Gene loci information

Transcript annotation

  • This transcript has been annotated as 5’-3’ exoribonuclease 2-like protein.

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 g8673 g8673.t1 TSS g8673.t1 32185667 32185667
chr_2 g8673 g8673.t1 isoform g8673.t1 32185768 32188489
chr_2 g8673 g8673.t1 exon g8673.t1.exon1 32185768 32185842
chr_2 g8673 g8673.t1 cds g8673.t1.CDS1 32185768 32185842
chr_2 g8673 g8673.t1 exon g8673.t1.exon2 32185918 32186334
chr_2 g8673 g8673.t1 cds g8673.t1.CDS2 32185918 32186334
chr_2 g8673 g8673.t1 exon g8673.t1.exon3 32186399 32188134
chr_2 g8673 g8673.t1 cds g8673.t1.CDS3 32186399 32188134
chr_2 g8673 g8673.t1 exon g8673.t1.exon4 32188199 32188421
chr_2 g8673 g8673.t1 cds g8673.t1.CDS4 32188199 32188421
chr_2 g8673 g8673.t1 exon g8673.t1.exon5 32188481 32188489
chr_2 g8673 g8673.t1 cds g8673.t1.CDS5 32188481 32188489
chr_2 g8673 g8673.t1 TTS g8673.t1 NA NA

Sequences

>g8673.t1 Gene=g8673 Length=2460
ATGGGAGTTCCAGCATTCTTTAGATGGTTATCAAGAAAGTATCCTAGTGTGATTATTGAA
TGTACAGAAAATAAGCGTGTTGATGAAGAAACAGGAAAGAATGTATACGAAGATTCATCA
TTACCCAATCCAAATGATATAGAATTTGACAATCTTTATCTCGATATGAACGGAATTATT
CATCCTTGCACACATCCAGAAGATAAACCGCCTCCAAAAAATGAAAATGAGATGATGATT
GCCATTTTTGAATGCATTGATCGACTTTTCTCAATTGTAAGACCAAGAAAATTACTTTAT
ATGGCAATTGATGGCGTTGCACCTCGAGCTAAAATGAATCAGCAACGTTCAAGACGTTTT
CGAGCTTCAAAAGAAGCTGCCGAAAAAGCAGCTGAAATTGCTCGAATAAGAGAAGAATTG
AAAGAAAAAGGAGCTATTCTTCCACCTGAAAAACCAAAAGAACATCATTTTGATTCAAAT
TGTATCACTCCTGGAACACCATTTATGGAGAGGCTAAGTAGATGTTTGCAGTACTACATT
CATGATCGTTTAAATAATGATCCAGGATGGCGAAATATTAAAGTAATTTTGTCTGATGCA
AATGTTCCAGGTGAAGGTGAACACAAAATTATGGATTATATTCGTAAACAAAGAGCTCAA
CCTGATCACGATCCAAATACACAGCATGTACTTTGTGGGGCTGATGCTGATTTAATTATG
CTTGGGCTTGCAACTCATGAACCTAATTTTACTATCATTCGTGAAGAGTTTCTTCCCAAT
AAGCCTCGTCCCTGTGACATTTGTTCTCAAATGGGCCATGAAATGAAAGATTGTTCCGGT
TTAGATATGGAATATCATCAACAGCCTGAAATACAATTTGGAAAGGAAACACAATTTATT
TTTGTGCGTTTAAATGTGCTCAAAGAATATCTAGCTAAAGAACTTCAAATGCCTAATTTA
CCATTTAAATATGATTTTGAGAGAGTTATAGACGATTGGGTTTTCATGTGTTTCTTTGTT
GGAAATGATTTCCTTCCTCATTTGCCGAGTTTAGAAATTCGAGAGAATGCAATTGATCGA
TTAATTCATTTATATAAAAAGTGTGTATATAAAACTGGCGGTTATTTGACTGATTCGGGT
GATGTAGCACTGGAACGAGTTGAAATGATTATGCGTGATTTGGGTGCAGTTGAAGATGAA
ATTTTTAGAGAACGTCAGCAGAATGAGGAACGTATGAAGGCTAGAAATAAACGAATGAAA
CTTGAGCGTCAACAAAGACCAAATTTTGAAATGATTCATAAGACACAATTTGCACCAACT
GCTGTTGGAAGAGGCATTACACCGAATGCAATTGTAAATGCTAAAGAAGATATTTTGCGC
ATCAGTAAAATGGCAATGGAATCTACTGCATCAAATAATGATGCTTTAGAGTCAATGCTT
AAGCCTGTTGGTGAGAGTGATTCACCAAATAATCAAAATCGTAGAGGGATCAAAAGAAAA
GCAGAAGATGAGTCAGTAAAAGAAGAAGATGAAGAAGAGGATGATCAAGCACATGACGAA
GTTCGATTATGGGAAGATGGGTTTAAAGATCGGTATTATGAGTCTAAATTCGATGTTATG
CCAGATAACATTCAATTTCGTTATTCTGTTGCACTTCAATACGTAAAAGGTTTGTGCTGG
GTGCTGCAATATTATTATCAAGGTTGTGCAAGTTGGGAATGGTATTTTCCATTTCATTAT
GCTCCATTTGCTTCTGATTTTGTAAATATCAAGGGGTTAAGCAAGAAATTTGAAAAAGGG
ACTCCTTTTAAACCTTTGGAACAATTGATGGGCGTTTTTCCAGCAGCAAGTCGTCAGCAC
GTTCCACTACCTTTTGCAAAATTAATGCTTGATCCAAAATCACCCATAATCGACTTTTAC
CCAGAAGACTTTAATATTGATCTTAATGGAAAGAAATTTGCATGGCAAGGTGTTGCATTA
TTACCATTTGTAGATGAGAAAAGATTATTTAAAGCTGTAGCACCTTATCGTAAGGAATTG
ACTTTAGAAGAACAAAAACGTAATAAACAAGGTGAAGATCGTTTATACGTTGGTATTGGC
TGTCCAGACTATCAGTTATTGAAAAAATTCTCAGAGACTGAAACCGATTTGAACACTGAA
TATCCAATTTCAATTGATGGCATGCAAGGACTTGCTTTAGTATCTGAAGAAAATATTTCA
ATTGGAGGAACATTTCCATCGGTTATTCCAAATCTTCACGATATTACTGATAATCGTGTC
ATAATGGTAAATTTCCGTGATCCAAAATATCCGCGTGATTTTATTTTCCCTGCACGTGTT
TTGCCCAATGCCAAGCAACCGCCAAATGTTTTAAAACAAGGTGTCGACGAAGGCAATCCA
AATTATAGACCTATAATTGGATTTAATCACAATCGATCGCAATTCGCTAGTTGGAAATAA

