Gene loci information

Transcript annotation

  • This transcript has been annotated as Exosome RNA helicase MTR4.

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 g4983 g4983.t1 isoform g4983.t1 6284420 6287738
chr_2 g4983 g4983.t1 exon g4983.t1.exon1 6284420 6284535
chr_2 g4983 g4983.t1 cds g4983.t1.CDS1 6284420 6284535
chr_2 g4983 g4983.t1 exon g4983.t1.exon2 6284593 6284700
chr_2 g4983 g4983.t1 cds g4983.t1.CDS2 6284593 6284700
chr_2 g4983 g4983.t1 exon g4983.t1.exon3 6284756 6284979
chr_2 g4983 g4983.t1 cds g4983.t1.CDS3 6284756 6284979
chr_2 g4983 g4983.t1 exon g4983.t1.exon4 6285044 6286017
chr_2 g4983 g4983.t1 cds g4983.t1.CDS4 6285044 6286017
chr_2 g4983 g4983.t1 exon g4983.t1.exon5 6286074 6287738
chr_2 g4983 g4983.t1 cds g4983.t1.CDS5 6286074 6287738
chr_2 g4983 g4983.t1 TTS g4983.t1 6287809 6287809
chr_2 g4983 g4983.t1 TSS g4983.t1 NA NA

