Gene loci information

Transcript annotation

  • This transcript has been annotated as Exosome complex exonuclease RRP44.

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 g7153 g7153.t1 TTS g7153.t1 21552484 21552484
chr_2 g7153 g7153.t1 isoform g7153.t1 21552551 21556501
chr_2 g7153 g7153.t1 exon g7153.t1.exon1 21552551 21552820
chr_2 g7153 g7153.t1 cds g7153.t1.CDS1 21552551 21552820
chr_2 g7153 g7153.t1 exon g7153.t1.exon2 21552887 21553673
chr_2 g7153 g7153.t1 cds g7153.t1.CDS2 21552887 21553673
chr_2 g7153 g7153.t1 exon g7153.t1.exon3 21553734 21554230
chr_2 g7153 g7153.t1 cds g7153.t1.CDS3 21553734 21554230
chr_2 g7153 g7153.t1 exon g7153.t1.exon4 21554919 21555488
chr_2 g7153 g7153.t1 cds g7153.t1.CDS4 21554919 21555488
chr_2 g7153 g7153.t1 exon g7153.t1.exon5 21555549 21555981
chr_2 g7153 g7153.t1 cds g7153.t1.CDS5 21555549 21555981
chr_2 g7153 g7153.t1 exon g7153.t1.exon6 21556035 21556363
chr_2 g7153 g7153.t1 cds g7153.t1.CDS6 21556035 21556363
chr_2 g7153 g7153.t1 exon g7153.t1.exon7 21556448 21556501
chr_2 g7153 g7153.t1 cds g7153.t1.CDS7 21556448 21556501
chr_2 g7153 g7153.t1 TSS g7153.t1 NA NA

