General information for g9797.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 5’-3’ exoribonuclease 1.
Parent gene
- The parent gene g9797 is located on chr_1: 5236142..5239385 (- strand)
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 | g9797 | g9797.t1 | isoform | g9797.t1 | 5231251 | 5236142 |
| chr_1 | g9797 | g9797.t1 | exon | g9797.t1.exon1 | 5231251 | 5235138 |
| chr_1 | g9797 | g9797.t1 | cds | g9797.t1.CDS1 | 5231251 | 5235138 |
| chr_1 | g9797 | g9797.t1 | exon | g9797.t1.exon2 | 5235199 | 5235510 |
| chr_1 | g9797 | g9797.t1 | cds | g9797.t1.CDS2 | 5235199 | 5235510 |
| chr_1 | g9797 | g9797.t1 | exon | g9797.t1.exon3 | 5235563 | 5236003 |
| chr_1 | g9797 | g9797.t1 | cds | g9797.t1.CDS3 | 5235563 | 5236003 |
| chr_1 | g9797 | g9797.t1 | exon | g9797.t1.exon4 | 5236068 | 5236142 |
| chr_1 | g9797 | g9797.t1 | cds | g9797.t1.CDS4 | 5236068 | 5236142 |
| chr_1 | g9797 | g9797.t1 | TSS | g9797.t1 | 5236414 | 5236414 |
| chr_1 | g9797 | g9797.t1 | TTS | g9797.t1 | NA | NA |
Sequences
>g9797.t1 Gene=g9797 Length=4716
ATGGGTGTCCCGAAATTCTTCAGATATATCAGCGAAAGATATCCATGTCTTTCCGAACTC
GTAAGAGAAAATCAGGTTCCTGAATTTGACAATCTCTATCTCGATATGAATGGAATTATT
CATGCTTGTTCACATCCAAATGATAACGATGTTCACTTTAGAATCACAGAGGAGCAGATC
TTCAAAGATATTTTCTTTTATTTGGAGACTCTCTTCAATATGATCAAACCACAGAAATTG
TTCTTTCTCGCAGTCGATGGAGTTGCACCACGAGCAAAAATGAATCAACAACGTGGAAGA
AGATTTCGTTCTGCAAAGGAAGCCGAAATTCAAGAAGAAAAAGCGAGAGAAAAGGGAGAA
GTTTTACCTGAAGAAGCTCGTTTTGATTCAAATTGCATCACTCCTGGAACTCCATTCATG
TGTCGTTTAGATAAGGCTTTGAGATATTTTATTCAACACAAAATATCAACCTCTAAATCA
TGGCAGAATTGTAAAATTATTCTTAGCGGTCATCAGACACCCGGTGAAGGTGAACACAAA
ATTATGGAATACATAAGATATTTGAAAGCACAAAAGAAATTTGATCCCAATACGAGACAT
TGTCTTTATGGACTAGATGCTGATTTGATTATGCTAGGATTGTGCACACATGAAAGACAT
TTTTCACTATTACGAGAAGAAGTCAAGTTTGGAAAGAAGAGCAATAAAGCTGTATCTGTT
AGTCAGCAACGATTTTTCCTTCTTCATTTGAGTCTTTTGCGCGAATACTTGGAACAGGAA
TTTATCGCATTGAAAGATAATTTAAAATTCCAATTTGACATTGAAAAGATAATTGATGAT
TGGGTATTGATGGGATTTTTAGTTGGAAATGATTTCATTCCAAACATTCCAAATCTTCAT
ATCAATACAAACGCTTTGCCTATACTTTATCAAGCATACATCAAAACTCTGCCAAATTTA
GATGGTTATATAAATGAAGGAGGAAAACTAAATTTAAAGAGACTACAAGCTTATCTTGAA
AATCTCGCTGATTTTGATCGTGAAAATTTCTCTGCACAATATGATGATTTAAAATTTCTT
GAGACAAAACATCAATCAGGTTTCAATAATAGAAATGATGACACTTTTGGAGGCAACAAA
GAATTAATGGACATGGTAAAAGCTACTGAATTTGAATTTGACAGTCCTGATGAGGATAAT
GAAGTTTTTGAAGAAAATAAAGATGAAAGTAGTGACAGCGATCTCGATGATGATGCAATA
TATGAAAAAGAATTTTATCAACATCGACGCGATTATTACGTAAATAAAATGAAGTATCAA