Sequences

>g4983.t1 Gene=g4983 Length=3087
ATGGCAGAGATTGACGAGTTGTTTAGTTGTTTTGAAGAGGAAAATATTGAACAACAGCCT
ATGATTCCAGTTGTAGAAGAGGTAGAAAAGACAACAGTAGAAGCAGAAAGTATTTCGAAT
GACCCAAATATTTCAACTTCATCACATAAAAGAGCTTTAGAATGTAGTGATGATGATGAG
GCTCCTAAAAAACCTAGAGTGGAATCAATGTTAGACGATATAAATTTGGAACAAATTGAC
GCGCGAATAAAAATTCATGTATTAAAAAGTCCTGACGCTTGTGTCCATGAAGTTGCTGTT
CATCCTAATCAAGAATATGATCCACTTAAACCAGCAACACAACCACCAGCAAAAGAATAT
CCATTTATTTTGGATTCATTTCAAAAAGAAGCTATTCTTTGTATTGAGAATAATCAATCG
GTTCTAGTATCTGCTCATACATCAGCTGGTAAAACTGTCGTTGCCGAATATGCAGTTGCT
AGAGCACTATCAATGAAACAAAGAGTTATCTACACCACTCCCATAAAAGCATTGAGTAAT
CAAAAATATCGAGAATTTCATGAAGAATTTCAAGATGTTGGTTTAGTTACTGGTGATATT
ACTATCAATCCGACAGCTTCATGTTTAATTATGACAACAGAAATTCTACGAAATATGCTA
TACCGTGGTTCAGAAATAATGCGTGAAGTCGGTTGGGTTATCTTCGATGAGATACATTAC
ATGAGAGACAAAGAGCGTGGTGTTGTATGGGAAGAAACTTTGATTCTTTTGCCTGACAAT
GTGCATTATGTTTTCCTTTCGGCAACAATTCCTAATGCACGTCAATTTGCTGAATGGGTT
TGTCATATTCATCGCCAACCTTGTCATGTTGTCTACACTGATTATCGTCCAACACCATTA
CAACATTACATATTTCCAGCTGGTGGTGATGGAATTCATCTTGTGGTTGATGAAAAAGGA
AATTTCAAAGAAGATAATTTCAATGCTGCAATGAATGTTTTAATGAAAAGTGGTGCTGGA
AAAGGCGATGAAAAAGGTAGGAAAGGAGGGATAAAAGCAACTAATAAAACGAGTGGCGTA
ACAAACATCTTTAAAATTGTAAAAATGATCATGGAACGTAGTTTAGCGCCTGTAATTATT
TTCTCATTTAGTAAGAAAGAATGTGAAACAAATGCAATGCAAATGGCAAAATTAGATTTT
AATTCAGCTGAAGAAAAAAGACTTGTTGATGAAGTATTCAACAATGCAATGGATGTATTA
AATGAAGATGATAAAAAGCTTCCACAAGTTGAAAAATTACTACCACTATTAAAACGTGGT
ATAGGAGTGCATCATGGTGGTTTATTACCTATTTTAAAAGAAACAATCGAAATTCTTTTT
GGTGAAGGATTACTTAAAGCACTCTTTGCTACTGAAACATTTGCAATGGGATTAAATATG
CCTGCACGAACAGTAGTTTTTACAAGTAGTCAAAAGTTTGATGGTAAAAATTTCCGAACA
CTTGCTAGTGGTGAATACATACAAATGTCAGGAAGAGCAGGACGTCGTGGTCTTGATGAT
AAAGGTATTGTAATTCTTATGGTGGATGAGAAAGTTTCACCTGCAATCGGTCGTGAAATT
GTCCAAGGAAAACCTAATGCTATTAATTCAGCATTTCATCTTACTTACAATATGGTTCTC
AATTTGTTGCGTGTAGAAGAAATTAATCCTGAATATATGCTTGAACGTTCATTTTTCCAA
TTTCAAAATCAATCAACAATTCCTGACCTTTACAAAAAAGTTCAACAAAAACAAGACGAA
TTAATAGAATTTGTAGTGAAAGAAGAATCATCAATAAGAACTTATCATCATATTCGTGAA
CAATTGGATACATTAACGGAGAAATATCAACAATTTTATACTAATCCACAATATATAAGA
CCATTTCTTCAACCTGGACGTCTGTGTAAAATTAAAACTGGAGAGCATGAGTTTGATTGG
GGAATGGTAGTCAATAATAAAATCGAGCATACTGACAATTCAAAAAATCCACTCAAATCT
GATTCTAAATTGATAATTGAAGTTTTACTCCATATTGATGATACACCAGATAAATCAAAA
AATCCAATACCTTGTCCGCCTGGTAAAAAAGGATGTGCTGAAATTATTCCCATTACATCA
AACTTAGTTTCAAAGCTTAGTACATTAAGAATCTACTATCCTGATGATTTACGGCCAACT
GACAGTCGAAGAGCTGTGTTGAAAAGGATTGAAGAAGTGAAAAAGAAATTTCCAAATGGG
GCACCAATTTTGAATCCTGTCGAAGATATGCGAATCAAAGATAAAGAATTTTTAAACATT
ATAACTTTGCTTGAAAAATTTGAAAAACAACTTTATTCTCATCCACTTCATTCATCACCT
GAGCTAGCTGATATTTATAATTCATATTTAGCAAAATTACAATTAGAATCTGAGTTAGTT
GAAGCAAAGAAGAAATTGAAAGATGCTAAAAGTTTATTACAAATGGACGATTTGAAACAT
CGTAAAAGAGTTTTGAGACGTCTTGGTTATTGTACAAATTCCGATGTTATTGAATTCAAA
GGTCGAGTTGCATGCGAACTTTCTTCAGGCGATGAACTTTTGATTACCGAAATGATTTTT
AATGGCACTTTCAACGACTTGCAGCCTGCTCAGTGTGCTGCATTATTATCATGCTTTGTC
TGTGATGATAGAGCAGGCGAACTTAATATTGATGCTGAGCTTCAAGCGCCATTCAAACAA
ATGCAAGATTTTGCTCGTCGTATTGCAAAAGTGTCAAAAGAATGCAAAATGGATATTGAT
GAAGACGATTATGTGGAAAAATTCAAACCAACTCTGATGGATGTGGTATTAAAATGGTGT
AAGGGTGCATCATTTTCACAAATTTGTCAGATAACAGATGTATTTGAAGGTAATATTATT
CGATGCATGCGACGACTTGAAGAACTCATGCGACAAATGGTCCAAGCATCAAAAACAATT
GGAAATACTGATTTGGAAAATAAATTTTCTGAAGGTATTCGATTATTAAAACGTGATATT
GTTTTTGCTGCATCACTTTATCTTTAA

