General information for g11454.t4
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.t4 | TTS | g11454.t4 | 16353376 | 16353376 |
| chr_1 | g11454 | g11454.t4 | isoform | g11454.t4 | 16353591 | 16355484 |
| chr_1 | g11454 | g11454.t4 | exon | g11454.t4.exon1 | 16353591 | 16355021 |
| chr_1 | g11454 | g11454.t4 | cds | g11454.t4.CDS1 | 16353591 | 16355021 |
| chr_1 | g11454 | g11454.t4 | exon | g11454.t4.exon2 | 16355087 | 16355484 |
| chr_1 | g11454 | g11454.t4 | cds | g11454.t4.CDS2 | 16355087 | 16355314 |
| chr_1 | g11454 | g11454.t4 | TSS | g11454.t4 | 16355547 | 16355547 |
Sequences
>g11454.t4 Gene=g11454 Length=1829
ATGGAAACAAGTAAAAATAATCAAAAAGATCAAGAGAATATTGATCCTGCTTCTGAAGCA
CCAAAAATTTATACTTTGGAAGGTAAAATTTAAAACGATAAATAAAATAAATTTAAAAAT
TTGTCAATATTTTTTTTAACAAAATTTTAGTGCTTAGAATGATAAGAGATATGCAGCAAC
AACATGGATTGAGGCATGGTGATTATCAACGCTACCGTGGTTACTGTACTAGAAGAGTTA
AAAGATTGAGAAAGAATCTTAACCTACCACAAGGTGATCGAAAACATTTTAAGAAGAAAG
AAGTTAATATAAATCATCTTGAGAGTAAAAATTCAAATGAAAAATACATTCATATTCCTC
TTATTCTTGCTGAAAGATGCTGGGCTTATGCAATGCAGTTAAGACAAGAAGCAAATAGCG
AGCCTAGAAAAAAGTACCATCTTATATCTAAGCTTAAAAAAGCTTGTGTATATTCTCGAC
AATTGCTTTTCCTAGCTAATACTTCATTTTGTGATGCTAGAACAAAGCTCGAAGCAGAGG
CTTATGATTCATGGATACATGGCTCATTCTATTTTGAACTCAATCAGTGGAAGGAAGCTG
CTGAATATTTGAAAAAAACACAAATTGTTTATGAAAACTTGTTAAAGGCATTACCAGAGG
AAGAGCAAACCATTTATAGAGCAAAAATTGATGAATTAAGTCCAAGTCTTCGTTATTGTT
CTTATAATATTGGTGAAAATGCATCCGTCAATGATTTATTAGAAATTCAACGTGTTGGAT
TGTTGGATAACTTGGGTGCACTTGTTGCACAAACAAGAACTGAACAAACTGATGCATTTC
AAAGCACTGAATGGCGTGGCAGAAAAATTACTGTTCGCCCTCAAAAAGTTCGGATGTTCT
TATTGAGTGTTCAAGATTTAGATAAGTCAATTGAAAAAGCAAAAGAATTTCAAGCTAAAA
TCGATATTATCGAAAACGTTCTACTTGATTGCAAAGATGCTGTGCTGGCATTAAAGGATG
AAATAAGAAACGATCCAAAAAATCGTGTATCAAATCAAGAAGGACAATTATCTGGAATGC
AATTTTTGCTCTCATACATACAGTACATTCGAATGAAATTAACACTTGAACGAAATTTAT
ATTTGATTGGACAATTGAAACAAAACAAAGAAGACGATGGTACGACGAAAAAAAGTCGTC
CTCAAGACATTTCAAGATTATATGAGATAATTCTTCAAAATATAAGTGAAATGCAGCAAC
TAAATGGTCTTGAAAATGATACAGAGTATCAAAACGAAATAAAAGATTTAGCAAATGCTT
TTAAAGCATTTAGATGTTACTATATTGCTCTTACACTGGTTAATTTGAAACGTTGGAAAG
AAGCTGTAGCAATGTATGAACGTTCAACAAAATATGCGACACAAGCGATCAAAGCAAAAG
TCCACGAATTCAATTTACAAGCAGATCTTAACGAATTGCTAAAAAACATTGAAGGAAATA
AATTTTCCGCTCATGCTTATAGTGTTTTAGAATCTGATAATCAAGATGAGACAGTCTTTT
ATGGTAAAACACAAAAAACTACTAAACCTTTACTCGAGCGTCTCAATCAATACGTAGAGG
ATCCAACATTGAATTCAAAAAATCCTAATGTCTACAAATTAACTCCTGAAATGGAGGCTA
TTCCATGTAAACCTTTGTTTTTCGATTTGGCTTTAAATTTTATCGAATTTCCATCGCTTG
ATGATAAGAAAGAACAAGTAACGAATAAAAAAGTATCAGGAGTTGGAGGATTGATCAAAG
GCTTCCTTGGTTTTGGAGATAAAAAATAA
>g11454.t4 Gene=g11454 Length=552
MQQQHGLRHGDYQRYRGYCTRRVKRLRKNLNLPQGDRKHFKKKEVNINHLESKNSNEKYI
HIPLILAERCWAYAMQLRQEANSEPRKKYHLISKLKKACVYSRQLLFLANTSFCDARTKL
EAEAYDSWIHGSFYFELNQWKEAAEYLKKTQIVYENLLKALPEEEQTIYRAKIDELSPSL
RYCSYNIGENASVNDLLEIQRVGLLDNLGALVAQTRTEQTDAFQSTEWRGRKITVRPQKV
RMFLLSVQDLDKSIEKAKEFQAKIDIIENVLLDCKDAVLALKDEIRNDPKNRVSNQEGQL
SGMQFLLSYIQYIRMKLTLERNLYLIGQLKQNKEDDGTTKKSRPQDISRLYEIILQNISE
MQQLNGLENDTEYQNEIKDLANAFKAFRCYYIALTLVNLKRWKEAVAMYERSTKYATQAI
KAKVHEFNLQADLNELLKNIEGNKFSAHAYSVLESDNQDETVFYGKTQKTTKPLLERLNQ
YVEDPTLNSKNPNVYKLTPEMEAIPCKPLFFDLALNFIEFPSLDDKKEQVTNKKVSGVGG
LIKGFLGFGDKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11454.t4 | CDD | cd15481 | SRP68-RBD | 2 | 185 | 0.0e+00 |
| 4 | g11454.t4 | Gene3D | G3DSA:1.10.3450.40 | - | 1 | 190 | 0.0e+00 |
| 2 | g11454.t4 | PANTHER | PTHR12860 | SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN | 2 | 547 | 0.0e+00 |
| 5 | g11454.t4 | PIRSF | PIRSF038995 | SRP68 | 1 | 550 | 0.0e+00 |
| 1 | g11454.t4 | Pfam | PF16969 | RNA-binding signal recognition particle 68 | 7 | 518 | 0.0e+00 |
| 3 | g11454.t4 | SUPERFAMILY | SSF48452 | TPR-like | 94 | 417 | 8.5e-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.
