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.t18 TSS g1159.t18 8422719 8422719
chr_3 g1159 g1159.t18 isoform g1159.t18 8422830 8431942
chr_3 g1159 g1159.t18 exon g1159.t18.exon1 8422830 8422957
chr_3 g1159 g1159.t18 cds g1159.t18.CDS1 8422830 8422957
chr_3 g1159 g1159.t18 exon g1159.t18.exon2 8426427 8426467
chr_3 g1159 g1159.t18 cds g1159.t18.CDS2 8426427 8426467
chr_3 g1159 g1159.t18 exon g1159.t18.exon3 8426535 8426809
chr_3 g1159 g1159.t18 cds g1159.t18.CDS3 8426535 8426809
chr_3 g1159 g1159.t18 exon g1159.t18.exon4 8426874 8427099
chr_3 g1159 g1159.t18 cds g1159.t18.CDS4 8426874 8427099
chr_3 g1159 g1159.t18 exon g1159.t18.exon5 8427233 8427421
chr_3 g1159 g1159.t18 cds g1159.t18.CDS5 8427233 8427421
chr_3 g1159 g1159.t18 exon g1159.t18.exon6 8430922 8431131
chr_3 g1159 g1159.t18 cds g1159.t18.CDS6 8430922 8430971
chr_3 g1159 g1159.t18 exon g1159.t18.exon7 8431212 8431942
chr_3 g1159 g1159.t18 TTS g1159.t18 8431937 8431937

Sequences

>g1159.t18 Gene=g1159 Length=1800
ATGGCTGATGTACAAGAATACGATAACGGCGAACAAATGCAAGAAGATTTCCAGGGACAA
GGTGATCAATCTGGAGATAGTAACTATCAAAACGGAAATGGAGAAACTCAAGCTCGCGAT
GACGATCGAAAGCTGTTTGTCGGTGGTTTAAGTTGGGAAACAACAGAAAAGGAATTGCGT
GATCATTTTGGACAATATGGTGAAATTGACAGCATCAATGTTAAAACAGATCCTACAACT
GGTCGCTCACGTGGATTTGCATTCATTGTTTATAAAGCAGCTGATTCAATTGATAAAGTT
GTCGCTGCTGGTGATCATATCATTAACAACAAGAAAGTTGATCCTAAAAAAGCCAAGGCA
AGAACTGGCAAAATCTTTGTCGGTGGACTCATTCCAGAAATTAGTGATGATGAAATCAAG
GCATATTTCTCACAATTTGGAAATATTACTGAAATGGAAATGCCATTCGATAAGCAAAAG
AATCAACGTAAAGCTTTCTGCTTTATCACTTTTGACTCGGAAGCTGTTGTCAATGAATTA
TTAAAGTCTCCAAAACAAACAATCAGTGGAAAGGAAGTTGATGTCAAAAAAGCCACGCCA
AAACCAGATAATGCTCCAATGATGCAACGTGGTGGAGGACGAAATATGAGAGGTGGACGA
GGAGGACGCGGAAATTGGAACGGATATGGAGGTGGTTATGGCCAAAACGGCTGGAACCAA
GGCGGAGGCAGTTGGGGTGGAAACAACTATGACAATTATCAGGGTGGTTATGGTGGTAGT
GGTGTTGATTATCAGGGTAACTATGGCGGATACAACAATTATGATTATGGAAATTACGGC
GGCAGCGGTGGCAATTATGGTGGAAAACAAAGAGGTGGTGGGCGTCAACAAAGACATCAA
CCATATTAAGCCATTTTTCTTGGATTAAGTAAAAATACAAACAACTCATCCATCTCATTC
ACTCATTGAAATCCTTAATTGTATTTTTTGAACATAAATTATAATATCGACCGTGTCTTC
AAAATGAAAAAGAATATTAAACAATAGCAGCAAAAACCAATCAAGAAAAACTCTCATCAA
ATGTTGAATTTATATATGCGTATATAAAATTCTCACATACCATCATCAACAATAAATAAG
ATTTACAAGAACAACTCATTTTAATATACATTGTTGTATGGGCGATTCATTCCACATTAA
ATACACACACAAACAAACCATTTTTTACATTACTAAATAAATCAGAAGGAAATGTAAATT
TTTAATATTCTCTCTATCTCTCATTGTTCTGTATATTTTGACTGAATTTTTTTTTCTTTT
TAATTTCTATTTGTGAGATACTTATGAGAAAGGATAGTATGTAATTAAAACAATCAACAT
TTGAAATATCTTTAGCATTCAAAGACGACCTCGATATATAAGATCTTTAACATCAAAAAA
CAACCCTCCTCATACATAATTTTTTTATCCCTCTGATTTTCTTCATTAATGTCTTGCATT
CATAAATTAATAGCTTTTTGATTTTAAAAAATTTTTCTTACTCAATAATTGAGTTGACTA
AAAACACAAACAAATAGTACGGTTTTCGATTATTGAAGAAGGAAAATGAGTATATAAAAT
TTATAATTCTCTCATCAATTAAATTTATTACACAAAAATAGTAATTTAAATGATAAAAAG
AATAATTACAGTAGCGTTAATTCACTTGATAACTTTATAAAGAAAATAACTATTTTTAAT
CATCATTTCTAAGGATAAAAATTAATAAAACCTCTTATAAGATTAAATTTAAAACAAAAA

