Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L4.

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 g3343 g3343.t48 TTS g3343.t48 24752884 24752884
chr_3 g3343 g3343.t48 isoform g3343.t48 24753005 24754773
chr_3 g3343 g3343.t48 exon g3343.t48.exon1 24753005 24753703
chr_3 g3343 g3343.t48 cds g3343.t48.CDS1 24753005 24753664
chr_3 g3343 g3343.t48 exon g3343.t48.exon2 24753929 24754053
chr_3 g3343 g3343.t48 exon g3343.t48.exon3 24754120 24754533
chr_3 g3343 g3343.t48 exon g3343.t48.exon4 24754767 24754773
chr_3 g3343 g3343.t48 TSS g3343.t48 24754851 24754851

Sequences

>g3343.t48 Gene=g3343 Length=1245
ATGGTTAAGTAAATCAGCTGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGT
TATTAAAGATACAACAATTCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGT
CGTCAATGATGTACATCAATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGC
TGAAGCAGGCCATCAAACATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTAT
TCCTCGAGTTCGTGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTG
TCGTGGAGGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAA
TGTCAACTTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCT
TGACATATTATTGACGGAATTGCTGAACTTCCATTGGTTGTCTCAGATAAAGTTCAAGAA
TACAACAAGACCAAACAAGCTGTTTTGTTCTTACGTCGTAACAAGTTGTGGGGAGATGTT
TTGAAAGTTTATCGTTCAAAACGCTTTAGAGCTGGTCGTGGTAAAATGCGAAATCGTCGT
CGTATTCAACGTCGTGGACCATTAATTGTTTACTCGAAGGATGATGGCTTGCGTCGTGCA
TTCCGTAATATTCCCGGTGTTGATACAATGAGCGTTCACAAATTGAATTTGCTCAAATTG
GCTCCAGGTGGACATCTTGGACGATTGATTGTTTGGACCGAAGGCGCTTTCAAGCATTTG
AATGCATTGTTTGGAACATGGAGTGAGCCTTCAACAGTGAAAAAGGCTTACAATCTGCCA
CATCCAATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATCACAAGAAATCAAGAGC
GTTTTGAATGCACCTAAGAAGAGAGTTTTCCATCGTGTACGCCGCTTGAATCCATTGAAG
AACGCCAGACAAAAGACCAAGTTGAATCCATATTCAGAAGTTACTCGTCGTCGTGCATTG
TTGGCTAAAGAAAAGCGAAAGTATGAGACACAAATTGCCAAGGCAAAGAAGAAGAAGGTC
GAACTCAAGAGCAATCATCCAGCTATTGTGTATCAAAAGAATGTTGCTAATCGTTTGAAG
CTCTTAGCTGCATCAAAGAAAGCTAGACAAGCTCGCGCTGCTGAAAAGAAAAAAGCTGCT
GCTGGAAAGAAAGCAACAAAAAAGACCGCAGCCAAGAAAAAGTAA

>g3343.t48 Gene=g3343 Length=219
MRNRRRIQRRGPLIVYSKDDGLRRAFRNIPGVDTMSVHKLNLLKLAPGGHLGRLIVWTEG
AFKHLNALFGTWSEPSTVKKAYNLPHPIMSNTDLTRLLKSQEIKSVLNAPKKRVFHRVRR
LNPLKNARQKTKLNPYSEVTRRRALLAKEKRKYETQIAKAKKKKVELKSNHPAIVYQKNV
ANRLKLLAASKKARQARAAEKKKAAAGKKATKKTAAKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3343.t48 Coils Coil Coil 143 170 -
7 g3343.t48 Gene3D G3DSA:3.40.1370.10 - 1 108 9.3E-45
6 g3343.t48 MobiDBLite mobidb-lite consensus disorder prediction 192 219 -
3 g3343.t48 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 1 201 9.0E-61
4 g3343.t48 PANTHER PTHR19431:SF0 60S RIBOSOMAL PROTEIN L4 1 201 9.0E-61
1 g3343.t48 Pfam PF00573 Ribosomal protein L4/L1 family 5 66 8.3E-12
2 g3343.t48 Pfam PF14374 60S ribosomal protein L4 C-terminal domain 80 152 4.3E-24
5 g3343.t48 SUPERFAMILY SSF52166 Ribosomal protein L4 1 66 8.37E-20

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:0005840 ribosome CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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