>g8673.t1 Gene=g8673 Length=819
MGVPAFFRWLSRKYPSVIIECTENKRVDEETGKNVYEDSSLPNPNDIEFDNLYLDMNGII
HPCTHPEDKPPPKNENEMMIAIFECIDRLFSIVRPRKLLYMAIDGVAPRAKMNQQRSRRF
RASKEAAEKAAEIARIREELKEKGAILPPEKPKEHHFDSNCITPGTPFMERLSRCLQYYI
HDRLNNDPGWRNIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHVLCGADADLIM
LGLATHEPNFTIIREEFLPNKPRPCDICSQMGHEMKDCSGLDMEYHQQPEIQFGKETQFI
FVRLNVLKEYLAKELQMPNLPFKYDFERVIDDWVFMCFFVGNDFLPHLPSLEIRENAIDR
LIHLYKKCVYKTGGYLTDSGDVALERVEMIMRDLGAVEDEIFRERQQNEERMKARNKRMK
LERQQRPNFEMIHKTQFAPTAVGRGITPNAIVNAKEDILRISKMAMESTASNNDALESML
KPVGESDSPNNQNRRGIKRKAEDESVKEEDEEEDDQAHDEVRLWEDGFKDRYYESKFDVM
PDNIQFRYSVALQYVKGLCWVLQYYYQGCASWEWYFPFHYAPFASDFVNIKGLSKKFEKG
TPFKPLEQLMGVFPAASRQHVPLPFAKLMLDPKSPIIDFYPEDFNIDLNGKKFAWQGVAL
LPFVDEKRLFKAVAPYRKELTLEEQKRNKQGEDRLYVGIGCPDYQLLKKFSETETDLNTE
YPISIDGMQGLALVSEENISIGGTFPSVIPNLHDITDNRVIMVNFRDPKYPRDFIFPARV
LPNAKQPPNVLKQGVDEGNPNYRPIIGFNHNRSQFASWK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g8673.t1 CDD cd18673 PIN_XRN1-2-like 52 311 8.37282E-148
10 g8673.t1 Coils Coil Coil 123 143 -
9 g8673.t1 Coils Coil Coil 404 424 -
6 g8673.t1 Gene3D G3DSA:3.40.50.12390 - 1 141 1.0E-42
7 g8673.t1 Gene3D G3DSA:3.40.50.12390 - 157 355 2.9E-51
8 g8673.t1 Gene3D G3DSA:3.30.110.100 - 593 690 2.9E-31
5 g8673.t1 MobiDBLite mobidb-lite consensus disorder prediction 481 519 -
3 g8673.t1 PANTHER PTHR12341:SF41 5’-3’ EXORIBONUCLEASE 2 1 794 1.1E-291
4 g8673.t1 PANTHER PTHR12341 5’->3’ EXORIBONUCLEASE 1 794 1.1E-291
11 g8673.t1 PIRSF PIRSF037239 Exonuclease_Xrn2 1 816 0.0
2 g8673.t1 Pfam PF03159 XRN 5’-3’ exonuclease N-terminus 1 256 1.3E-102
1 g8673.t1 Pfam PF17846 Xrn1 helical domain 323 793 4.7E-165

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:0005634 nucleus CC
GO:0004527 exonuclease activity MF
GO:0004534 5’-3’ exoribonuclease activity MF
GO:0006139 nucleobase-containing compound metabolic process BP
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