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.t16 TSS g1159.t16 8422719 8422719
chr_3 g1159 g1159.t16 isoform g1159.t16 8422830 8431593
chr_3 g1159 g1159.t16 exon g1159.t16.exon1 8422830 8422957
chr_3 g1159 g1159.t16 cds g1159.t16.CDS1 8422830 8422957
chr_3 g1159 g1159.t16 exon g1159.t16.exon2 8426427 8426467
chr_3 g1159 g1159.t16 cds g1159.t16.CDS2 8426427 8426467
chr_3 g1159 g1159.t16 exon g1159.t16.exon3 8426535 8426809
chr_3 g1159 g1159.t16 cds g1159.t16.CDS3 8426535 8426809
chr_3 g1159 g1159.t16 exon g1159.t16.exon4 8426874 8427099
chr_3 g1159 g1159.t16 cds g1159.t16.CDS4 8426874 8427099
chr_3 g1159 g1159.t16 exon g1159.t16.exon5 8427224 8427409
chr_3 g1159 g1159.t16 cds g1159.t16.CDS5 8427224 8427409
chr_3 g1159 g1159.t16 exon g1159.t16.exon6 8430900 8431131
chr_3 g1159 g1159.t16 cds g1159.t16.CDS6 8430900 8430994
chr_3 g1159 g1159.t16 exon g1159.t16.exon7 8431212 8431593
chr_3 g1159 g1159.t16 TTS g1159.t16 8431937 8431937

Sequences

>g1159.t16 Gene=g1159 Length=1470
ATGGCTGATGTACAAGAATACGATAACGGCGAACAAATGCAAGAAGATTTCCAGGGACAA
GGTGATCAATCTGGAGATAGTAACTATCAAAACGGAAATGGAGAAACTCAAGCTCGCGAT
GACGATCGAAAGCTGTTTGTCGGTGGTTTAAGTTGGGAAACAACAGAAAAGGAATTGCGT
GATCATTTTGGACAATATGGTGAAATTGACAGCATCAATGTTAAAACAGATCCTACAACT
GGTCGCTCACGTGGATTTGCATTCATTGTTTATAAAGCAGCTGATTCAATTGATAAAGTT
GTCGCTGCTGGTGATCATATCATTAACAACAAGAAAGTTGATCCTAAAAAAGCCAAGGCA
AGAACTGGCAAAATCTTTGTCGGTGGACTCATTCCAGAAATTAGTGATGATGAAATCAAG
GCATATTTCTCACAATTTGGAAATATTACTGAAATGGAAATGCCATTCGATAAGCAAAAG
AATCAACGTAAAGCTTTCTGCTTTATCACTTTTGACTCGGAAGCTGTTGTCAATGAATTA
TTAAAGTCTCCAAAACAAACAATCAGTGGAAAGGAAGTTGATGTCAAAAAAGCCACGCCA
AAACCAGATAATGCTCCAATGATGCAACGTGGTGGAGGACGAAATATGAGAGGTGGACGA
GGAGGACGCGGATTTCAAGGAAATTGGAACGGATATGGAGGTGGTTATGGCCAAAACGGC
TGGAACCAAGGCGGAGGCAGTTGGGGTGGAAACAACTATGACAATTATCAGGGTGGTTAT
GGTGGTAGTGGTGTTGATTATCAGGGTAACTATGGCGGATACAACAATTATGATTATGGA
AATTACGGCGGCAGCGAAATTAGGCGGAAACTACCAAGGTGGAAAACAAAGAGGTGGTGG
GCGTCAACAAAGACATCAACCATATTAAGCCATTTTTCTTGGATTAAGTAAAAATACAAA
CAACTCATCCATCTCATTCACTCATTGAAATCCTTAATTGTATTTTTTGAACATAAATTA
TAATATCGACCGTGTCTTCAAAATGAAAAAGAATATTAAACAATAGCAGCAAAAACCAAT
CAAGAAAAACTCTCATCAAATGTTGAATTTATATATGCGTATATAAAATTCTCACATACC
ATCATCAACAATAAATAAGATTTACAAGAACAACTCATTTTAATATACATTGTTGTATGG
GCGATTCATTCCACATTAAATACACACACAAACAAACCATTTTTTACATTACTAAATAAA
TCAGAAGGAAATGTAAATTTTTAATATTCTCTCTATCTCTCATTGTTCTGTATATTTTGA
CTGAATTTTTTTTTCTTTTTAATTTCTATTTGTGAGATACTTATGAGAAAGGATAGTATG
TAATTAAAACAATCAACATTTGAAATATCTTTAGCATTCAAAGACGACCTCGATATATAA
GATCTTTAACATCAAAAAACAACCCTCCTC

>g1159.t16 Gene=g1159 Length=316
MADVQEYDNGEQMQEDFQGQGDQSGDSNYQNGNGETQARDDDRKLFVGGLSWETTEKELR
DHFGQYGEIDSINVKTDPTTGRSRGFAFIVYKAADSIDKVVAAGDHIINNKKVDPKKAKA
RTGKIFVGGLIPEISDDEIKAYFSQFGNITEMEMPFDKQKNQRKAFCFITFDSEAVVNEL
LKSPKQTISGKEVDVKKATPKPDNAPMMQRGGGRNMRGGRGGRGFQGNWNGYGGGYGQNG
WNQGGGSWGGNNYDNYQGGYGGSGVDYQGNYGGYNNYDYGNYGGSEIRRKLPRWKTKRWW
ASTKTSTILSHFSWIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1159.t16 CDD cd12325 RRM1_hnRNPA_hnRNPD_like 45 116 6.76871E-37
9 g1159.t16 CDD cd12329 RRM2_hnRNPD_like 124 198 2.94918E-38
7 g1159.t16 Gene3D G3DSA:3.30.70.330 - 37 115 8.7E-25
8 g1159.t16 Gene3D G3DSA:3.30.70.330 - 116 231 1.4E-21
14 g1159.t16 MobiDBLite mobidb-lite consensus disorder prediction 1 42 -
13 g1159.t16 MobiDBLite mobidb-lite consensus disorder prediction 11 35 -
15 g1159.t16 MobiDBLite mobidb-lite consensus disorder prediction 192 219 -
3 g1159.t16 PANTHER PTHR48033:SF8 RNA-BINDING PROTEIN SQUID 9 284 3.9E-106
4 g1159.t16 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 9 284 3.9E-106
2 g1159.t16 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 45 111 3.5E-17
1 g1159.t16 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 125 192 3.9E-12
16 g1159.t16 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 43 125 17.097
17 g1159.t16 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 123 200 14.812
12 g1159.t16 SMART SM00360 rrm1_1 44 116 8.1E-24
11 g1159.t16 SMART SM00360 rrm1_1 124 196 2.2E-16
5 g1159.t16 SUPERFAMILY SSF54928 RNA-binding domain, RBD 40 122 9.27E-25
6 g1159.t16 SUPERFAMILY SSF54928 RNA-binding domain, RBD 119 228 2.85E-19

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