Gene loci information

Transcript annotation

  • This transcript has been annotated as 116 kDa U5 small nuclear ribonucleoprotein component.

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_3 g3792 g3792.t1 isoform g3792.t1 27970663 27973631
chr_3 g3792 g3792.t1 exon g3792.t1.exon1 27970663 27973467
chr_3 g3792 g3792.t1 cds g3792.t1.CDS1 27970663 27973467
chr_3 g3792 g3792.t1 exon g3792.t1.exon2 27973536 27973631
chr_3 g3792 g3792.t1 cds g3792.t1.CDS2 27973536 27973631
chr_3 g3792 g3792.t1 TSS g3792.t1 NA NA
chr_3 g3792 g3792.t1 TTS g3792.t1 NA NA

Sequences

>g3792.t1 Gene=g3792 Length=2901
ATGGATTCTGATTTATATGATGAGTTTGGAAACTATATTGGACCTGATTTAGAAAGTGAT
TCTGAAGAGGAAGAATATGATGAACAAGATGTCGATGACGATGCCAATGAAGAAGATGAA
GCTGAAATGGATGTCGATGATGAAGAAAAAACATCAAAAGCTATTGTTTTACATGAAGAT
AAGCGTTATTATCAAACAGCGTTAGAAGTTTACGGTCCAGATGTAGAAACAATTGTTCAA
GAAGAAGATGCACAGCCATTAGATAAGCCACTTATTGAACCAACAAAAAAAGTTAAATTT
CAGCTTAAAGAGCAAGATTTACCACAAACTACATATTCGATAGAATTTCTAAGTGATTTG
ATGGATATTCCAGAACTAATTCGAAATGTTGCTCTAATTGGTCATCTTCATCATGGAAAA
ACGACTTTTGTTGATTGTCTCATCAAACAAACTCATCCGCAATTTCAAGATATGGAGGAA
AGAAATCTTAGATATACAGACACATTATTTACTGAGCAAGAAAGAGGTGTCAGTATAAAA
TCTACACCAGTTACACTCGTCTTGCAAGATGTCAAGGAAAAGAGCTATTTAATGAATGTT
TTTGATACACCGGGACATGTTAATTTTTCAGACGAAGTAACTGCTGCAATGAGAATGGTT
GATGGTGTTGTACTTTTTGTTGATGCAGCTGAAGGTGTCATGCTCAACACTGAAAGATTA
TTAAAGCATGCAATTCAAGAAAAACTTGCTATAACCGTTTGCATCAACAAAATTGATCGT
TTAATTCTCGAACTTAAATTACCACCACAAGATGCATATTTTAAATTGAAACATATCATT
GATGAAATCAATGGATTAATCACTTTATATGGTAATACAAATCCTCAACTCTCTCCGATT
ATTGGAAATGTATGTTTTGCAAGTTCACAATATGGTTTCTGTTTTACTTTGAAATCATTT
GCTAAACTCTATACTGACACTTTCCCTGGTGTATCGACAACTGAATTTGCTCGAAGATTA
TGGGGCGATATGTATTTCAACAGTAAAACTCGAAAGTTTTCTAAAAAGCCTGCTCATAAT
TCAGCTCCGAGAAGCTTTATTGAATTTATTTTGGAACCAATTTATAAACTTTTTGCTCAA
