Gene loci information

Transcript annotation

  • This transcript has been annotated as PAN2-PAN3 deadenylation complex catalytic subunit PAN2.

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_1 g10385 g10385.t1 TSS g10385.t1 9379690 9379690
chr_1 g10385 g10385.t1 isoform g10385.t1 9379792 9383659
chr_1 g10385 g10385.t1 exon g10385.t1.exon1 9379792 9379813
chr_1 g10385 g10385.t1 cds g10385.t1.CDS1 9379792 9379813
chr_1 g10385 g10385.t1 exon g10385.t1.exon2 9379875 9382884
chr_1 g10385 g10385.t1 cds g10385.t1.CDS2 9379875 9382884
chr_1 g10385 g10385.t1 exon g10385.t1.exon3 9383036 9383218
chr_1 g10385 g10385.t1 cds g10385.t1.CDS3 9383036 9383218
chr_1 g10385 g10385.t1 exon g10385.t1.exon4 9383274 9383425
chr_1 g10385 g10385.t1 cds g10385.t1.CDS4 9383274 9383425
chr_1 g10385 g10385.t1 exon g10385.t1.exon5 9383496 9383659
chr_1 g10385 g10385.t1 cds g10385.t1.CDS5 9383496 9383659
chr_1 g10385 g10385.t1 TTS g10385.t1 9383744 9383744