Sequences

>g7153.t1 Gene=g7153 Length=2940
ATGTTAACTAATAAAGTTTTTATAAGAAAGAACAAACGTGGAAACGTTCTAAAGATCATA
AGAGAACATTATCTTCGTACAGATTTATGGTGTGGAAGCTGTTGCTGTATAATTTGTCCT
CATGAGAAGCATGATTTAATTCTAGCAGAGAATCCTCCATCAAAAAGTTCAATTTTTAAA
GAACCTCATTATCTCATGGTTGATACAAATGTAATACTGGATCAAATAGATGTATTTGAA
GAAGATGTTATTAGTAATGTAATTATTGTGCAAACAGTAATTGATGAAGTCAAACATAGA
AGTTCAGCAATTTATAAACGTTTAAGAGACATTTTAACAAATCCAGCTAGAAAGTTTTAT
ACATTTGTGAATGAACATCACCGCGATACTTATATTGAACGAGAACAGAAAGAATCGTCT
AATGATCGCAATGATCGTGCTATTAGAAAAGCTGCTTTGTGGTATCAAAATCATTTGAAC
AAAAGCACAAAAGAATCAAAGAAACCAAAAATTACAATCATACTTCTGACAGACGATGCT
GAAAACAGAAGAAAGGCACAAGAAGAGGATAAGCTTGTTTCATGTTCTGTACAAACATAT
GTTAGATCACTTTCGGAACATCCATATTTGCAAGATAAATTATGCATCAAAGAATATGCA
TCCGAGAGTGACAAACATCCTGTCTATCCACCACATTTAACTGTTGTGCAAATGCATGAA
GGAATAAAAAGTGGTAAATTATATCAAGGTTCTTTTGTTGCATCTAGAGAGAATTTCCTC
GAAGGTAGTGTTAATGTTGAATGCTTTGAAAAATTTATACTTGTTCAAGGTCGTGAAGCA
TTGAATAGAGCTATTGACGGTGATACAGTTTGCGTTGAGCTGTTACCTGAAAACGAATGG
ACATGCCCAAGTGAAATTGTTCTTGAGGATAATGAAAATGATCCTATAGTTGAAACTATC
GAAGAAGATGAAAATGAAAAAATTCTCAAAGAATCTGCAAGCAAAAAACAAGAAAAGCAA
CCAACAGGAAAAATTGTTGGAATAATCAAACGAAAATGGCGTCAATACTGTGGAATACTT
AAACCTAATGAAATCAAAGGTACATCTCGTCACATCTTTATTCCAGCCGAAAGAAAAATA
CCACGTGTGCGAATTGAAACACGACAGGCAGAGAAGCTTTACAGTAAAAGAATTATTGTT
GCAATTGATCAATGGCCAAGACATTCGAGATATCCTCAAGGTCATTTTGTGCGCGCTCTT
GGTCCATTAGGTGATAAAGAGACAGAAAATGAAGTCTTATTAATTGAGCATGATGTTCCA
CACAGTAAATTTTCACAAGAAGTTCTTAATTGTCTTCCATCTTTACCGTGGATTATTTCG
GAACAGGATTACAAAGAACGTGTGGATTTAAGAAAAATAGCTATTTGTAGTGTTGATCCA
CCTGGTTGCACGGATATAGATGACGCACTTCACAGCAGATTACTTCCGAATGGCAATATT
GAAGTTGGTGTTCATATTGCTGATGTTAGTCATTTTATAAGACCAGGAACAGCAATCGAT
AAAGAAGCAGCTTCACGTGCTACTACAGTATATCTCGTTGATAAACGAATTGACATGGTG
CCAGAATTATTATCCTCCAATCTTTGTTCACTTAGAGGAAATGTTGAACGTTTTGCATTT
TCATGTATATGGGAATTAGATAAAAATGCAAATATCATTGCTACTAAATTTCACAAAAGT
GTTATTAAATCAAAAGCTGCATTAACATACGAAGAGGCACAATTGATTATTGATGACAAA
AATAAAAATGATGACATTGCTAAATCTCTTCGACGTTTAAATGAATTGGCAAAAATTTTA
AAACGTAGACGAACTGAGAATGGTGCTTTAGTTTTGGCTTCTCCTGAAATTAGATTTCAC
ATTGATAGTGAAACAAACGATCCTATTGAAGTTGCGGTTAAACAATTAAGAGAAACAAAT
TCAATGGTTGAAGAATTTATGTTGCTTGCGAATGTATCTGTTGCAGAAAAAATTGAGAAA
GAATTTCCTGAACATGCTATGCTACGTCGTCATCCGATACCACCTCAAACAAATTTTGAA
CCATTAATAAAAGCTGTTAGACATCAAGGATTCGACATAGATACAAGTTCAGGCAAACAC
CTTGCAATTTCTTTGGATAACATTGTTAAAGACGATAATCCATATTTCAATACAATGTTG
AGAATATTAGCAACGCGTTGCATGTTGCAAGCAGTTTATTTCATAAGTGGAACATTAACT
CGTTCAGAATTCTTTCATTATGGTTTAGCTGCTCCAATTTATACACATTTTACTTCACCA
ATTCGTCGTTATGCCGATATTATCGTTCATAGATTACTTGCTGCATGCATTGGTGCGGAT
TCAACTTATGCTGATTTATTGGACAAAACAAAGAATTCTTTATTATGCAACAATTTAAAT
TATCGAAATCGAATGGCACAATATGCGGGTCGAGCATCTGTAGCATTAAATACACATCTC
TTTTTTAGAAACCGTTCGGAGGAAGTCGAAGGTTATGTTTTATTTGTTCGTAAGAATGCA
TTGCAAATTCTAGTACCAAAATATGGACTCGAGGGTACAATATATCTTAGTGGAAAGAAT
ATTAATGCCAAGTTTATTTACAACGAAGAGAATCAATCACAACAGTGTGAAAATATCGTT
TTCCATTCATTTGATCCCGTTATTGTACGTCTTAGTCTTGATTCAACGAATGTTCAGCAC
GAAAAGCTTGTTTTTGAGCTTGTGAAACCATTTATTGAAGGCTTCAGTATACAATCGAAT
GACAACGTAATGGAAATTGATGAAACTCCTCAGTCTCCTACGATGAAAAGAAAACCTATG
GAGGAGGCAGTGGCAGTAGGAAGCGGAAAGAAAGCAGGAAATAAAAAGAAGAAAAAGTAA