GTTGTAGGAGATGTTGATGGTACACTTGCTGATACACTTGCAGAGTTAAACATTCGAATT
ACAAAAGAAGAAATGAAATGCAACATAAGACCACTTTTACGACTCATTTGTAATCGATTC
TTTGGTGATTTCACTGGTTTTGTAGATATGTGCGTTGAACACATTTTATCACCAGCTGGG
AATTCTAAAAATAAAATCGATCATATTTATACTGGTCCAAAAGAAGGCGTGCTTTATGAT
GATATGCTGAATTGCAATCAAGATGGAAATTTAGTCGTTCACACAAGCAAAATGTATCCA
ACAGATGATTGTAACATTTTTTTAGTTCTTGCTCGCGTTATGAATGGAACTCTTTATAGT
GGACAAGAAGTACGAATTCTTGGTGAAAATTACACACTACTTGATGAAGAAGACTCGCGT
ATTGTAAAAGTTGGCCGTTTATGGGTATATGAGGCTCGTTATAAAATTGAATTAAATAGA
GTTCCAGCTGGAACTTGGGTTTTAATTGAGTCAATCGATCAAAGTATTGTCAAAACTTCT
ACTATTGTCGATGCAAATGTTCAAGAAGATTTATACATCTTTAGACCACTCAAATTCAAC
ACACAGAGTATCATAAAAATTGCAGTTGAACCTGTTAATCCATCTGAATTACCAAAAATG
CTTGATGGTTTGAGAAAAGTGAACAAAAGTTACCCACTTTTATCAACTCGTGTTGAAGAG
TCTGGTGAGCATGTAATTTTAGGTACTGGAGAACTTTATCTAGATTGTGTTATGCATGAC
TTGAGAAAAATGTATTCAGAAATTGACATTAAAGTTGCCGATCCAGTTACAATGTTTACA
GAAACATGTGTAGAAACTTCAGCAATCAAATGTTTCTCAGAAACTCCAAACAAAAAGAAT
AAAATCACCATGATTTCGGAACCACTCGAGAAAGGATTAGCAGAGGATATTGAAAATGAA
AATGTTTCAATAAATTGGAGTAAAAAGAAAATTGGTGAATTCTTCCAAAAAACATATGAT
TGGGATTTGCTTGCGGCACGTTCAATTTGGTCATTTGGTCCAGATAATTGTGGTGCAAAT
ATTCTTGTTGATGACACATTACCATCAGAGGTTGACAAATCTTTATTGCTCTCAATTAAA
GATTCAATAGTTCAAGGATTTCAATGGGCTACAAGGGAAGGTCCATTGTGTGAAGAGCCA
ATTAGAAATGTAAAATTTAAAGTATTGGATGCAGTGATTGCAAACGAACCTATACACAGA
GGAGGTGGTCAAATTATTCCAACTGCTCGGCGCGTTTCATATTCTGCATTTTTAATGGCA
ACACCAAGATTAATGGAACCATATTTATTTGTCGAAGTTCAAGCTCCAGCTGATTGTGTA
TCATCTGTTTATACAGTGTTAGCGAAAAGACGTGGACATGTGACACAAGATGCTCCAATA
CCAGGTTCTCCTTTATATATTGTCAAAGCTTTTATTCCAGCAATTGATTCGTTTGGATTT
GAAACGGATTTGAGAACACACACTCAAGGACAAGCATTTTGTCAATCAGTCTTTCATCAC
TGGCAAATAGTACCAGGTGATCCTCTAGACAAATCAATCATCATTCGACCACTTGAACCA
CAACCAGCTACACATTTAGCACGTGAATTTATGATTAAAACTCGTCGACGCAAGGGTCTT
TCTGAAGATGTCTCTATCAACAAATTCTTTGATGATCCAATGTTGCTCGAGTTAGCAAAA
CAAGATGTTTTATTAAATTAA

