General information for g11454.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal recognition particle subunit SRP68.
Parent gene
- The parent gene g11454 is located on chr_1: 16355484..16357660 (- strand)
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 | g11454 | g11454.t2 | isoform | g11454.t2 | 16344748 | 16355484 |
| chr_1 | g11454 | g11454.t2 | exon | g11454.t2.exon1 | 16344748 | 16344996 |
| chr_1 | g11454 | g11454.t2 | exon | g11454.t2.exon2 | 16353572 | 16355021 |
| chr_1 | g11454 | g11454.t2 | cds | g11454.t2.CDS1 | 16353591 | 16355021 |
| chr_1 | g11454 | g11454.t2 | exon | g11454.t2.exon3 | 16355087 | 16355334 |
| chr_1 | g11454 | g11454.t2 | cds | g11454.t2.CDS2 | 16355087 | 16355334 |
| chr_1 | g11454 | g11454.t2 | exon | g11454.t2.exon4 | 16355403 | 16355484 |
| chr_1 | g11454 | g11454.t2 | cds | g11454.t2.CDS3 | 16355403 | 16355484 |
| chr_1 | g11454 | g11454.t2 | TSS | g11454.t2 | 16355547 | 16355547 |
| chr_1 | g11454 | g11454.t2 | TTS | g11454.t2 | NA | NA |
Sequences
>g11454.t2 Gene=g11454 Length=2029
ATGGAAACAAGTAAAAATAATCAAAAAGATCAAGAGAATATTGATCCTGCTTCTGAAGCA
CCAAAAATTTATACTTTGGAAGTGCTTAGAATGATAAGAGATATGCAGCAACAACATGGA
TTGAGGCATGGTGATTATCAACGCTACCGTGGTTACTGTACTAGAAGAGTTAAAAGATTG
AGAAAGAATCTTAACCTACCACAAGGTGATCGAAAACATTTTAAGAAGAAAGAAGTTAAT
ATAAATCATCTTGAGAGTAAAAATTCAAATGAAAAATACATTCATATTCCTCTTATTCTT
GCTGAAAGATGCTGGGCTTATGCAATGCAGTTAAGACAAGAAGCAAATAGCGAGCCTAGA
AAAAAGTACCATCTTATATCTAAGCTTAAAAAAGCTTGTGTATATTCTCGACAATTGCTT
TTCCTAGCTAATACTTCATTTTGTGATGCTAGAACAAAGCTCGAAGCAGAGGCTTATGAT
TCATGGATACATGGCTCATTCTATTTTGAACTCAATCAGTGGAAGGAAGCTGCTGAATAT
TTGAAAAAAACACAAATTGTTTATGAAAACTTGTTAAAGGCATTACCAGAGGAAGAGCAA
ACCATTTATAGAGCAAAAATTGATGAATTAAGTCCAAGTCTTCGTTATTGTTCTTATAAT
ATTGGTGAAAATGCATCCGTCAATGATTTATTAGAAATTCAACGTGTTGGATTGTTGGAT
AACTTGGGTGCACTTGTTGCACAAACAAGAACTGAACAAACTGATGCATTTCAAAGCACT
GAATGGCGTGGCAGAAAAATTACTGTTCGCCCTCAAAAAGTTCGGATGTTCTTATTGAGT
GTTCAAGATTTAGATAAGTCAATTGAAAAAGCAAAAGAATTTCAAGCTAAAATCGATATT
ATCGAAAACGTTCTACTTGATTGCAAAGATGCTGTGCTGGCATTAAAGGATGAAATAAGA
AACGATCCAAAAAATCGTGTATCAAATCAAGAAGGACAATTATCTGGAATGCAATTTTTG
CTCTCATACATACAGTACATTCGAATGAAATTAACACTTGAACGAAATTTATATTTGATT
GGACAATTGAAACAAAACAAAGAAGACGATGGTACGACGAAAAAAAGTCGTCCTCAAGAC
ATTTCAAGATTATATGAGATAATTCTTCAAAATATAAGTGAAATGCAGCAACTAAATGGT
CTTGAAAATGATACAGAGTATCAAAACGAAATAAAAGATTTAGCAAATGCTTTTAAAGCA
TTTAGATGTTACTATATTGCTCTTACACTGGTTAATTTGAAACGTTGGAAAGAAGCTGTA
GCAATGTATGAACGTTCAACAAAATATGCGACACAAGCGATCAAAGCAAAAGTCCACGAA