GAAATGACGCCTGAAGTGTTAGTTGAACAAGCTCAATGTTATGTTACTGCATTACAATGG
ACTCTACACTATTATTATCATGGAGTTAAATCATGGAGTTATTATTATCCACACCATTAC
GCTCCATTCATTAGTGATGTAAAAAATTTCAAGGATTTCATACCTAAATTTGAACTTGGG
AAACCATTTCTTCCTTTTCAACAATTAATGAGTGTATTACCCGCTGGTAGTCGTGACCAT
GTTCCTGAATGTTACAAGCAATTAATGACAAATCCTGAGAGTGAACTTATTGAATTTTAT
CCAACAAACTTTGAAACTGACCTAAATGGTAAGAAACAAGATTGGGAAGCTGTTGTGCTT
ATTCCGTTCATTGACGAAGAAAAATTGTTAAGAACATTGAAGAAATACGATAATGAATTG
ACAAGCGATGAAAAGGAACGAAATGTGCATGGACCAATGTTTGTTTACACATACAGTAGT
GTCAGTCAAGGTTCTCTAGCAGGACCGCTCAATTTTCCCAGTATTGGCAATCTTTTGTGT
AAAGAACAAAAAGTTTATCGTGAAGAGATCCAAATTCCTGAAGACAAACTTGTTCTCGGT
CCATCAAAGGGAGCTTTGCAACATATTTATTATGCTGGTTTTCCTACAATGAAACATTTG
AATTATAAAAGTGAATTCAAAGTACAACATGTAAGAGTTTTTGATCAGCCATCACGAGGT
GAGAATATGATTATAATTTTGGAACCAAGCAATTATCCTGAAAAACCAATTGAAATTATT
GTAAAAGAAATGATGTCTAAAACAGTACACGTTGGCTGGCCTCATTTAGTAGAGGCTAAA
ATCGTGAGAATTACTGATAAAGACAATACATTTTTCTCTGATGGAAGTTCCGATAAGACT
AATCCTCAAAAATGGAAAATTGAAGTACAATCAATCAAAGAACATCACATAAATAGAATG
GGAATCGATATTGGAGAAGTAACAAAAATTGTACATGTCTTGAGACAAACAGGAGAAGAA
TATAAGTTTGATCCTAAATTAAGAATATACCGCTGTTTCAAGACATACTCGAAAATTGAA
ACTGCATATGCATTGCAAACTGTTGTTACAAACATCAAAGCATACCGACAAAAAATGAAG
GAAGAATTACCACTTTATGAAGCATTTAAAAGTGGGACAGAAGTGTTTATGCTTGGTGAT
CGATATTATGGTTCGAAAGGTGAAGTAATGGACACAACTTGCTTTGAAAAAAGTGGTCGT
GTAAAAGTTCTTCTAACAGTTCACGAAGAGCCGAAATTTGAAGGTATCTGGAAAATGCAT
CAAACATCTCAAGACTCATACCTAAATACGTATCAAGCTGCATCACGTCTAAGCATATCT
GACAACGTATTTAATCGAATTACAGGAAGTGTGCTAGTCATTGCTGGAATTAAGCGACAA
ATTGCAGAAGGAACTTCAAAAATGAATATTGGATTACAATTGAAATTTAACAAGCAAAAT
GAAGAATTAACTGGATATACAAAGAAAGAAAGAGTATGGCTTTATTCTGAAAAGACTGTC
AATTTAGTTCAAGAATATTATTGTAAATTTCCTCAAATTTTCGAAGTCATGGAGAGAAGA
TCTTCAAATAGTAATAATGATGTTTATTTCGAGTCTGATTTCTTTGAAAAGACTGATGGA
GAAGATTGCTTACATAATTTGATGAAATGGTTAAATCAACTGCCACATAATAAAGCTGAA
AGACGGACAATTGGCACTGAAGCTGTTGAAAAGGACGTAATTGAAGAAGTAAAGAAACAA
GTAATTGAAGCAAATAAATTACCAATGAAACGTTCGACTGTGCAAGTAAAGCCACATTTG
CTTTATGTTCCATCTCTATCAAAAATGACTTCAAAATCACCTGACGATAAAGCAGATTTT
CAACTCTTTGATCGAGTAGTTGTCATAAGAGATACTGATCAATACTCGATTGGTGCTAGA
GGAACTGTAATTGGAATAAATCGTGTTAAAGACTTGAATCCTGTTCGTCAAGATTGCATT
AATAAGGAAGACATCTATTGCCTAGTATTGTTGGATGAAAGCAAACAAAATAATGGAGTT
GTAAGAATTCCTCAAGAAAACCTTATCAACATATCATATGGATTAACTAAAGATGGTGTT
GAAAGAATTGCAAGTACACGAAATCAGCCACTTGCTCAAATTGGAAAAGAAGAGCCAGTA
AAAAATGCAGAACTGCCAAAACTCACTGAAAGTTATTCATCTATGCTTCAAAATTCAAAT
AAAAATCAAAAGAAAGGTCCAAATACGAGTCAGGCATTTTTAGATTTTTGGAATGCTGCA
AAAAATAAAACAACTTCAGCAGCAGCTGTAGCTAAAATAAATAATACGACAGTTGTTGCT
