General information for g4685.t1
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.t1 | isoform | g4685.t1 | 4167830 | 4170973 |
| chr_2 | g4685 | g4685.t1 | exon | g4685.t1.exon1 | 4167830 | 4167911 |
| chr_2 | g4685 | g4685.t1 | cds | g4685.t1.CDS1 | 4167830 | 4167911 |
| chr_2 | g4685 | g4685.t1 | exon | g4685.t1.exon2 | 4170092 | 4170255 |
| chr_2 | g4685 | g4685.t1 | cds | g4685.t1.CDS2 | 4170092 | 4170255 |
| chr_2 | g4685 | g4685.t1 | exon | g4685.t1.exon3 | 4170326 | 4170531 |
| chr_2 | g4685 | g4685.t1 | cds | g4685.t1.CDS3 | 4170326 | 4170531 |
| chr_2 | g4685 | g4685.t1 | exon | g4685.t1.exon4 | 4170604 | 4170973 |
| chr_2 | g4685 | g4685.t1 | cds | g4685.t1.CDS4 | 4170604 | 4170973 |
| chr_2 | g4685 | g4685.t1 | TTS | g4685.t1 | 4171747 | 4171747 |
| chr_2 | g4685 | g4685.t1 | TSS | g4685.t1 | NA | NA |
Sequences
>g4685.t1 Gene=g4685 Length=822
ATGATGGTGTATCCAGAGGAGCCATCAATTTGGTCAATTCCACATCTTCCTGCATTATAT
GAAGACGATGGCGATTACGGCGTGAATGTCGTTGAGGCTTTACAAGAATTTTGGCAAATG
AAACAGGCTCGTGGCGCTGATTTAAAGAATGGCGCATTAGTCATTTATGAGTCGGTTCCC
TCAACAAGTCAACCATATGTTTGCTACGTTACATTACCTGGAGGTAGTTGCTTTGGTAGT
TTTCAAAATTGTCCGACAAAGGCAGAAGCACGAAGAAGCTCAGCAAAAATCGCACTCATG
AATTCAGTTTTTAATGAACATCCATCACGACGAATAAGTGATGAATTTATAGAAAAAGCT
GTAAATGAGGCGAGAGCATCGTTTAAAGGTGATAGTGGTGCAGACGATGATGATAGTAGT
GCTGATGATGGAGGTGGTGTTGGTGCTTTTAGATTTATGCTTGAATCAAATAAAGGAAGA
ACAATGCTTGAATTTCAAGAGCTAATGACAGTTTTTCAACTACTTCATTGGAATGGATCA
TTAAAAGCAATGCGTGAAAGACAATGTTCTCGTCAAGAAGTTGTTGCTCACTATTCAAAT
CGATCATTAGACGATGATATGCGTACTCAAATGGCTCTTGATTGGATTGCACGTGAGCAA
GAGAATCCTGGCACACTGAGTCGTGAATTGTCACAAGCTGAGAGAGAATTAGAGACTGCG
AGACTTGCCGGTCGGGAACTTAGATTTCCGAAAGAAAAGAAAGACATTTTGATGCTCGCA
CTCACACAAATGGGCGGTGGTAATAATACGATGAACAGTTGA
>g4685.t1 Gene=g4685 Length=273
MMVYPEEPSIWSIPHLPALYEDDGDYGVNVVEALQEFWQMKQARGADLKNGALVIYESVP
STSQPYVCYVTLPGGSCFGSFQNCPTKAEARRSSAKIALMNSVFNEHPSRRISDEFIEKA
VNEARASFKGDSGADDDDSSADDGGGVGAFRFMLESNKGRTMLEFQELMTVFQLLHWNGS
LKAMRERQCSRQEVVAHYSNRSLDDDMRTQMALDWIAREQENPGTLSRELSQAERELETA
RLAGRELRFPKEKKDILMLALTQMGGGNNTMNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4685.t1 | CDD | cd00048 | DSRM_SF | 49 | 99 | 0.0086391 |
| 2 | g4685.t1 | PANTHER | PTHR31139 | ECTOPIC P GRANULES PROTEIN 5 HOMOLOG | 26 | 268 | 0.0000000 |
| 3 | g4685.t1 | PANTHER | PTHR31139:SF3 | LIX1-LIKE PROTEIN | 26 | 268 | 0.0000000 |
| 1 | g4685.t1 | Pfam | PF14954 | Limb expression 1 | 24 | 263 | 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 transcript has been annotated with K16673 (LIX1-like protein)
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. There were no conditions that were differentially expressed