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.t3 TTS g6001.t3 13448960 13448960
chr_2 g6001 g6001.t3 isoform g6001.t3 13449151 13450575
chr_2 g6001 g6001.t3 exon g6001.t3.exon1 13449151 13449353
chr_2 g6001 g6001.t3 cds g6001.t3.CDS1 13449330 13449353
chr_2 g6001 g6001.t3 exon g6001.t3.exon2 13449456 13450394
chr_2 g6001 g6001.t3 cds g6001.t3.CDS2 13449456 13450370
chr_2 g6001 g6001.t3 exon g6001.t3.exon3 13450568 13450575
chr_2 g6001 g6001.t3 TSS g6001.t3 13450637 13450637

Sequences

>g6001.t3 Gene=g6001 Length=1150
ATTAGAAGAAATAAACACAAAAAAGCGTCATAATGACTGAAAAAGTTGAAACTGTTGCAA
ACCAAGGAGGACAAGAAGATAAGAATGATGGTGATCATTCACAGACAGATCTTACACAGC
TTGAACTCGACATTATCAAACAAATTGAATATTACTTTGGAGAAAGTAATTTAAGACGTG
ATAAATTTTTAAACAGCAAAATTGCAGAGGACAAAGATGGATGGGTTCCGATTAGCGTTT
TGCTTACTTTTAATCGTTTAAAAGCCCTTACAGAGGATGCAAATGTCATTGCTGAAAGTG
TTGATAAATCTTCAAATGGATTAGTACAAGTCAGTGAAGATAAACAGAAAATTCGTCGTC
ATCCCGAAAATCCATTACCTGAATTTAATGAAGAACGCCGAAAAGAATTACAAGCTAGAA
CTGCATATGCAAAAGGATTTCCACTTGATTCAACTATGAATACACTTCTTGAATATTTCA
AAAACAATTTTGATAAAGTTGAAAACGTCATGATGAGAAAATATTATTGCCCTAAAACAA
AAGTATACCTTTTTAAAGGTTCTGTTTATGTTCTTTTTTCTAATAAAGAAAATGCTGAAG
AATTTGTACAGCGACCAGATTTAAAATATGGCGAAAAAGACTTGTTGCGTTATATGCAAA
AGGATTATTTAGAAAAGAAGAAAACTGAAAAATCAAAGTATGACAAGAAACAAAAGAAAA
AGGAAGAAGATAAAGATGAAATTGTATTGCCTAAGAACGCAGTTATTCATTTTACCGGAG
TGGAAGGTGATATTATGAGAGAGGATATTAAGAAAAGAGTCTTGGAAATCGATCCATCAC
TTGTTATTGCATTCGTTCATTTTGAACGTGGAGCTAAAGAAGGTCAATTACGATTCTCAA
AAGAAGATGATGGTAAAAAGTTTTTGGAAAAACTTGAAAATGGAAAGGTGAACAAGAGGA
GACATTCTTGAAAGAAGCAATTGAAGATATGAGGAAAGCTCGTCAACGTGGACAACAAAA
GAATAACAAAGGTCGTAAAGGTGGTGGAAAGAACGATCGTAAGCGTAAACATGAAAATGA
AAGTGAAGATGTACCAACTAAGCAAACTAAAGTCGATGAGGAACCTTCTGTTGTAACTGT
AGCTGAATAA

>g6001.t3 Gene=g6001 Length=312
MTEKVETVANQGGQEDKNDGDHSQTDLTQLELDIIKQIEYYFGESNLRRDKFLNSKIAED
KDGWVPISVLLTFNRLKALTEDANVIAESVDKSSNGLVQVSEDKQKIRRHPENPLPEFNE
ERRKELQARTAYAKGFPLDSTMNTLLEYFKNNFDKVENVMMRKYYCPKTKVYLFKGSVYV
LFSNKENAEEFVQRPDLKYGEKDLLRYMQKDYLEKKKTEKSKYDKKQKKKEEDKDEIVLP
KNAVIHFTGVEGDIMREDIKKRVLEIDPSLVIAFVHFERGAKEGQLRFSKEDDGKKFLEK
LENGKVNKRRHS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g6001.t3 CDD cd12291 RRM1_La 130 206 4.25118E-18
15 g6001.t3 Coils Coil Coil 213 236 -
14 g6001.t3 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 17 108 9.5E-30
12 g6001.t3 Gene3D G3DSA:3.30.70.330 - 118 218 1.8E-13
13 g6001.t3 Gene3D G3DSA:3.30.70.330 - 225 311 2.3E-12
18 g6001.t3 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
3 g6001.t3 PANTHER PTHR22792 LUPUS LA PROTEIN-RELATED 30 303 2.4E-49
4 g6001.t3 PANTHER PTHR22792:SF140 LUPUS LA PROTEIN HOMOLOG 30 303 2.4E-49
7 g6001.t3 PRINTS PR00302 Lupus La protein signature 37 54 5.4E-34
8 g6001.t3 PRINTS PR00302 Lupus La protein signature 63 78 5.4E-34
5 g6001.t3 PRINTS PR00302 Lupus La protein signature 96 109 5.4E-34
9 g6001.t3 PRINTS PR00302 Lupus La protein signature 123 139 5.4E-34
6 g6001.t3 PRINTS PR00302 Lupus La protein signature 174 192 5.4E-34
2 g6001.t3 Pfam PF05383 La domain 34 90 1.4E-22
1 g6001.t3 Pfam PF08777 RNA binding motif 244 308 1.6E-10
19 g6001.t3 ProSiteProfiles PS50961 La-type HTH domain profile. 24 117 27.492
20 g6001.t3 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 129 226 8.876
17 g6001.t3 SMART SM00715 la 28 110 6.9E-36
11 g6001.t3 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 26 120 1.9E-26
10 g6001.t3 SUPERFAMILY SSF54928 RNA-binding domain, RBD 121 207 1.78E-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