Gene loci information

Transcript annotation

  • This transcript has been annotated as Poly(U)-binding-splicing factor half pint.

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 g1138 g1138.t5 isoform g1138.t5 8377916 8381516
chr_3 g1138 g1138.t5 exon g1138.t5.exon1 8377916 8378082
chr_3 g1138 g1138.t5 exon g1138.t5.exon2 8379578 8379860
chr_3 g1138 g1138.t5 cds g1138.t5.CDS1 8379745 8379860
chr_3 g1138 g1138.t5 exon g1138.t5.exon3 8380086 8380666
chr_3 g1138 g1138.t5 cds g1138.t5.CDS2 8380086 8380666
chr_3 g1138 g1138.t5 exon g1138.t5.exon4 8380732 8381346
chr_3 g1138 g1138.t5 cds g1138.t5.CDS3 8380732 8381346
chr_3 g1138 g1138.t5 exon g1138.t5.exon5 8381407 8381516
chr_3 g1138 g1138.t5 cds g1138.t5.CDS4 8381407 8381516
chr_3 g1138 g1138.t5 TTS g1138.t5 8381717 8381717
chr_3 g1138 g1138.t5 TSS g1138.t5 NA NA

Sequences

>g1138.t5 Gene=g1138 Length=1756
CTTTCTCTCAAATTATCAAAATCAATCTTTCAAATTTATAAAACTAAACTGTTCGCGATA
CTATCGTAGTAAAAACAATAGTATGATTACGAAATGTGATTAGGGGCGCAATAATGGACG
ACAAATGTGATGGATTGAGTGCACACACAAACACATAAAAATCATTGATTCATCTTCCTC
CAAGCGTGATTTCAGAAAGGAGCCAATTTACAACATTAAGCAAATAGGTGACGTTTCATT
TGGTCCGGGTACCCGTTCTGCTGTTTTTGGTGGTGGTTTACCGCAATTGAACAGTGAACA
AAAGGATACTGTAAAGAAGGCGAAAAAATATGCAATGGAACAAAGTATTAGAATGGTTCT
CATGAAACAAACACTTGCACACCAACAACAACAATTAGCAAGTCAAAGAACTCAAGTTCA
AAGGCAGCAAGCACTTGCTCTTATGTGCAGAGTCTATGTTGGGAGTATTTCATTTGAACT
TAAAGAAGATACAATTCGTGCAGCGTTTCTTCCTTTTGGTCCAATCAAATCAATCAATAT
GTCTTGGGATCCTGTGACACAAAAACATAAAGGATTTGCTTTTGTTGAATATGAGATTCC
TGAAGGAGCTCAACTTGCTTTAGAACAAATGAATGGAGCAATGTTAGGTGGAAGAAACAT
CAAAGTGGGAAGACCAAGTAACATGCCTCAGGCACAACAAGTGATTGATGAAATTCAAGA
GGAAGCCAAAAATTATAATCGTATTTACATCGCATCAATTCATCCAGAATTGACTGAAGA
GGATATTAAAAGTGTATTCGAAGCGTTTGGTGCGATTGTTTTCTGCAAATTAGCGCAAGG
CACATCACCTGGAAGTCATAAAGGATATGGCTTTATTGAATACAATACAAACCAAGCAGC
TCTCGAATCAATCGCAAGTATGAATCTATTTGACTTGGGAGGACAATTATTAAGAGTAGG
CAGGGCAATCACACCACCCAATGCTTTAGTTAGTCCTGCAGTAAATTCTTCAATGCCAAC
TGCAGCTGCTGTTGCTGCAGCTGCAGCTACCGCAAAAATTCAAGCAATGGATGCTGTGCA
AGCGAATGTTCTTGGTGCAGCAGCTCCCACACTTGGTTTGAAAACTCTTGCAGCATCAAC
TCCCGCAGTAACTCTTCCAACTCCAATTGTAACTCAAACAACAATTACTCCACCTGTCGT
ACTTCCCGTAGCAGCAGTGCTTCAACAAAGTCACATCACACCAATTGGCGTCTCTACAAA
TTTACCTTCATTGATATCAAATGAAACACAACAGAATGCAGAAGAATTGGTAAAACAAAA
ACAAGAAGAATTACAAAAGAAATTATTAGAAGAGGGTGAACCAACTTTACAACAACAAGA
ATCAATGTCCATCAAAGGTCAAAATGCAAGACATTTAGTCATGCAAAGACTTATGAGACC
ACGTGAAAGTAAAGTTGTAATTTTAAGAAATATGGTTGGACCTGAAGATGTTGATGAGAC
ACTTCAAGAAGAAATTCAAGATGAATGCAGTAAATATGGTGTTGTAGAGAAAGTTATTAT
TTATAAAGAGAAACAAACTGACAATGATGATGACGATTATGGTGATGTTATTGTAAAAAT
TTTCGTAGAATTTTCGATGTCATCTGAAGCTGACAAGGCAAGTTCTGGTTTAAATGGTCG
ATTTTTTGGAGGACGATTGGTTAAAGCTGAGAGCTACGACCAAGCACTTTTTGACCACAG
TGACTTTTCTGGTTGA

