Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L7a.

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_1 g12102 g12102.t23 TSS g12102.t23 20939009 20939009
chr_1 g12102 g12102.t23 isoform g12102.t23 20939077 20940413
chr_1 g12102 g12102.t23 exon g12102.t23.exon1 20939077 20939091
chr_1 g12102 g12102.t23 cds g12102.t23.CDS1 20939077 20939091
chr_1 g12102 g12102.t23 exon g12102.t23.exon2 20939358 20939631
chr_1 g12102 g12102.t23 cds g12102.t23.CDS2 20939358 20939631
chr_1 g12102 g12102.t23 exon g12102.t23.exon3 20939691 20939911
chr_1 g12102 g12102.t23 cds g12102.t23.CDS3 20939691 20939911
chr_1 g12102 g12102.t23 exon g12102.t23.exon4 20940190 20940413
chr_1 g12102 g12102.t23 cds g12102.t23.CDS4 20940190 20940219
chr_1 g12102 g12102.t23 TTS g12102.t23 20940505 20940505

Sequences

>g12102.t23 Gene=g12102 Length=734
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAG
GTTCCACCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTA
TTTAAAGTTTTGGAAAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAG
AAAAAGGCTGAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACA
TTGAGAGCTGGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTT
GTCATCTCACATGACGTTGATCCAATCGAATGGTTCATCGCAAAACATGCACAACTTTAG
CTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAATCAATTA
AGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGTTTACTCG
GACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAATTAGCCC
AAAAACAAGGATAA

>g12102.t23 Gene=g12102 Length=179
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLK
KKAEEKVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIEWFIAKHAQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12102.t23 Gene3D G3DSA:3.30.1330.210 - 62 175 1.4E-47
12 g12102.t23 MobiDBLite mobidb-lite consensus disorder prediction 23 46 -
2 g12102.t23 PANTHER PTHR23105:SF134 - 12 173 8.4E-57
3 g12102.t23 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 173 8.4E-57
8 g12102.t23 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 9.8E-46
5 g12102.t23 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 9.8E-46
7 g12102.t23 PRINTS PR00882 Ribosomal protein L7A family signature 78 97 9.8E-46
4 g12102.t23 PRINTS PR00882 Ribosomal protein L7A family signature 102 115 9.8E-46
6 g12102.t23 PRINTS PR00882 Ribosomal protein L7A family signature 137 157 9.8E-46
10 g12102.t23 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 141 155 5.1E-7
9 g12102.t23 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 160 173 5.1E-7
1 g12102.t23 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 135 170 1.9E-7
11 g12102.t23 SUPERFAMILY SSF55315 L30e-like 97 171 3.73E-13
13 g12102.t23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 19 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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