AGTGCTTCAGTTTCTATTCTTCCAAATAATACGAATCAACTGACAGAAGAAGAAGAAGCT
ATAGCAAAATCACTTGATTCTCAGAAGAAGCTCAATGAAGCAATAAACAAGAAAATGTCT
GAGTTAACAGTAAATAAGAAGAATTCACCAACACCTAATGAACAATCAGTTCCCATGATG
ATGATACCTCCAACGAAATTGCCTACACCTCCTATTGAGTGGTTAAATGGAGAAGCAAAG
AATAGCAGTTTTACAGAAGTTAAGCCATTTACAATCGTAGATGCTCCTAAATCATCTTTT
CCTACTAGTTTTGGTGAAAATCCAACACCTCGTCCAAAAATTGAATTACCAACACCACCA
GTTCAACATTCAATGCACTTTTATGGAAATCAACAGCAAATTCGTCCTCATCCATTTCCC
GCAATGCATTCGCAAAAATTCCAACAACACGGTCATCATCCATCGCATCATATGATGCAT
CCAATGCATATTCGACATCAATTTCCTGGTGGGTTTAAACCTCACAATATGAATTCTCCA
ATCGGACCATTTTTTGCAAATAATCATCACCAACAACAGCAACAAAGACATCATAATCCT
CAGCCAAGATTCTTCCATAATAATAATATTTTCCGACAAACAATGAAATTTAGACAACCA
CTGTCACAGCAAGTGCAAACTCCTCATTCTGCACCTATATTATCATCAAATTCTCAAGGC
AATCCATTTATTCCATTGCAAGCTGCCAGAAAGTCATCAAAGGGAAAAGAAGAACCAACA
CGATCAGCATCAACAACTTTGCCTGATAAAGAAGTTTCATCAACAACACCTCAACAATCA
CAGAATATTGAGAAGAAGTCTGAAGAAAAACAGGATTTTGAAACACCACAAGCTGCTGTC
GTACTTGAAGAAAAGAAAGACGAACAAAAAAAGCCAGTTTCTGCAAATAAACCGACTGTT
GACTCAAGAAAATCAAGACTCGCCATAAAATTCTAA
>g9797.t1 Gene=g9797 Length=1571
MGVPKFFRYISERYPCLSELVRENQVPEFDNLYLDMNGIIHACSHPNDNDVHFRITEEQI
FKDIFFYLETLFNMIKPQKLFFLAVDGVAPRAKMNQQRGRRFRSAKEAEIQEEKAREKGE
VLPEEARFDSNCITPGTPFMCRLDKALRYFIQHKISTSKSWQNCKIILSGHQTPGEGEHK
IMEYIRYLKAQKKFDPNTRHCLYGLDADLIMLGLCTHERHFSLLREEVKFGKKSNKAVSV
SQQRFFLLHLSLLREYLEQEFIALKDNLKFQFDIEKIIDDWVLMGFLVGNDFIPNIPNLH
INTNALPILYQAYIKTLPNLDGYINEGGKLNLKRLQAYLENLADFDRENFSAQYDDLKFL
ETKHQSGFNNRNDDTFGGNKELMDMVKATEFEFDSPDEDNEVFEENKDESSDSDLDDDAI
YEKEFYQHRRDYYVNKMKYQEMTPEVLVEQAQCYVTALQWTLHYYYHGVKSWSYYYPHHY
APFISDVKNFKDFIPKFELGKPFLPFQQLMSVLPAGSRDHVPECYKQLMTNPESELIEFY
PTNFETDLNGKKQDWEAVVLIPFIDEEKLLRTLKKYDNELTSDEKERNVHGPMFVYTYSS
VSQGSLAGPLNFPSIGNLLCKEQKVYREEIQIPEDKLVLGPSKGALQHIYYAGFPTMKHL
NYKSEFKVQHVRVFDQPSRGENMIIILEPSNYPEKPIEIIVKEMMSKTVHVGWPHLVEAK
IVRITDKDNTFFSDGSSDKTNPQKWKIEVQSIKEHHINRMGIDIGEVTKIVHVLRQTGEE
YKFDPKLRIYRCFKTYSKIETAYALQTVVTNIKAYRQKMKEELPLYEAFKSGTEVFMLGD
RYYGSKGEVMDTTCFEKSGRVKVLLTVHEEPKFEGIWKMHQTSQDSYLNTYQAASRLSIS
DNVFNRITGSVLVIAGIKRQIAEGTSKMNIGLQLKFNKQNEELTGYTKKERVWLYSEKTV
NLVQEYYCKFPQIFEVMERRSSNSNNDVYFESDFFEKTDGEDCLHNLMKWLNQLPHNKAE
RRTIGTEAVEKDVIEEVKKQVIEANKLPMKRSTVQVKPHLLYVPSLSKMTSKSPDDKADF
QLFDRVVVIRDTDQYSIGARGTVIGINRVKDLNPVRQDCINKEDIYCLVLLDESKQNNGV
VRIPQENLINISYGLTKDGVERIASTRNQPLAQIGKEEPVKNAELPKLTESYSSMLQNSN
KNQKKGPNTSQAFLDFWNAAKNKTTSAAAVAKINNTTVVASASVSILPNNTNQLTEEEEA
IAKSLDSQKKLNEAINKKMSELTVNKKNSPTPNEQSVPMMMIPPTKLPTPPIEWLNGEAK
