Gene loci information

Transcript annotation

  • This transcript has been annotated as La protein-like protein.

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_2 g6001 g6001.t5 TTS g6001.t5 13448960 13448960
chr_2 g6001 g6001.t5 isoform g6001.t5 13449471 13450575
chr_2 g6001 g6001.t5 exon g6001.t5.exon1 13449471 13450394
chr_2 g6001 g6001.t5 cds g6001.t5.CDS1 13449471 13450370
chr_2 g6001 g6001.t5 exon g6001.t5.exon2 13450568 13450575
chr_2 g6001 g6001.t5 TSS g6001.t5 13450637 13450637

Sequences

>g6001.t5 Gene=g6001 Length=932
ATTAGAAGAAATAAACACAAAAAAGCGTCATAATGACTGAAAAAGTTGAAACTGTTGCAA
ACCAAGGAGGACAAGAAGATAAGAATGATGGTGATCATTCACAGACAGATCTTACACAGC
TTGAACTCGACATTATCAAACAAATTGAATATTACTTTGGAGAAAGTAATTTAAGACGTG
ATAAATTTTTAAACAGCAAAATTGCAGAGGACAAAGATGGATGGGTTCCGATTAGCGTTT
TGCTTACTTTTAATCGTTTAAAAGCCCTTACAGAGGATGCAAATGTCATTGCTGAAAGTG
TTGATAAATCTTCAAATGGATTAGTACAAGTCAGTGAAGATAAACAGAAAATTCGTCGTC
ATCCCGAAAATCCATTACCTGAATTTAATGAAGAACGCCGAAAAGAATTACAAGCTAGAA
CTGCATATGCAAAAGGATTTCCACTTGATTCAACTATGAATACACTTCTTGAATATTTCA
AAAACAATTTTGATAAAGTTGAAAACGTCATGATGAGAAAATATTATTGCCCTAAAACAA
AAGTATACCTTTTTAAAGGTTCTGTTTATGTTCTTTTTTCTAATAAAGAAAATGCTGAAG
AATTTGTACAGCGACCAGATTTAAAATATGGCGAAAAAGACTTGTTGCGTTATATGCAAA
AGGATTATTTAGAAAAGAAGAAAACTGAAAAATCAAAGTATGACAAGAAACAAAAGAAAA
AGGAAGAAGATAAAGATGAAATTGTATTGCCTAAGAACGCAGTTATTCATTTTACCGGAG
TGGAAGGTGATATTATGAGAGAGGATATTAAGAAAAGAGTCTTGGAAATCGATCCATCAC
TTGTTATTGCATTCGTTCATTTTGAACGTGGAGCTAAAGAAGGTCAATTACGATTCTCAA
AAGAAGATGATGGTAAAAAGTTTTTGGAAAAA

>g6001.t5 Gene=g6001 Length=300
MTEKVETVANQGGQEDKNDGDHSQTDLTQLELDIIKQIEYYFGESNLRRDKFLNSKIAED
KDGWVPISVLLTFNRLKALTEDANVIAESVDKSSNGLVQVSEDKQKIRRHPENPLPEFNE
ERRKELQARTAYAKGFPLDSTMNTLLEYFKNNFDKVENVMMRKYYCPKTKVYLFKGSVYV
LFSNKENAEEFVQRPDLKYGEKDLLRYMQKDYLEKKKTEKSKYDKKQKKKEEDKDEIVLP
KNAVIHFTGVEGDIMREDIKKRVLEIDPSLVIAFVHFERGAKEGQLRFSKEDDGKKFLEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g6001.t5 CDD cd12291 RRM1_La 130 206 4.79288E-18
15 g6001.t5 Coils Coil Coil 213 236 -
14 g6001.t5 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 17 108 8.8E-30
13 g6001.t5 Gene3D G3DSA:3.30.70.330 - 118 218 1.7E-13
12 g6001.t5 Gene3D G3DSA:3.30.70.330 - 224 300 2.4E-11
18 g6001.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
3 g6001.t5 PANTHER PTHR22792 LUPUS LA PROTEIN-RELATED 30 298 5.9E-49
4 g6001.t5 PANTHER PTHR22792:SF140 LUPUS LA PROTEIN HOMOLOG 30 298 5.9E-49
7 g6001.t5 PRINTS PR00302 Lupus La protein signature 37 54 4.6E-34
8 g6001.t5 PRINTS PR00302 Lupus La protein signature 63 78 4.6E-34
5 g6001.t5 PRINTS PR00302 Lupus La protein signature 96 109 4.6E-34
9 g6001.t5 PRINTS PR00302 Lupus La protein signature 123 139 4.6E-34
6 g6001.t5 PRINTS PR00302 Lupus La protein signature 174 192 4.6E-34
2 g6001.t5 Pfam PF05383 La domain 34 90 1.3E-22
1 g6001.t5 Pfam PF08777 RNA binding motif 244 300 3.6E-9
19 g6001.t5 ProSiteProfiles PS50961 La-type HTH domain profile. 24 117 27.492
20 g6001.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 129 226 8.876
17 g6001.t5 SMART SM00715 la 28 110 6.9E-36
11 g6001.t5 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 26 120 1.72E-26
10 g6001.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 121 207 1.65E-8

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:0006396 RNA processing BP
GO:0005634 nucleus CC
GO:0003723 RNA binding MF
GO:1990904 ribonucleoprotein complex CC
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. There were no conditions that were differentially expressed