>g1138.t5 Gene=g1138 Length=473
MEQSIRMVLMKQTLAHQQQQLASQRTQVQRQQALALMCRVYVGSISFELKEDTIRAAFLP
FGPIKSINMSWDPVTQKHKGFAFVEYEIPEGAQLALEQMNGAMLGGRNIKVGRPSNMPQA
QQVIDEIQEEAKNYNRIYIASIHPELTEEDIKSVFEAFGAIVFCKLAQGTSPGSHKGYGF
IEYNTNQAALESIASMNLFDLGGQLLRVGRAITPPNALVSPAVNSSMPTAAAVAAAAATA
KIQAMDAVQANVLGAAAPTLGLKTLAASTPAVTLPTPIVTQTTITPPVVLPVAAVLQQSH
ITPIGVSTNLPSLISNETQQNAEELVKQKQEELQKKLLEEGEPTLQQQESMSIKGQNARH
LVMQRLMRPRESKVVILRNMVGPEDVDETLQEEIQDECSKYGVVEKVIIYKEKQTDNDDD
DYGDVIVKIFVEFSMSSEADKASSGLNGRFFGGRLVKAESYDQALFDHSDFSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1138.t5 CDD cd12370 RRM1_PUF60 38 113 6.23302E-54
12 g1138.t5 CDD cd12371 RRM2_PUF60 135 211 2.18676E-45
11 g1138.t5 Coils Coil Coil 117 137 -
10 g1138.t5 Coils Coil Coil 315 339 -
8 g1138.t5 Gene3D G3DSA:3.30.70.330 - 26 134 1.6E-30
7 g1138.t5 Gene3D G3DSA:3.30.70.330 - 135 228 1.8E-17
9 g1138.t5 Gene3D G3DSA:3.30.70.330 - 372 462 1.6E-26
3 g1138.t5 PANTHER PTHR47330 POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED 1 473 1.0E-214
4 g1138.t5 PANTHER PTHR47330:SF1 POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED 1 473 1.0E-214
1 g1138.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 40 110 2.2E-18
2 g1138.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 137 206 6.7E-12
22 g1138.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 38 116 17.353
21 g1138.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 135 213 15.221
23 g1138.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 373 463 9.729
14 g1138.t5 SMART SM00361 rrm2_1 39 112 0.28
17 g1138.t5 SMART SM00360 rrm1_1 39 112 5.2E-24
16 g1138.t5 SMART SM00361 rrm2_1 136 209 11.0
19 g1138.t5 SMART SM00360 rrm1_1 136 209 9.7E-16
15 g1138.t5 SMART SM00361 rrm2_1 374 459 8.6E-14
18 g1138.t5 SMART SM00360 rrm1_1 374 459 0.02
5 g1138.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 17 117 2.42E-25
6 g1138.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 134 459 1.99E-25
20 g1138.t5 TIGRFAM TIGR01645 half-pint: poly-U binding splicing factor, half-pint family 1 291 5.1E-149

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