General information for g4685.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein limb expression 1-like protein.
Parent gene
- The parent gene g4685 is located on chr_2: 4170604..4171754 (+ 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_2 | g4685 | g4685.t4 | isoform | g4685.t4 | 4170092 | 4171357 |
| chr_2 | g4685 | g4685.t4 | exon | g4685.t4.exon1 | 4170092 | 4170255 |
| chr_2 | g4685 | g4685.t4 | cds | g4685.t4.CDS1 | 4170127 | 4170255 |
| chr_2 | g4685 | g4685.t4 | exon | g4685.t4.exon2 | 4170326 | 4170531 |
| chr_2 | g4685 | g4685.t4 | cds | g4685.t4.CDS2 | 4170326 | 4170531 |
| chr_2 | g4685 | g4685.t4 | exon | g4685.t4.exon3 | 4170604 | 4171357 |
| chr_2 | g4685 | g4685.t4 | cds | g4685.t4.CDS3 | 4170604 | 4170973 |
| chr_2 | g4685 | g4685.t4 | TTS | g4685.t4 | 4171747 | 4171747 |
| chr_2 | g4685 | g4685.t4 | TSS | g4685.t4 | NA | NA |
Sequences
>g4685.t4 Gene=g4685 Length=1124
TGAATGTCGTTGAGGCTTTACAAGAATTTTGGCAAATGAAACAGGCTCGTGGCGCTGATT
TAAAGAATGGCGCATTAGTCATTTATGAGTCGGTTCCCTCAACAAGTCAACCATATGTTT
GCTACGTTACATTACCTGGAGGTAGTTGCTTTGGTAGTTTTCAAAATTGTCCGACAAAGG
CAGAAGCACGAAGAAGCTCAGCAAAAATCGCACTCATGAATTCAGTTTTTAATGAACATC
CATCACGACGAATAAGTGATGAATTTATAGAAAAAGCTGTAAATGAGGCGAGAGCATCGT
TTAAAGGTGATAGTGGTGCAGACGATGATGATAGTAGTGCTGATGATGGAGGTGGTGTTG
GTGCTTTTAGATTTATGCTTGAATCAAATAAAGGAAGAACAATGCTTGAATTTCAAGAGC
TAATGACAGTTTTTCAACTACTTCATTGGAATGGATCATTAAAAGCAATGCGTGAAAGAC
AATGTTCTCGTCAAGAAGTTGTTGCTCACTATTCAAATCGATCATTAGACGATGATATGC
GTACTCAAATGGCTCTTGATTGGATTGCACGTGAGCAAGAGAATCCTGGCACACTGAGTC
GTGAATTGTCACAAGCTGAGAGAGAATTAGAGACTGCGAGACTTGCCGGTCGGGAACTTA
GATTTCCGAAAGAAAAGAAAGACATTTTGATGCTCGCACTCACACAAATGGGCGGTGGTA
ATAATACGATGAACAGTTGAACTGTCATGAAGAAATGTTAGCTGGTTTTTCTTTCTTTTT
TGCCATCTTTCTTGAAATTTTCTTATTTTTTTTGCATTTAAAATGTAACACAAATTAATT
TTTAAGAAATATTGAAAGTTTTTTTATCTATTAGATTTTAAGATAGAAATTTTAAAAAAA
TCAAAACAAAATAAATTTAAAGCTCAAGTTATTGTGATTACAAGCAAGTAGAAATTAGAA
TTTTCTTTTTTGAAATTAAGCAATATTTTTCTTCTTTTAACAGTTTTTTTTCATAAACAA
TTATAACACAGTACATGAAGAAATAGTTTAACATTTCATTTGGTGGCGGTCGTCAATTCA
AACTATCAAAACAAATCAAATAAATGAAAATAGTTTAAGTTAAA
>g4685.t4 Gene=g4685 Length=234
MKQARGADLKNGALVIYESVPSTSQPYVCYVTLPGGSCFGSFQNCPTKAEARRSSAKIAL
MNSVFNEHPSRRISDEFIEKAVNEARASFKGDSGADDDDSSADDGGGVGAFRFMLESNKG
RTMLEFQELMTVFQLLHWNGSLKAMRERQCSRQEVVAHYSNRSLDDDMRTQMALDWIARE
QENPGTLSRELSQAERELETARLAGRELRFPKEKKDILMLALTQMGGGNNTMNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4685.t4 | CDD | cd00048 | DSRM_SF | 10 | 60 | 0.0087492 |
| 2 | g4685.t4 | PANTHER | PTHR31139 | ECTOPIC P GRANULES PROTEIN 5 HOMOLOG | 1 | 229 | 0.0000000 |
| 3 | g4685.t4 | PANTHER | PTHR31139:SF3 | LIX1-LIKE PROTEIN | 1 | 229 | 0.0000000 |
| 1 | g4685.t4 | Pfam | PF14954 | Limb expression 1 | 1 | 224 | 0.0000000 |
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