>g3792.t1 Gene=g3792 Length=966
MDSDLYDEFGNYIGPDLESDSEEEEYDEQDVDDDANEEDEAEMDVDDEEKTSKAIVLHED
KRYYQTALEVYGPDVETIVQEEDAQPLDKPLIEPTKKVKFQLKEQDLPQTTYSIEFLSDL
MDIPELIRNVALIGHLHHGKTTFVDCLIKQTHPQFQDMEERNLRYTDTLFTEQERGVSIK
STPVTLVLQDVKEKSYLMNVFDTPGHVNFSDEVTAAMRMVDGVVLFVDAAEGVMLNTERL
LKHAIQEKLAITVCINKIDRLILELKLPPQDAYFKLKHIIDEINGLITLYGNTNPQLSPI
IGNVCFASSQYGFCFTLKSFAKLYTDTFPGVSTTEFARRLWGDMYFNSKTRKFSKKPAHN
SAPRSFIEFILEPIYKLFAQVVGDVDGTLADTLAELNIRITKEEMKCNIRPLLRLICNRF
FGDFTGFVDMCVEHILSPAGNSKNKIDHIYTGPKEGVLYDDMLNCNQDGNLVVHTSKMYP
TDDCNIFLVLARVMNGTLYSGQEVRILGENYTLLDEEDSRIVKVGRLWVYEARYKIELNR
VPAGTWVLIESIDQSIVKTSTIVDANVQEDLYIFRPLKFNTQSIIKIAVEPVNPSELPKM
LDGLRKVNKSYPLLSTRVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVTMFT
ETCVETSAIKCFSETPNKKNKITMISEPLEKGLAEDIENENVSINWSKKKIGEFFQKTYD
WDLLAARSIWSFGPDNCGANILVDDTLPSEVDKSLLLSIKDSIVQGFQWATREGPLCEEP
IRNVKFKVLDAVIANEPIHRGGGQIIPTARRVSYSAFLMATPRLMEPYLFVEVQAPADCV
SSVYTVLAKRRGHVTQDAPIPGSPLYIVKAFIPAIDSFGFETDLRTHTQGQAFCQSVFHH
WQIVPGDPLDKSIIIRPLEPQPATHLAREFMIKTRRRKGLSEDVSINKFFDDPMLLELAK
QDVLLN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g3792.t1 CDD cd04167 Snu114p 128 325 4.54877E-107
26 g3792.t1 CDD cd04090 EF2_II_snRNP 471 564 2.40755E-42
29 g3792.t1 CDD cd16264 snRNP_III 583 654 8.65664E-40
28 g3792.t1 CDD cd01683 EF2_IV_snRNP 654 831 1.83023E-113
27 g3792.t1 CDD cd04098 eEF2_C_snRNP 826 905 1.31576E-50
19 g3792.t1 Gene3D G3DSA:3.40.50.300 - 121 437 3.2E-166
23 g3792.t1 Gene3D G3DSA:2.40.30.10 Translation factors 157 564 3.2E-166
24 g3792.t1 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 317 421 3.2E-166
21 g3792.t1 Gene3D G3DSA:3.30.70.870 Elongation Factor G (Translational Gtpase) 581 657 6.9E-28
22 g3792.t1 Gene3D G3DSA:3.30.70.240 - 661 940 1.7E-118
20 g3792.t1 Gene3D G3DSA:3.30.230.10 - 666 943 1.7E-118
33 g3792.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 52 -
34 g3792.t1 MobiDBLite mobidb-lite consensus disorder prediction 17 46 -
7 g3792.t1 PANTHER PTHR42908:SF6 116 KDA U5 SMALL NUCLEAR RIBONUCLEOPROTEIN COMPONENT 53 960 0.0
8 g3792.t1 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 53 960 0.0
13 g3792.t1 PRINTS PR00315 GTP-binding elongation factor signature 129 142 1.2E-10
9 g3792.t1 PRINTS PR00315 GTP-binding elongation factor signature 174 182 1.2E-10
10 g3792.t1 PRINTS PR00315 GTP-binding elongation factor signature 199 209 1.2E-10
12 g3792.t1 PRINTS PR00315 GTP-binding elongation factor signature 215 226 1.2E-10
11 g3792.t1 PRINTS PR00315 GTP-binding elongation factor signature 251 260 1.2E-10
5 g3792.t1 Pfam PF16004 116 kDa U5 small nuclear ribonucleoprotein component N-terminus 4 108 7.4E-35
4 g3792.t1 Pfam PF00009 Elongation factor Tu GTP binding domain 127 316 4.5E-48
3 g3792.t1 Pfam PF03144 Elongation factor Tu domain 2 488 562 6.9E-9
1 g3792.t1 Pfam PF14492 Elongation Factor G, domain III 583 645 1.7E-6
2 g3792.t1 Pfam PF03764 Elongation factor G, domain IV 703 820 9.8E-26
6 g3792.t1 Pfam PF00679 Elongation factor G C-terminus 823 911 1.7E-23
32 g3792.t1 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 167 182 -
36 g3792.t1 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 125 333 43.193
30 g3792.t1 SMART SM00889 EFG_IV_2 701 821 4.6E-21
31 g3792.t1 SMART SM00838 EFG_C_a 823 912 4.1E-16
15 g3792.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 112 435 3.91E-84
18 g3792.t1 SUPERFAMILY SSF50447 Translation proteins 437 569 7.07E-34
16 g3792.t1 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 582 655 5.04E-17
14 g3792.t1 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 659 825 1.74E-56
17 g3792.t1 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 826 912 3.45E-27
35 g3792.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 128 262 2.6E-14

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:0005525 GTP binding MF
GO:0003924 GTPase 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