>g4983.t1 Gene=g4983 Length=1028
MAEIDELFSCFEEENIEQQPMIPVVEEVEKTTVEAESISNDPNISTSSHKRALECSDDDE
APKKPRVESMLDDINLEQIDARIKIHVLKSPDACVHEVAVHPNQEYDPLKPATQPPAKEY
PFILDSFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAVARALSMKQRVIYTTPIKALSN
QKYREFHEEFQDVGLVTGDITINPTASCLIMTTEILRNMLYRGSEIMREVGWVIFDEIHY
MRDKERGVVWEETLILLPDNVHYVFLSATIPNARQFAEWVCHIHRQPCHVVYTDYRPTPL
QHYIFPAGGDGIHLVVDEKGNFKEDNFNAAMNVLMKSGAGKGDEKGRKGGIKATNKTSGV
TNIFKIVKMIMERSLAPVIIFSFSKKECETNAMQMAKLDFNSAEEKRLVDEVFNNAMDVL
NEDDKKLPQVEKLLPLLKRGIGVHHGGLLPILKETIEILFGEGLLKALFATETFAMGLNM
PARTVVFTSSQKFDGKNFRTLASGEYIQMSGRAGRRGLDDKGIVILMVDEKVSPAIGREI
VQGKPNAINSAFHLTYNMVLNLLRVEEINPEYMLERSFFQFQNQSTIPDLYKKVQQKQDE
LIEFVVKEESSIRTYHHIREQLDTLTEKYQQFYTNPQYIRPFLQPGRLCKIKTGEHEFDW
GMVVNNKIEHTDNSKNPLKSDSKLIIEVLLHIDDTPDKSKNPIPCPPGKKGCAEIIPITS
NLVSKLSTLRIYYPDDLRPTDSRRAVLKRIEEVKKKFPNGAPILNPVEDMRIKDKEFLNI
ITLLEKFEKQLYSHPLHSSPELADIYNSYLAKLQLESELVEAKKKLKDAKSLLQMDDLKH
RKRVLRRLGYCTNSDVIEFKGRVACELSSGDELLITEMIFNGTFNDLQPAQCAALLSCFV
CDDRAGELNIDAELQAPFKQMQDFARRIAKVSKECKMDIDEDDYVEKFKPTLMDVVLKWC
KGASFSQICQITDVFEGNIIRCMRRLEELMRQMVQASKTIGNTDLENKFSEGIRLLKRDI
VFAASLYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4983.t1 CDD cd18024 DEXHc_Mtr4-like 94 296 1.1036E-153
15 g4983.t1 CDD cd18795 SF2_C_Ski2 296 529 1.886E-61
13 g4983.t1 Coils Coil Coil 812 832 -
8 g4983.t1 Gene3D G3DSA:3.40.50.300 - 93 296 8.9E-82
9 g4983.t1 Gene3D G3DSA:3.40.50.300 - 297 549 6.6E-86
12 g4983.t1 Gene3D G3DSA:1.10.3380.30 - 556 1019 1.9E-171
10 g4983.t1 Gene3D G3DSA:1.20.1500.20 - 578 828 1.9E-171
11 g4983.t1 Gene3D G3DSA:2.40.30.300 - 644 760 1.9E-171
22 g4983.t1 MobiDBLite mobidb-lite consensus disorder prediction 31 65 -
20 g4983.t1 MobiDBLite mobidb-lite consensus disorder prediction 35 50 -
21 g4983.t1 MobiDBLite mobidb-lite consensus disorder prediction 51 65 -
5 g4983.t1 PANTHER PTHR12131:SF7 EXOSOME RNA HELICASE MTR4 65 1027 0.0
6 g4983.t1 PANTHER PTHR12131 ATP-DEPENDENT RNA AND DNA HELICASE 65 1027 0.0
14 g4983.t1 PIRSF PIRSF005198 SKI2 6 1028 0.0
1 g4983.t1 Pfam PF00270 DEAD/DEAH box helicase 127 271 4.9E-17
3 g4983.t1 Pfam PF00271 Helicase conserved C-terminal domain 413 517 4.4E-6
4 g4983.t1 Pfam PF13234 rRNA-processing arch domain 571 828 1.7E-70
2 g4983.t1 Pfam PF08148 DSHCT (NUC185) domain 855 1023 2.5E-52
24 g4983.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 132 288 24.165
23 g4983.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 362 566 12.7
19 g4983.t1 SMART SM00487 ultradead3 120 303 3.3E-33
18 g4983.t1 SMART SM00490 helicmild6 428 517 4.4E-16
17 g4983.t1 SMART SM01142 DSHCT_2 852 1028 4.9E-95
7 g4983.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 136 531 4.57E-47

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:0006401 RNA catabolic process BP
GO:0003723 RNA binding MF
GO:0005524 ATP binding MF
GO:0003724 RNA helicase activity 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