATTAAAAATATTTTATTGAAATTAAATTCAAAATTGAATGGCACAAATCAC
ATGATTCGTGAAGAATCTTACAATACGTTCAATGCATTCAATAAAAATTCTGGTGTGATG
TTTATTGGCGCAGACGTTACTCATCCAAGCCCTGATGCAAAAGATATACCATCAGTTGTT
GGCGTGGCTTCTTCGCATGATGATGTCGGATTTCGATATTGCTGCGCGTGGAGATTGCAA
GATCCCACAAAAGAAATGATTGTTGATTTAGAAGAAATCGTTGCTCAACATTTACATTTT
TATAAAGAGAAAAATAAGAAACTTCCTGGTAAAATAATGTATTACCGTGATGGAGTTAGT
GAAGGTCAATTTAGACAAGTGCTTGATATTGAAATGACTGCTATAAGAAATGCAATGCGA
CGAATTTATGGAACGAATCAACCTGCACAGGTTACTTTTATTGTTGTTCAAAAACGTCAT
CATACAAGATTTTTCCCACTTGATCCGAACTTTACTGAGGGAAAATTCAAAAATATCTCA
CCAGGAACTGTTGTTGATAAAGATATTATGCATCCATTTCAATACCAATTTTTCATGGCT
TCTCATGCTGCTATACAGGGTGTAACAAAACCAACAAAATATTGCATTTTGATTAACGAA
TCGAAGATTGATCCGGACGTTTTACAAGCTATCACATATTCTTTATGTCATTTGTTTACT
CGATGTAATCGTGCTGTCTCTTATCCAGCACCAACTTATTATGCTCATTTAGTTGCTGCC
AGAGGTAAAAATTATATTGTCGGCGAAAGGCTCAATATGGGAAACTTGCAAAAAGAATTT
AATATTCGACAAATTCGACCTGAATTCAATAATAATACACCTATGTTTTTTGTCTAA

>g34.t1 Gene=g34 Length=1058
MGKKKNKNLSDEPDNTQQQQTVATSQQTQASQVPQQQKQQSQQPKQQKKSQSDDSQTAST
SQQSHQKKSQPQQQSVQSQPSQEGQQQKQSKKKQQSGDAQVSQEGQQQQRYQWKDKKPKG
DGQKQQQPEHSKNIQQSQPPQSTLGPKQGQQSQQQRGQPQSAWGPKQGPQSQRPASQSQQ
QREKQQTGPRSSTSGVSVSSLSSSMKKLSIVPYNAKIPIETSPDGRVYEGKKGRKCKVQV
NYGTISFDPKKFPQKAYHYDISFDPNAPKKMLPFALRAFMTNYFRNYLYGTDERSNLYTS
QKLAINGTDIEVYTNEAKAVMGDRTRDFKVTIKFAREVDLGILLNYQNPQNETLDQPATA
VQVLDIILRSAFNNLLAENRAVRAGRQVFFVPPKQMPLGDGMELWYGLFQSAILGRSRLY
LNVDVLHKAFPSQMLVLDYLASICRDGRVPQRLDERSGEFRQLKEFLSMLSIQYRTKDNE
PFKTYGVNGLIGSSRQERFEQDGRSMSVEEYYRNFKNINLRFPDLPCLWVGSRQRRIALP
MEFCYIPPGQATNKKCSSRTVAEIIRYSATTTDDRKRKILDLLRQINYANDPTVSGFGIR
VDPNFQDIDARVISPPQLEYKGEKLVTPRNGVWREETYARTNNQEINWAIVNCDDRTNNV
ALENLKNNIVSEARRQNINLRDIRSNDFIRINAYQSRNLKQDLENIFEKCKNNACQLVIV
IIIDQKDCYARVKQAAELRVGILTQCIKANTIFRMGKGNPMMTIKNILLKLNSKLNGTNH
MIREESYNTFNAFNKNSGVMFIGADVTHPSPDAKDIPSVVGVASSHDDVGFRYCCAWRLQ
DPTKEMIVDLEEIVAQHLHFYKEKNKKLPGKIMYYRDGVSEGQFRQVLDIEMTAIRNAMR
RIYGTNQPAQVTFIVVQKRHHTRFFPLDPNFTEGKFKNISPGTVVDKDIMHPFQYQFFMA
SHAAIQGVTKPTKYCILINESKIDPDVLQAITYSLCHLFTRCNRAVSYPAPTYYAHLVAA
RGKNYIVGERLNMGNLQKEFNIRQIRPEFNNNTPMFFV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g34.t1 CDD cd02846 PAZ_argonaute_like 436 546 1.61752E-15
13 g34.t1 CDD cd04657 Piwi_ago-like 592 1026 6.59455E-160
10 g34.t1 Gene3D G3DSA:2.170.260.10 paz domain 432 554 8.4E-25
12 g34.t1 Gene3D G3DSA:3.40.50.2300 - 612 784 1.1E-29
11 g34.t1 Gene3D G3DSA:3.30.420.10 - 793 1058 2.9E-94
19 g34.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 200 -
21 g34.t1 MobiDBLite mobidb-lite consensus disorder prediction 12 109 -
20 g34.t1 MobiDBLite mobidb-lite consensus disorder prediction 110 126 -
18 g34.t1 MobiDBLite mobidb-lite consensus disorder prediction 127 200 -
6 g34.t1 PANTHER PTHR22891 EUKARYOTIC TRANSLATION INITIATION FACTOR 2C 50 1056 3.9E-247
7 g34.t1 PANTHER PTHR22891:SF66 PROTEIN ARGONAUTE-2 50 1056 3.9E-247
5 g34.t1 Pfam PF16486 N-terminal domain of argonaute 234 368 5.3E-15
4 g34.t1 Pfam PF08699 Argonaute linker 1 domain 387 431 2.6E-11
2 g34.t1 Pfam PF02170 PAZ domain 446 560 4.9E-13
3 g34.t1 Pfam PF16488 Argonaute linker 2 domain 574 620 9.5E-12
1 g34.t1 Pfam PF02171 Piwi domain 718 1026 6.5E-85
23 g34.t1 ProSiteProfiles PS50821 PAZ domain profile. 479 548 16.897
22 g34.t1 ProSiteProfiles PS50822 Piwi domain profile. 717 1027 39.204
15 g34.t1 SMART SM01163 DUF1785_2 382 433 6.5E-10
16 g34.t1 SMART SM00949 PAZ_2_a_3 434 570 4.9E-4
17 g34.t1 SMART SM00950 Piwi_a_2 717 1027 9.7E-102
9 g34.t1 SUPERFAMILY SSF101690 PAZ domain 429 588 7.69E-31
8 g34.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 702 1029 6.32E-80

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