Sequences

>g10385.t1 Gene=g10385 Length=3531
ATGAACGCAGCGTTTAATCCAATTTACGAACCAGAATCATTATTTAATATTGGCCAAGGC
GATGCAGAATATCTTGAATTAGGCACCACTTTGAGCAATAATTTATCATGTGGCATAACA
ACAGTAAAATTTGATACTCATGAAGAATTAATTTGGACTGGAAATCAGTCTGGCTATGTC
AGCAGCTTTTATGGCTCAACAATGCAAAAATACACTTCATTTCGTGTCCATCAGACAGAA
ATCGTTCATCAAATTGAAACAAATTCAGAGGGAATTTTTGCACTGACCAGTACATCATTG
CGGCATCAAATTCGTCGTGGAATTCCAAAATTCACACATCGTTCGAAAAATCTTACAGAT
GCACTATGTATGTTTGCATTATCACCAACGCGACTCTTAATTGCAGGACATCAACCAAAT
TTGATTGATTTTGACCTCACAACTATGACTGAGCAGGCAATTATTGATGTTGGTGAACAT
GGTTGTGCTATAATAAAGAAATATGATCATTCAAGATTTCTATGCTGTGGAGATGTTAAT
GGTTTCATTACCCTTCGTGATCCTTTGACTCTTCATGAAGAACATAAATTACCAACTCAT
TCAGCATCACTTAATGATTTTGATGTGCAAGGAAATTATTTAGTCTCATGTGGATTCAGT
GATATAAATGGAAAATTGACTGTTGATAGATTTTTATTGGTTTATGACATGAGAATGCTG
AGACTTGTTTCTCCAATTCAAACTCTAATTGATCCAACTTTGCTTAGCTTTCTTCCATCT
TTTGTGTCGCGTTTAGCAATTGTTTCTCCAATAGGACAATTGCAATTGGTTGATACAGTT
GAATTAACACAACCACGTGTGTGCATGTATCAGGTCAATATAGCGAGTCAGTGCATGTCA
TTTGATATTTCATCATCAAATCAAGCAATGGCATTTGGCGATAACACTGGTCAATTGAGT
CTCATAAGTGCAATTTCATCGCCTGAACCGCAATTCAATAATTATTCACGTGAGACTGAA
TTTGCTGATACACCAGAACCCCTGCCTTTTGTATCAATTACAGATATGAATTTTCCGCTT
TCATCAATTTTACTTCCAAAATTACAAAGTGGAAATTGGTTAAGTGATTTACCTAAAGAA
ATGTGTGAATATCATTATCGAAAACCTAAACCTATTGATCCAATTATTCTCAGTACAATG
AAACAACAAGGCACAATCAGTTATGCACCAAATCCACGAACAACTCGTCGCAATCAAATT
CCTTATATTATGGAAAATGAAGCTCAATCAGATGATCCAGAAGTGTCAGCTAATACAAAC
ATTTCAATTTTTTCATCACATGCAATTCCAAAACATTATCAAAAAATTGACATTAAATAC
AAAGCTGGAACAACACTCGAATTTGATTTTAGTGAATTTAATCAGACAGAATTTTGTGGA
CTTGAAAATCTTCTTCCTAATGCTTATTGTAATTCGATGCTCCAAATTCTTTTTTATTTG
TTTCCATTGCGACAAGCTTTGATTACTCATACTTGCTCGAAGGAAGTCTGTTTGAGTTGT
GAACTTGGTTTTCTGTTTCACATGCTTGCTAATAATAAAAGTAAGCAACCATGTCAGGCA
AGCAATTTCTTACGTTCATTCAGAACAGTTCCTGAAGTTGCAGCACTTTCTTTAGTAATT
AGCGATAGAAATCCAAGTCGAAATATCAATCTGATTCGTCTCATTCAAAATTGGAATCGT
TTTATTCTTCATCAAATTCACAATGAATTACTTGACGCTGGCAAAAGAAATAGTGTTCCA
ATGCAAAGTGTTGATATCACAAATTTAATTTCATCAGTAAGCAAGAGACTTGAAGAAGCA
TCATTAGCAGAAGAAAAAGAGCAAACAGAAGATGAAGAAAAAGATGAAATTGAGCAGGAT
CGATATCAATTTTTAGAAACTGAAAAGAAAGAGGATCAAGAACATGAAGTTTCATCTGAA
GTGAGTTCATTATTTGGCATTAAACAACGTGTTGTTCATCGGTGTCTAAAATGTAATGAA
AAGAAGCTCAAAAATAATGTGGTTTTGGTATGCAATTTAATCTATCCACTAACATCACCA
ACTCATGAATCTTGTGACTTTCTTAAAATTCTCAAAAATTCACTGAATTTAGAAAAAACA
CTTTCGGCATGGTGTGACATTTGCAATCGTTTTAGTCCACACAATCACTGTGCAAGTGTT
ACTGATTTGCCTAATTTATTGGCTATCAATTGTGGTCTTGATAATGAAAAAGAAATTGAG
TTGTTGAAACGTCATTTAAACCAATTCAATTCCGATTTTATTCAGAGTCCAGTAAATGAA
TCAGAAAATGCAATTAAAAAGCAATGTCGTTATGGAATCAAATGCACACGTACTGATTGT
CATTTTTCACATCCACATATGAGACGCATAACAACATCAAGTGAATCATCAAATGGAACA
AATGGTAAATTGTCCGATCGATGGTTTCCAACGAGTTTTAAAATTACTATTGCCGGTGAA
AACATTTCAATTGATGATATTCAAAATAGTGATGATGATACATCACAAATTTACAATCTA
CAAGCCGTTGTATATTGCATTGACAATGGACAACAGAGAAATCTAATTTCGTTCATATTG
CGCAATGGTCAATGGTATATTTTCAATGATTTTTGCATTAAAAACGTACAGGAGGATGAA
GTTTTGTCATTTATGTTAGATTGGAAAATTCCGAGTGTATTGTTTTATAAAAACAAAAAT
TACGAATGGAATGAGCATGATAACAGCACCTATGAGAGTCCATTTACAAGCAATTTGTTA
CTCGAAGAAATTTTGAATACAAACGTAGAACAAGATGTTTCAAATTTCATGCCATTAGAG
CCACATGAAGTTCCAAAACAGGGAGATATTGTTGCTATGGATGCAGAGTTTGTTACATTA
AATCCAGAGGAAAGTGAGATAAGTAGTGATGGAAAAATGACTACTTTCAAGCCACGCGTT
GCTAGTGTTGCAAGAATTAGTTGTATTCGAGGTCCTGGCAATGAAAGAGAAGGAGTTGCT
TTTATTGATGATTATATTCTGACGCAAGAACAAGTATCAGATTATTTGACAAAATTCAGT
GGAATAAAACCAGGTGATCTCGATGCAAATTTAAGCAATAAAAGACTGACAACATTAAAG
AGATCATATCAAAAGCTGAGATATTTGGTTGATAGTGGTGTAATTTTCGTCGGTCATGGG
TTAAAGAACGATTTTCGTGTGGTTAATTTGCACGTTCCTTCTAAGCAAATAATCGATACC
GTTTATCTTTTTCACATTCCACATCATCGAATGGTTTCATTAAAGTTCTTAGCTTGGCAT
TTCTTAGGAATTAGCATTCAATCAGAAACTCATGATTCTATTGAAGATGCAAGGACGTCA
CTACAACTTTATAAACACTATTTAAAACTTCAAGAAGAAGATCGTGTCAATGCTGCATTG
AATAATTTATATGACATTGGTAAACAGTTACAATGGAAAGTTCCAGAATAA

