Gene loci information

Transcript annotation

  • This transcript has been annotated as RNA-binding protein squid.

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 g1159 g1159.t9 TSS g1159.t9 8422719 8422719
chr_3 g1159 g1159.t9 isoform g1159.t9 8422830 8427421
chr_3 g1159 g1159.t9 exon g1159.t9.exon1 8422830 8422957
chr_3 g1159 g1159.t9 cds g1159.t9.CDS1 8422830 8422957
chr_3 g1159 g1159.t9 exon g1159.t9.exon2 8426427 8426467
chr_3 g1159 g1159.t9 cds g1159.t9.CDS2 8426427 8426467
chr_3 g1159 g1159.t9 exon g1159.t9.exon3 8426535 8426809
chr_3 g1159 g1159.t9 cds g1159.t9.CDS3 8426535 8426809
chr_3 g1159 g1159.t9 exon g1159.t9.exon4 8426874 8427099
chr_3 g1159 g1159.t9 cds g1159.t9.CDS4 8426874 8427099
chr_3 g1159 g1159.t9 exon g1159.t9.exon5 8427224 8427421
chr_3 g1159 g1159.t9 cds g1159.t9.CDS5 8427224 8427420
chr_3 g1159 g1159.t9 TTS g1159.t9 8427624 8427624

Sequences

>g1159.t9 Gene=g1159 Length=868
ATGGCTGATGTACAAGAATACGATAACGGCGAACAAATGCAAGAAGATTTCCAGGGACAA
GGTGATCAATCTGGAGATAGTAACTATCAAAACGGAAATGGAGAAACTCAAGCTCGCGAT
GACGATCGAAAGCTGTTTGTCGGTGGTTTAAGTTGGGAAACAACAGAAAAGGAATTGCGT
GATCATTTTGGACAATATGGTGAAATTGACAGCATCAATGTTAAAACAGATCCTACAACT
GGTCGCTCACGTGGATTTGCATTCATTGTTTATAAAGCAGCTGATTCAATTGATAAAGTT
GTCGCTGCTGGTGATCATATCATTAACAACAAGAAAGTTGATCCTAAAAAAGCCAAGGCA
AGAACTGGCAAAATCTTTGTCGGTGGACTCATTCCAGAAATTAGTGATGATGAAATCAAG
GCATATTTCTCACAATTTGGAAATATTACTGAAATGGAAATGCCATTCGATAAGCAAAAG
AATCAACGTAAAGCTTTCTGCTTTATCACTTTTGACTCGGAAGCTGTTGTCAATGAATTA
TTAAAGTCTCCAAAACAAACAATCAGTGGAAAGGAAGTTGATGTCAAAAAAGCCACGCCA
AAACCAGATAATGCTCCAATGATGCAACGTGGTGGAGGACGAAATATGAGAGGTGGACGA
GGAGGACGCGGATTTCAAGGAAATTGGAACGGATATGGAGGTGGTTATGGCCAAAACGGC
TGGAACCAAGGCGGAGGCAGTTGGGGTGGAAACAACTATGACAATTATCAGGGTGGTTAT
GGTGGTAGTGGTGTTGATTATCAGGGTAACTATGGCGGATACAACAATTATGATTATGGA
AATTACGGCGGCAGCGGTGGCAATTATG

>g1159.t9 Gene=g1159 Length=289
MADVQEYDNGEQMQEDFQGQGDQSGDSNYQNGNGETQARDDDRKLFVGGLSWETTEKELR
DHFGQYGEIDSINVKTDPTTGRSRGFAFIVYKAADSIDKVVAAGDHIINNKKVDPKKAKA
RTGKIFVGGLIPEISDDEIKAYFSQFGNITEMEMPFDKQKNQRKAFCFITFDSEAVVNEL
LKSPKQTISGKEVDVKKATPKPDNAPMMQRGGGRNMRGGRGGRGFQGNWNGYGGGYGQNG
WNQGGGSWGGNNYDNYQGGYGGSGVDYQGNYGGYNNYDYGNYGGSGGNY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1159.t9 CDD cd12325 RRM1_hnRNPA_hnRNPD_like 45 116 6.8517E-37
8 g1159.t9 Gene3D G3DSA:3.30.70.330 - 30 118 4.8E-25
7 g1159.t9 Gene3D G3DSA:3.30.70.330 - 119 231 1.3E-21
13 g1159.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 42 -
12 g1159.t9 MobiDBLite mobidb-lite consensus disorder prediction 11 35 -
14 g1159.t9 MobiDBLite mobidb-lite consensus disorder prediction 192 219 -
3 g1159.t9 PANTHER PTHR48033:SF8 RNA-BINDING PROTEIN SQUID 9 287 5.9E-106
4 g1159.t9 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 9 287 5.9E-106
2 g1159.t9 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 45 111 3.0E-17
1 g1159.t9 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 125 192 3.4E-12
15 g1159.t9 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 43 125 17.097
16 g1159.t9 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 123 200 14.812
11 g1159.t9 SMART SM00360 rrm1_1 44 116 8.1E-24
10 g1159.t9 SMART SM00360 rrm1_1 124 196 2.2E-16
5 g1159.t9 SUPERFAMILY SSF54928 RNA-binding domain, RBD 40 122 6.58E-25
6 g1159.t9 SUPERFAMILY SSF54928 RNA-binding domain, RBD 115 228 3.12E-24

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

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