TTCAATTTACAAGCAGATCTTAACGAATTGCTAAAAAACATTGAAGGAAATAAATTTTCC
GCTCATGCTTATAGTGTTTTAGAATCTGATAATCAAGATGAGACAGTCTTTTATGGTAAA
ACACAAAAAACTACTAAACCTTTACTCGAGCGTCTCAATCAATACGTAGAGGATCCAACA
TTGAATTCAAAAAATCCTAATGTCTACAAATTAACTCCTGAAATGGAGGCTATTCCATGT
AAACCTTTGTTTTTCGATTTGGCTTTAAATTTTATCGAATTTCCATCGCTTGATGATAAG
AAAGAACAAGTAACGAATAAAAAAGTATCAGGAGTTGGAGGATTGATCAAAGGCTTCCTT
GGTTTTGGAGATAAAAAATAATTTCTTTTTTGATTTATAGGAGGAGACCATGAAGTATAA
TTATATTGATTAGCGACGCCCCGTTGTCGTTCTAGTTCATCATGTAACCATTCGACAGCA
CCCGACCATGCCTGTGAAATCGTTGGATTGCTATGCAACATATTTAAGGCAATGGGACTT
TTGCGGAACAAATGAACCAAACATTTAATGCATTGGTATGCTCGTTTTTGGTAATTCATC
CGATTTCGTTGAATCGTATCTAAAAGACCTTCTCTATCTTCAGGAAATC
>g11454.t2 Gene=g11454 Length=586
METSKNNQKDQENIDPASEAPKIYTLEVLRMIRDMQQQHGLRHGDYQRYRGYCTRRVKRL
RKNLNLPQGDRKHFKKKEVNINHLESKNSNEKYIHIPLILAERCWAYAMQLRQEANSEPR
KKYHLISKLKKACVYSRQLLFLANTSFCDARTKLEAEAYDSWIHGSFYFELNQWKEAAEY
LKKTQIVYENLLKALPEEEQTIYRAKIDELSPSLRYCSYNIGENASVNDLLEIQRVGLLD
NLGALVAQTRTEQTDAFQSTEWRGRKITVRPQKVRMFLLSVQDLDKSIEKAKEFQAKIDI
IENVLLDCKDAVLALKDEIRNDPKNRVSNQEGQLSGMQFLLSYIQYIRMKLTLERNLYLI
GQLKQNKEDDGTTKKSRPQDISRLYEIILQNISEMQQLNGLENDTEYQNEIKDLANAFKA
FRCYYIALTLVNLKRWKEAVAMYERSTKYATQAIKAKVHEFNLQADLNELLKNIEGNKFS
AHAYSVLESDNQDETVFYGKTQKTTKPLLERLNQYVEDPTLNSKNPNVYKLTPEMEAIPC
KPLFFDLALNFIEFPSLDDKKEQVTNKKVSGVGGLIKGFLGFGDKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11454.t2 | CDD | cd15481 | SRP68-RBD | 27 | 219 | 0.0e+00 |
| 4 | g11454.t2 | Gene3D | G3DSA:1.10.3450.40 | - | 23 | 224 | 0.0e+00 |
| 2 | g11454.t2 | PANTHER | PTHR12860 | SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN | 13 | 581 | 0.0e+00 |
| 5 | g11454.t2 | PIRSF | PIRSF038995 | SRP68 | 23 | 584 | 0.0e+00 |
| 1 | g11454.t2 | Pfam | PF16969 | RNA-binding signal recognition particle 68 | 41 | 552 | 0.0e+00 |
| 3 | g11454.t2 | SUPERFAMILY | SSF48452 | TPR-like | 129 | 451 | 9.3e-06 |
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:0006614 | SRP-dependent cotranslational protein targeting to membrane | BP |
| GO:0003723 | RNA binding | MF |
| GO:0005786 | signal recognition particle, endoplasmic reticulum targeting | CC |
| GO:0005515 | protein binding | MF |
| GO:0030942 | endoplasmic reticulum signal peptide binding | MF |
| GO:0005047 | signal recognition particle binding | MF |
| GO:0008312 | 7S RNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03107 (signal recognition particle subunit SRP68)
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.
