Gene loci information

Transcript annotation

  • This transcript has been annotated as 39S ribosomal protein L2, mitochondrial.

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 g3799 g3799.t1 TTS g3799.t1 27992846 27992846
chr_3 g3799 g3799.t1 isoform g3799.t1 27992901 27993965
chr_3 g3799 g3799.t1 exon g3799.t1.exon1 27992901 27993561
chr_3 g3799 g3799.t1 cds g3799.t1.CDS1 27992901 27993561
chr_3 g3799 g3799.t1 exon g3799.t1.exon2 27993620 27993770
chr_3 g3799 g3799.t1 cds g3799.t1.CDS2 27993620 27993770
chr_3 g3799 g3799.t1 exon g3799.t1.exon3 27993833 27993965
chr_3 g3799 g3799.t1 cds g3799.t1.CDS3 27993833 27993965
chr_3 g3799 g3799.t1 TSS g3799.t1 27993978 27993978

Sequences

>g3799.t1 Gene=g3799 Length=945
ATGAGTTTCAAAATTTTAAGACACTCATTAAATTTATTTTCTAAACAATTACCAGCTCTG
CCAGTCATTTCAAATCACATTAATCTTCAACTTGTACGTGCTCTTCCTCATTTCGTTGAT
AAACCAACACCGGGAAAAGATCATAAACAATATAGAAGAACTGTTCATTTCCCCGAAGAT
GGAAATTATACCATAAAACCACTTGATAACACACATTTAGCTGGTCGAGATCCAGTAACA
GGAAGAGTTGTTGCAAAAGGTATTGGCGGAGGAATAAAATTCAAATATCATTGGATTAAA
TATAATAGAGATGGACCAGAAGAAGGACCTCCACAAGAAGAAAGAGTGTTACAAATTCTC
AAATGCGGTTGCAGAACAGCAGACGTTGCTCTTGTCGGTGTTGGAAAGGAACTCAAATAC
ATTTTAGCAACTGAGAATATGAAGGCTGGCGATATTATTAAAACGTCAAAATTCATTCCG
AGAATTCCTGTTAGAGCAAATGAAGGCGATGCATATCCTCTTGGTGCTCTACCAGTAGGC
ACAATCGTTCACAACATTGAAAAATATCCTGGCTGTAATAAACATTTTGTGCATGCTGCT
GGTGTATTTGCTACTATTCTGAGAAAATTTGATGATCGAGTAGTTATATTGATGCCAAAC
AAAAGAGAATATGCTTTGCTAGAGAAATGTATGGCAACTGTAGGTCGATTATCAAATGTT
GAACACTCGAGAACACCAATTCCCTCAGTACACAGATGGCGTGAACTTGGAAACCGACCA
AGATCGGGACTTTGGCAAAGAAAGAGCGGTAGACATGGTAGAAAAATTAAGAAACCACCA
CCAATGAAACTACATGGACCTCCAAAGCAGCCAGAAAAGCCACCATTAAAGCTCACAATC
AATCGTGTTTCAAAAGGAGGAGGAACATATATTAATCCACTCTAA

>g3799.t1 Gene=g3799 Length=314
MSFKILRHSLNLFSKQLPALPVISNHINLQLVRALPHFVDKPTPGKDHKQYRRTVHFPED
GNYTIKPLDNTHLAGRDPVTGRVVAKGIGGGIKFKYHWIKYNRDGPEEGPPQEERVLQIL
KCGCRTADVALVGVGKELKYILATENMKAGDIIKTSKFIPRIPVRANEGDAYPLGALPVG
TIVHNIEKYPGCNKHFVHAAGVFATILRKFDDRVVILMPNKREYALLEKCMATVGRLSNV
EHSRTPIPSVHRWRELGNRPRSGLWQRKSGRHGRKIKKPPPMKLHGPPKQPEKPPLKLTI
NRVSKGGGTYINPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3799.t1 Gene3D G3DSA:2.40.50.140 - 38 151 2.2E-16
11 g3799.t1 Gene3D G3DSA:2.30.30.30 - 163 239 2.6E-21
10 g3799.t1 MobiDBLite mobidb-lite consensus disorder prediction 259 296 -
9 g3799.t1 MobiDBLite mobidb-lite consensus disorder prediction 265 282 -
3 g3799.t1 PANTHER PTHR13691:SF5 39S RIBOSOMAL PROTEIN L2, MITOCHONDRIAL 71 288 1.2E-33
4 g3799.t1 PANTHER PTHR13691 RIBOSOMAL PROTEIN L2 71 288 1.2E-33
1 g3799.t1 Pfam PF00181 Ribosomal Proteins L2, RNA binding domain 75 154 1.2E-16
2 g3799.t1 Pfam PF03947 Ribosomal Proteins L2, C-terminal domain 168 261 4.1E-19
7 g3799.t1 SMART SM01383 Ribosomal_L2_2 75 155 6.0E-21
8 g3799.t1 SMART SM01382 Ribosomal_L2_C_2 166 288 4.3E-14
5 g3799.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 50 157 5.88E-16
6 g3799.t1 SUPERFAMILY SSF50104 Translation proteins SH3-like domain 169 290 5.84E-30

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

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