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.t4 TTS g6001.t4 13448960 13448960
chr_2 g6001 g6001.t4 isoform g6001.t4 13449151 13450575
chr_2 g6001 g6001.t4 exon g6001.t4.exon1 13449151 13449396
chr_2 g6001 g6001.t4 cds g6001.t4.CDS1 13449151 13449396
chr_2 g6001 g6001.t4 exon g6001.t4.exon2 13449471 13450394
chr_2 g6001 g6001.t4 cds g6001.t4.CDS2 13449471 13450370
chr_2 g6001 g6001.t4 exon g6001.t4.exon3 13450568 13450575
chr_2 g6001 g6001.t4 TSS g6001.t4 13450637 13450637

Sequences

>g6001.t4 Gene=g6001 Length=1178
ATTAGAAGAAATAAACACAAAAAAGCGTCATAATGACTGAAAAAGTTGAAACTGTTGCAA
ACCAAGGAGGACAAGAAGATAAGAATGATGGTGATCATTCACAGACAGATCTTACACAGC
TTGAACTCGACATTATCAAACAAATTGAATATTACTTTGGAGAAAGTAATTTAAGACGTG
ATAAATTTTTAAACAGCAAAATTGCAGAGGACAAAGATGGATGGGTTCCGATTAGCGTTT
TGCTTACTTTTAATCGTTTAAAAGCCCTTACAGAGGATGCAAATGTCATTGCTGAAAGTG
TTGATAAATCTTCAAATGGATTAGTACAAGTCAGTGAAGATAAACAGAAAATTCGTCGTC
ATCCCGAAAATCCATTACCTGAATTTAATGAAGAACGCCGAAAAGAATTACAAGCTAGAA
CTGCATATGCAAAAGGATTTCCACTTGATTCAACTATGAATACACTTCTTGAATATTTCA
AAAACAATTTTGATAAAGTTGAAAACGTCATGATGAGAAAATATTATTGCCCTAAAACAA
AAGTATACCTTTTTAAAGGTTCTGTTTATGTTCTTTTTTCTAATAAAGAAAATGCTGAAG
AATTTGTACAGCGACCAGATTTAAAATATGGCGAAAAAGACTTGTTGCGTTATATGCAAA
AGGATTATTTAGAAAAGAAGAAAACTGAAAAATCAAAGTATGACAAGAAACAAAAGAAAA
AGGAAGAAGATAAAGATGAAATTGTATTGCCTAAGAACGCAGTTATTCATTTTACCGGAG
TGGAAGGTGATATTATGAGAGAGGATATTAAGAAAAGAGTCTTGGAAATCGATCCATCAC
TTGTTATTGCATTCGTTCATTTTGAACGTGGAGCTAAAGAAGGTCAATTACGATTCTCAA
AAGAAGATGATGGTAAAAAGTTTTTGGAAAAAATGAAACTTAAAGAATTGGAACTTACAA
TGTCACTTGTTGAAGGTGAACAAGAGGAGACATTCTTGAAAGAAGCAATTGAAGATATGA
GGAAAGCTCGTCAACGTGGACAACAAAAGAATAACAAAGGTCGTAAAGGTGGTGGAAAGA
ACGATCGTAAGCGTAAACATGAAAATGAAAGTGAAGATGTACCAACTAAGCAAACTAAAG
TCGATGAGGAACCTTCTGTTGTAACTGTAGCTGAATAA

>g6001.t4 Gene=g6001 Length=381
MTEKVETVANQGGQEDKNDGDHSQTDLTQLELDIIKQIEYYFGESNLRRDKFLNSKIAED
KDGWVPISVLLTFNRLKALTEDANVIAESVDKSSNGLVQVSEDKQKIRRHPENPLPEFNE
ERRKELQARTAYAKGFPLDSTMNTLLEYFKNNFDKVENVMMRKYYCPKTKVYLFKGSVYV
LFSNKENAEEFVQRPDLKYGEKDLLRYMQKDYLEKKKTEKSKYDKKQKKKEEDKDEIVLP
KNAVIHFTGVEGDIMREDIKKRVLEIDPSLVIAFVHFERGAKEGQLRFSKEDDGKKFLEK
MKLKELELTMSLVEGEQEETFLKEAIEDMRKARQRGQQKNNKGRKGGGKNDRKRKHENES
EDVPTKQTKVDEEPSVVTVAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6001.t4 CDD cd12291 RRM1_La 130 206 2.25209E-17
15 g6001.t4 Coils Coil Coil 213 236 -
16 g6001.t4 Coils Coil Coil 322 342 -
14 g6001.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 17 108 1.4E-29
13 g6001.t4 Gene3D G3DSA:3.30.70.330 - 118 214 2.7E-13
12 g6001.t4 Gene3D G3DSA:3.30.70.330 - 215 343 1.1E-17
22 g6001.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
19 g6001.t4 MobiDBLite mobidb-lite consensus disorder prediction 324 381 -
21 g6001.t4 MobiDBLite mobidb-lite consensus disorder prediction 336 351 -
20 g6001.t4 MobiDBLite mobidb-lite consensus disorder prediction 352 369 -
3 g6001.t4 PANTHER PTHR22792 LUPUS LA PROTEIN-RELATED 30 362 5.5E-56
4 g6001.t4 PANTHER PTHR22792:SF140 LUPUS LA PROTEIN HOMOLOG 30 362 5.5E-56
7 g6001.t4 PRINTS PR00302 Lupus La protein signature 37 54 1.2E-33
8 g6001.t4 PRINTS PR00302 Lupus La protein signature 63 78 1.2E-33
5 g6001.t4 PRINTS PR00302 Lupus La protein signature 96 109 1.2E-33
9 g6001.t4 PRINTS PR00302 Lupus La protein signature 123 139 1.2E-33
6 g6001.t4 PRINTS PR00302 Lupus La protein signature 174 192 1.2E-33
2 g6001.t4 Pfam PF05383 La domain 34 90 1.9E-22
1 g6001.t4 Pfam PF08777 RNA binding motif 244 344 3.6E-17
23 g6001.t4 ProSiteProfiles PS50961 La-type HTH domain profile. 24 117 27.492
24 g6001.t4 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 129 226 8.876
18 g6001.t4 SMART SM00715 la 28 110 6.9E-36
11 g6001.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 26 120 2.81E-26
10 g6001.t4 SUPERFAMILY SSF54928 RNA-binding domain, RBD 121 206 2.61E-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.

Raw TPM values