Gene loci information

Transcript annotation

  • This transcript has been annotated as Heterogeneous nuclear ribonucleoprotein 87F.

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 g1607 g1607.t6 isoform g1607.t6 12100324 12101444
chr_3 g1607 g1607.t6 exon g1607.t6.exon1 12100324 12100566
chr_3 g1607 g1607.t6 cds g1607.t6.CDS1 12100326 12100566
chr_3 g1607 g1607.t6 exon g1607.t6.exon2 12100837 12101069
chr_3 g1607 g1607.t6 cds g1607.t6.CDS2 12100837 12101069
chr_3 g1607 g1607.t6 exon g1607.t6.exon3 12101331 12101444
chr_3 g1607 g1607.t6 cds g1607.t6.CDS3 12101331 12101444
chr_3 g1607 g1607.t6 TSS g1607.t6 12101603 12101603
chr_3 g1607 g1607.t6 TTS g1607.t6 NA NA

Sequences

>g1607.t6 Gene=g1607 Length=590
ATGAGTGAAAACGTACATGACGGCGAATGCAGCAATGCTCAAATGGAAAATTCCGAAATG
AATGGAAATAACGAGCATTATGAAGACAATGGTAATCAAAATGAACAATATGATGATGAT
ATTAAAGAACCAGAATGCACGCGAAAACTTTTTATTGGTGGGCTTGACTATAGAACAACT
GACGAAACATTAAAGAGTTATTTTGAAAAATGGGGAAAAATAGTTGATGTAGTTGTAATG
AAAGATCCTAAGACTAAACGTTCACGTGGGTTTGGTTTCATCACTTACTCGCGTTCAAGC
ATGGTTGATGCAGCACAAGCAGCTCGTCCTCATAAAATTGACTCTCGTACTGTTGAACCA
AAACGTGCGGTGCCTAGAAATGATATTAATCGCCCGGAGGCGGGTTCTTCTGTGAAGAAA
CTGTTTGTTGGAGGCCTTAAAGACGACTTTGAAGAAGAAGATTTGCGTGAATATTTCTCA
CAATTTGGAAATATCACATCTGTAATCATTGTTAGTGATAAAGAAAGTGGAAAAAAACGT
GGATTTGGATTCGTTGAATATGACGATTATGATCCTGTTGATAAAATTTG

>g1607.t6 Gene=g1607 Length=196
MSENVHDGECSNAQMENSEMNGNNEHYEDNGNQNEQYDDDIKEPECTRKLFIGGLDYRTT
DETLKSYFEKWGKIVDVVVMKDPKTKRSRGFGFITYSRSSMVDAAQAARPHKIDSRTVEP
KRAVPRNDINRPEAGSSVKKLFVGGLKDDFEEEDLREYFSQFGNITSVIIVSDKESGKKR
GFGFVEYDDYDPVDKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g1607.t6 CDD cd12578 RRM1_hnRNPA_like 49 126 5.15266E-50
7 g1607.t6 Coils Coil Coil 10 30 -
5 g1607.t6 Gene3D G3DSA:3.30.70.330 - 9 135 2.0E-25
6 g1607.t6 Gene3D G3DSA:3.30.70.330 - 136 196 8.2E-20
11 g1607.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 30 -
12 g1607.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 41 -
3 g1607.t6 PANTHER PTHR48026 HOMOLOGOUS TO DROSOPHILA SQD (SQUID) PROTEIN 29 196 1.6E-65
1 g1607.t6 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 50 116 2.9E-16
2 g1607.t6 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 141 194 4.5E-15
14 g1607.t6 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 48 125 15.75
13 g1607.t6 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 139 196 16.602
9 g1607.t6 SMART SM00360 rrm1_1 49 121 6.0E-23
10 g1607.t6 SMART SM00360 rrm1_1 140 196 3.4E-6
4 g1607.t6 SUPERFAMILY SSF54928 RNA-binding domain, RBD 46 195 3.8E-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:0003676 nucleic acid binding MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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