NSSFTEVKPFTIVDAPKSSFPTSFGENPTPRPKIELPTPPVQHSMHFYGNQQQIRPHPFP
AMHSQKFQQHGHHPSHHMMHPMHIRHQFPGGFKPHNMNSPIGPFFANNHHQQQQQRHHNP
QPRFFHNNNIFRQTMKFRQPLSQQVQTPHSAPILSSNSQGNPFIPLQAARKSSKGKEEPT
RSASTTLPDKEVSSTTPQQSQNIEKKSEEKQDFETPQAAVVLEEKKDEQKKPVSANKPTV
DSRKSRLAIKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g9797.t1 | CDD | cd18673 | PIN_XRN1-2-like | 32 | 257 | 1.42124E-128 |
| 19 | g9797.t1 | Coils | Coil | Coil | 566 | 586 | - |
| 15 | g9797.t1 | Gene3D | G3DSA:3.40.50.12390 | - | 1 | 129 | 3.3E-45 |
| 16 | g9797.t1 | Gene3D | G3DSA:3.40.50.12390 | - | 130 | 314 | 1.5E-59 |
| 17 | g9797.t1 | Gene3D | G3DSA:3.30.110.100 | - | 495 | 590 | 2.3E-30 |
| 18 | g9797.t1 | Gene3D | G3DSA:2.170.260.40 | - | 657 | 821 | 1.4E-26 |
| 14 | g9797.t1 | Gene3D | G3DSA:2.30.30.750 | - | 1067 | 1161 | 3.1E-5 |
| 12 | g9797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 119 | - |
| 8 | g9797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 100 | 119 | - |
| 9 | g9797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1460 | 1486 | - |
| 11 | g9797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1460 | 1571 | - |
| 13 | g9797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1499 | 1522 | - |
| 10 | g9797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1523 | 1554 | - |
| 6 | g9797.t1 | PANTHER | PTHR12341:SF7 | 5’-3’ EXORIBONUCLEASE 1 | 1 | 1224 | 3.1E-261 |
| 7 | g9797.t1 | PANTHER | PTHR12341 | 5’->3’ EXORIBONUCLEASE | 1 | 1224 | 3.1E-261 |
| 20 | g9797.t1 | PIRSF | PIRSF006743 | Exonuclease_Xnr1 | 1 | 391 | 2.6E-230 |
| 21 | g9797.t1 | PIRSF | PIRSF006743 | Exonuclease_Xnr1 | 387 | 1565 | 2.9E-200 |
| 5 | g9797.t1 | Pfam | PF03159 | XRN 5’-3’ exonuclease N-terminus | 1 | 227 | 1.1E-94 |
| 4 | g9797.t1 | Pfam | PF17846 | Xrn1 helical domain | 271 | 596 | 7.2E-87 |
| 3 | g9797.t1 | Pfam | PF18332 | Exoribonuclease Xrn1 D1 domain | 650 | 814 | 7.5E-28 |
| 1 | g9797.t1 | Pfam | PF18334 | Exoribonuclease Xrn1 D2/D3 domain | 824 | 910 | 9.6E-9 |
| 2 | g9797.t1 | Pfam | PF18129 | Xrn1 SH3-like domain | 1079 | 1133 | 1.9E-7 |
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:0008409 | 5’-3’ exonuclease activity | MF |
| GO:0004527 | exonuclease activity | MF |
| GO:0003676 | nucleic acid binding | MF |
| GO:0000956 | nuclear-transcribed mRNA catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K12618 (5’-3’ exoribonuclease 1 [EC:3.1.13.-])
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.