>g1159.t18 Gene=g1159 Length=302
MADVQEYDNGEQMQEDFQGQGDQSGDSNYQNGNGETQARDDDRKLFVGGLSWETTEKELR
DHFGQYGEIDSINVKTDPTTGRSRGFAFIVYKAADSIDKVVAAGDHIINNKKVDPKKAKA
RTGKIFVGGLIPEISDDEIKAYFSQFGNITEMEMPFDKQKNQRKAFCFITFDSEAVVNEL
LKSPKQTISGKEVDVKKATPKPDNAPMMQRGGGRNMRGGRGGRGNWNGYGGGYGQNGWNQ
GGGSWGGNNYDNYQGGYGGSGVDYQGNYGGYNNYDYGNYGGSGGNYGGKQRGGGRQQRHQ
PY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1159.t18 CDD cd12325 RRM1_hnRNPA_hnRNPD_like 45 116 5.1476E-37
9 g1159.t18 CDD cd12329 RRM2_hnRNPD_like 124 198 6.10367E-38
8 g1159.t18 Gene3D G3DSA:3.30.70.330 - 30 118 5.2E-25
7 g1159.t18 Gene3D G3DSA:3.30.70.330 - 119 229 1.5E-21
15 g1159.t18 MobiDBLite mobidb-lite consensus disorder prediction 1 42 -
14 g1159.t18 MobiDBLite mobidb-lite consensus disorder prediction 11 35 -
13 g1159.t18 MobiDBLite mobidb-lite consensus disorder prediction 192 220 -
3 g1159.t18 PANTHER PTHR48033:SF8 RNA-BINDING PROTEIN SQUID 9 302 3.2E-109
4 g1159.t18 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 9 302 3.2E-109
2 g1159.t18 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 45 111 3.3E-17
1 g1159.t18 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 125 192 3.6E-12
16 g1159.t18 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 43 125 17.097
17 g1159.t18 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 123 200 14.812
12 g1159.t18 SMART SM00360 rrm1_1 44 116 8.1E-24
11 g1159.t18 SMART SM00360 rrm1_1 124 196 2.2E-16
6 g1159.t18 SUPERFAMILY SSF54928 RNA-binding domain, RBD 40 122 8.6E-25
5 g1159.t18 SUPERFAMILY SSF54928 RNA-binding domain, RBD 116 232 3.94E-25

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