>g10385.t1 Gene=g10385 Length=1176
MNAAFNPIYEPESLFNIGQGDAEYLELGTTLSNNLSCGITTVKFDTHEELIWTGNQSGYV
SSFYGSTMQKYTSFRVHQTEIVHQIETNSEGIFALTSTSLRHQIRRGIPKFTHRSKNLTD
ALCMFALSPTRLLIAGHQPNLIDFDLTTMTEQAIIDVGEHGCAIIKKYDHSRFLCCGDVN
GFITLRDPLTLHEEHKLPTHSASLNDFDVQGNYLVSCGFSDINGKLTVDRFLLVYDMRML
RLVSPIQTLIDPTLLSFLPSFVSRLAIVSPIGQLQLVDTVELTQPRVCMYQVNIASQCMS
FDISSSNQAMAFGDNTGQLSLISAISSPEPQFNNYSRETEFADTPEPLPFVSITDMNFPL
SSILLPKLQSGNWLSDLPKEMCEYHYRKPKPIDPIILSTMKQQGTISYAPNPRTTRRNQI
PYIMENEAQSDDPEVSANTNISIFSSHAIPKHYQKIDIKYKAGTTLEFDFSEFNQTEFCG
LENLLPNAYCNSMLQILFYLFPLRQALITHTCSKEVCLSCELGFLFHMLANNKSKQPCQA
SNFLRSFRTVPEVAALSLVISDRNPSRNINLIRLIQNWNRFILHQIHNELLDAGKRNSVP
MQSVDITNLISSVSKRLEEASLAEEKEQTEDEEKDEIEQDRYQFLETEKKEDQEHEVSSE
VSSLFGIKQRVVHRCLKCNEKKLKNNVVLVCNLIYPLTSPTHESCDFLKILKNSLNLEKT
LSAWCDICNRFSPHNHCASVTDLPNLLAINCGLDNEKEIELLKRHLNQFNSDFIQSPVNE
SENAIKKQCRYGIKCTRTDCHFSHPHMRRITTSSESSNGTNGKLSDRWFPTSFKITIAGE
NISIDDIQNSDDDTSQIYNLQAVVYCIDNGQQRNLISFILRNGQWYIFNDFCIKNVQEDE
VLSFMLDWKIPSVLFYKNKNYEWNEHDNSTYESPFTSNLLLEEILNTNVEQDVSNFMPLE
PHEVPKQGDIVAMDAEFVTLNPEESEISSDGKMTTFKPRVASVARISCIRGPGNEREGVA
FIDDYILTQEQVSDYLTKFSGIKPGDLDANLSNKRLTTLKRSYQKLRYLVDSGVIFVGHG
LKNDFRVVNLHVPSKQIIDTVYLFHIPHHRMVSLKFLAWHFLGISIQSETHDSIEDARTS
LQLYKHYLKLQEEDRVNAALNNLYDIGKQLQWKVPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10385.t1 CDD cd06143 PAN2_exo 971 1145 2.50118E-103
10 g10385.t1 Coils Coil Coil 619 640 -
8 g10385.t1 Gene3D G3DSA:2.130.10.10 - 26 325 4.1E-67
9 g10385.t1 Gene3D G3DSA:3.30.420.10 - 966 1169 4.8E-43
4 g10385.t1 Hamap MF_03182 PAN2-PAN3 deadenylation complex catalytic subunit PAN2 [PAN2]. 2 1176 11.623149
3 g10385.t1 PANTHER PTHR15728 DEADENYLATION COMPLEX CATALYTIC SUBUNIT PAN2 29 1175 0.0
2 g10385.t1 Pfam PF13423 Ubiquitin carboxyl-terminal hydrolase 480 893 4.7E-86
1 g10385.t1 Pfam PF00929 Exonuclease 971 1144 2.6E-20
13 g10385.t1 ProSiteProfiles PS50235 Ubiquitin specific protease (USP) domain profile. 479 919 20.233
12 g10385.t1 SMART SM00479 exoiiiendus 969 1153 1.1E-23
7 g10385.t1 SUPERFAMILY SSF50978 WD40 repeat-like 37 327 4.3E-16
6 g10385.t1 SUPERFAMILY SSF54001 Cysteine proteinases 477 922 2.55E-27
5 g10385.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 968 1153 3.15E-23

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:0006397 mRNA processing BP
GO:0004535 poly(A)-specific ribonuclease activity MF
GO:0005515 protein binding MF
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening BP
GO:0031251 PAN complex CC
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