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.t1 TTS g6001.t1 13448960 13448960
chr_2 g6001 g6001.t1 isoform g6001.t1 13449151 13450370
chr_2 g6001 g6001.t1 exon g6001.t1.exon1 13449151 13449396
chr_2 g6001 g6001.t1 cds g6001.t1.CDS1 13449151 13449396
chr_2 g6001 g6001.t1 exon g6001.t1.exon2 13449456 13450370
chr_2 g6001 g6001.t1 cds g6001.t1.CDS2 13449456 13450370
chr_2 g6001 g6001.t1 TSS g6001.t1 13450637 13450637

Sequences

>g6001.t1 Gene=g6001 Length=1161
ATGACTGAAAAAGTTGAAACTGTTGCAAACCAAGGAGGACAAGAAGATAAGAATGATGGT
GATCATTCACAGACAGATCTTACACAGCTTGAACTCGACATTATCAAACAAATTGAATAT
TACTTTGGAGAAAGTAATTTAAGACGTGATAAATTTTTAAACAGCAAAATTGCAGAGGAC
AAAGATGGATGGGTTCCGATTAGCGTTTTGCTTACTTTTAATCGTTTAAAAGCCCTTACA
GAGGATGCAAATGTCATTGCTGAAAGTGTTGATAAATCTTCAAATGGATTAGTACAAGTC
AGTGAAGATAAACAGAAAATTCGTCGTCATCCCGAAAATCCATTACCTGAATTTAATGAA
GAACGCCGAAAAGAATTACAAGCTAGAACTGCATATGCAAAAGGATTTCCACTTGATTCA
ACTATGAATACACTTCTTGAATATTTCAAAAACAATTTTGATAAAGTTGAAAACGTCATG
ATGAGAAAATATTATTGCCCTAAAACAAAAGTATACCTTTTTAAAGGTTCTGTTTATGTT
CTTTTTTCTAATAAAGAAAATGCTGAAGAATTTGTACAGCGACCAGATTTAAAATATGGC
GAAAAAGACTTGTTGCGTTATATGCAAAAGGATTATTTAGAAAAGAAGAAAACTGAAAAA
TCAAAGTATGACAAGAAACAAAAGAAAAAGGAAGAAGATAAAGATGAAATTGTATTGCCT
AAGAACGCAGTTATTCATTTTACCGGAGTGGAAGGTGATATTATGAGAGAGGATATTAAG
AAAAGAGTCTTGGAAATCGATCCATCACTTGTTATTGCATTCGTTCATTTTGAACGTGGA
GCTAAAGAAGGTCAATTACGATTCTCAAAAGAAGATGATGGTAAAAAGTTTTTGGAAAAA
CTTGAAAATGGAAAGATGAAACTTAAAGAATTGGAACTTACAATGTCACTTGTTGAAGGT
GAACAAGAGGAGACATTCTTGAAAGAAGCAATTGAAGATATGAGGAAAGCTCGTCAACGT
GGACAACAAAAGAATAACAAAGGTCGTAAAGGTGGTGGAAAGAACGATCGTAAGCGTAAA
CATGAAAATGAAAGTGAAGATGTACCAACTAAGCAAACTAAAGTCGATGAGGAACCTTCT
GTTGTAACTGTAGCTGAATAA

>g6001.t1 Gene=g6001 Length=386
MTEKVETVANQGGQEDKNDGDHSQTDLTQLELDIIKQIEYYFGESNLRRDKFLNSKIAED
KDGWVPISVLLTFNRLKALTEDANVIAESVDKSSNGLVQVSEDKQKIRRHPENPLPEFNE
ERRKELQARTAYAKGFPLDSTMNTLLEYFKNNFDKVENVMMRKYYCPKTKVYLFKGSVYV
LFSNKENAEEFVQRPDLKYGEKDLLRYMQKDYLEKKKTEKSKYDKKQKKKEEDKDEIVLP
KNAVIHFTGVEGDIMREDIKKRVLEIDPSLVIAFVHFERGAKEGQLRFSKEDDGKKFLEK
LENGKMKLKELELTMSLVEGEQEETFLKEAIEDMRKARQRGQQKNNKGRKGGGKNDRKRK
HENESEDVPTKQTKVDEEPSVVTVAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g6001.t1 CDD cd12291 RRM1_La 130 206 2.32118E-17
16 g6001.t1 Coils Coil Coil 213 236 -
17 g6001.t1 Coils Coil Coil 327 347 -
15 g6001.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 17 108 1.4E-29
14 g6001.t1 Gene3D G3DSA:3.30.70.330 - 118 214 2.7E-13
13 g6001.t1 Gene3D G3DSA:3.30.70.330 - 215 348 2.6E-20
22 g6001.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
20 g6001.t1 MobiDBLite mobidb-lite consensus disorder prediction 329 386 -
21 g6001.t1 MobiDBLite mobidb-lite consensus disorder prediction 341 356 -
23 g6001.t1 MobiDBLite mobidb-lite consensus disorder prediction 357 374 -
3 g6001.t1 PANTHER PTHR22792 LUPUS LA PROTEIN-RELATED 30 367 3.3E-58
4 g6001.t1 PANTHER PTHR22792:SF140 LUPUS LA PROTEIN HOMOLOG 30 367 3.3E-58
7 g6001.t1 PRINTS PR00302 Lupus La protein signature 37 54 1.3E-33
8 g6001.t1 PRINTS PR00302 Lupus La protein signature 63 78 1.3E-33
5 g6001.t1 PRINTS PR00302 Lupus La protein signature 96 109 1.3E-33
9 g6001.t1 PRINTS PR00302 Lupus La protein signature 123 139 1.3E-33
6 g6001.t1 PRINTS PR00302 Lupus La protein signature 174 192 1.3E-33
2 g6001.t1 Pfam PF05383 La domain 34 90 2.0E-22
1 g6001.t1 Pfam PF08777 RNA binding motif 244 349 3.3E-20
24 g6001.t1 ProSiteProfiles PS50961 La-type HTH domain profile. 24 117 27.492
25 g6001.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 129 226 8.876
19 g6001.t1 SMART SM00715 la 28 110 6.9E-36
12 g6001.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 26 120 2.9E-26
11 g6001.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 121 206 2.74E-8
10 g6001.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 239 342 8.21E-5

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.

Raw TPM values