>g7153.t1 Gene=g7153 Length=979
MLTNKVFIRKNKRGNVLKIIREHYLRTDLWCGSCCCIICPHEKHDLILAENPPSKSSIFK
EPHYLMVDTNVILDQIDVFEEDVISNVIIVQTVIDEVKHRSSAIYKRLRDILTNPARKFY
TFVNEHHRDTYIEREQKESSNDRNDRAIRKAALWYQNHLNKSTKESKKPKITIILLTDDA
ENRRKAQEEDKLVSCSVQTYVRSLSEHPYLQDKLCIKEYASESDKHPVYPPHLTVVQMHE
GIKSGKLYQGSFVASRENFLEGSVNVECFEKFILVQGREALNRAIDGDTVCVELLPENEW
TCPSEIVLEDNENDPIVETIEEDENEKILKESASKKQEKQPTGKIVGIIKRKWRQYCGIL
KPNEIKGTSRHIFIPAERKIPRVRIETRQAEKLYSKRIIVAIDQWPRHSRYPQGHFVRAL
GPLGDKETENEVLLIEHDVPHSKFSQEVLNCLPSLPWIISEQDYKERVDLRKIAICSVDP
PGCTDIDDALHSRLLPNGNIEVGVHIADVSHFIRPGTAIDKEAASRATTVYLVDKRIDMV
PELLSSNLCSLRGNVERFAFSCIWELDKNANIIATKFHKSVIKSKAALTYEEAQLIIDDK
NKNDDIAKSLRRLNELAKILKRRRTENGALVLASPEIRFHIDSETNDPIEVAVKQLRETN
SMVEEFMLLANVSVAEKIEKEFPEHAMLRRHPIPPQTNFEPLIKAVRHQGFDIDTSSGKH
LAISLDNIVKDDNPYFNTMLRILATRCMLQAVYFISGTLTRSEFFHYGLAAPIYTHFTSP
IRRYADIIVHRLLAACIGADSTYADLLDKTKNSLLCNNLNYRNRMAQYAGRASVALNTHL
FFRNRSEEVEGYVLFVRKNALQILVPKYGLEGTIYLSGKNINAKFIYNEENQSQQCENIV
FHSFDPVIVRLSLDSTNVQHEKLVFELVKPFIEGFSIQSNDNVMEIDETPQSPTMKRKPM
EEAVAVGSGKKAGNKKKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g7153.t1 CDD cd09862 PIN_Rrp44-like 9 200 2.38432E-83
15 g7153.t1 Coils Coil Coil 603 623 -
12 g7153.t1 Gene3D G3DSA:3.40.50.1010 - 9 213 1.5E-69
13 g7153.t1 Gene3D G3DSA:2.40.50.690 - 217 326 1.8E-31
14 g7153.t1 Gene3D G3DSA:2.40.50.700 - 353 424 8.8E-29
20 g7153.t1 MobiDBLite mobidb-lite consensus disorder prediction 948 979 -
6 g7153.t1 PANTHER PTHR23355 RIBONUCLEASE 3 930 0.0
7 g7153.t1 PANTHER PTHR23355:SF35 EXOSOME COMPLEX EXONUCLEASE RRP44 3 930 0.0
2 g7153.t1 Pfam PF13638 PIN domain 66 189 2.7E-12
1 g7153.t1 Pfam PF17216 Rrp44-like cold shock domain 229 327 8.4E-21
4 g7153.t1 Pfam PF17849 Dis3-like cold-shock domain 2 (CSD2) 372 438 1.2E-18
3 g7153.t1 Pfam PF00773 RNB domain 467 796 2.3E-97
5 g7153.t1 Pfam PF17215 S1 domain 849 891 4.1E-5
17 g7153.t1 ProSitePatterns PS01175 Ribonuclease II family signature. 766 790 -
19 g7153.t1 SMART SM00670 PIN_9 63 184 4.9E-20
18 g7153.t1 SMART SM00955 RNB_2 467 799 4.2E-143
8 g7153.t1 SUPERFAMILY SSF88723 PIN domain-like 62 189 5.1E-11
10 g7153.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 227 421 1.37E-38
9 g7153.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 427 844 1.37E-131
11 g7153.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 847 924 1.39E-12

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:0003723 RNA binding MF
GO:0004540 ribonuclease activity 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