General information for g5065.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Low density lipoprotein receptor adapter protein 1-B.
Parent gene
- The parent gene g5065 is located on chr_2: 6722334..6725663 (- 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 | g5065 | g5065.t2 | TTS | g5065.t2 | 6722238 | 6722238 |
| chr_2 | g5065 | g5065.t2 | isoform | g5065.t2 | 6722334 | 6725663 |
| chr_2 | g5065 | g5065.t2 | exon | g5065.t2.exon1 | 6722334 | 6722583 |
| chr_2 | g5065 | g5065.t2 | cds | g5065.t2.CDS1 | 6722334 | 6722583 |
| chr_2 | g5065 | g5065.t2 | exon | g5065.t2.exon2 | 6722646 | 6723207 |
| chr_2 | g5065 | g5065.t2 | cds | g5065.t2.CDS2 | 6722646 | 6723207 |
| chr_2 | g5065 | g5065.t2 | exon | g5065.t2.exon3 | 6725615 | 6725663 |
| chr_2 | g5065 | g5065.t2 | cds | g5065.t2.CDS3 | 6725615 | 6725663 |
| chr_2 | g5065 | g5065.t2 | TSS | g5065.t2 | 6725847 | 6725847 |
Sequences
>g5065.t2 Gene=g5065 Length=861
ATGTCATTCCTTTTCAAATCAATGTGGAAAAATAACTGCAAGCATCATAAGCTTAATGAG
GAACTAGCATTAGCAAGTAGCATACGAGATTTTGCTGAAAGTCCACTAGATTTAAATGAT
GAAGAACTGACTGATGATGCCATTGTTTATAATTTAAAATATCTTGGTAGTACACAATTA
CTTCCACAAGCCAAAAATGAAGAAACAAAAAAGACCAAATTTAATAAGAAAACTAATCTT
GCGACAACGAGTGCCATCAAAAAAATCATTGCAGCATCAAAGAGTCAAAAGAAATTGCCT
GAAGTGACTATTTCAATTTCGCCCAGAGGAATTGAGTCATTCAATACAGCTACAGAAGAG
CCTATTCTACAAATTCCTATTTATAAAATTTCATACTGTTCTGTGGATGCATCACATGAT
ACAATTTTTTCCTTCGTCTGTTCAAATTCGGAGAAGGAAGAACATTTTGAAGTAAATCAA
TTCGGATCACCTGATTCACCTTCTGGGCATTTGGAATCAGCTTCAGTTGACGAAGATAGC
GATTTAGTACTTCATGCTTTTCAATGTAACAAACGCAAGATTGCAACAACTGTGACTTTA
TCTGTCGCACGATCATTTGAGCGTGCTTTTCAGATTTATCAGAATGAACAATTTTTAAAG
GAAGTTCGTGAAAAGAAAACTAACAAAGAAAATATTGCTGAGACACAAAACAATGCTGCT
AACATTAAAAACATCATTTCAAATGGAAAAGATGACGATAAGTGCTTGATTGATCTTGAC
GATGGCCCTCAACTGAATTATTTGTACTCTAAGGAAAGAAATCGTGAATATTTCAAGACA
ACTTGGGTCAATTTTGAGTGA
>g5065.t2 Gene=g5065 Length=286
MSFLFKSMWKNNCKHHKLNEELALASSIRDFAESPLDLNDEELTDDAIVYNLKYLGSTQL
LPQAKNEETKKTKFNKKTNLATTSAIKKIIAASKSQKKLPEVTISISPRGIESFNTATEE
PILQIPIYKISYCSVDASHDTIFSFVCSNSEKEEHFEVNQFGSPDSPSGHLESASVDEDS
DLVLHAFQCNKRKIATTVTLSVARSFERAFQIYQNEQFLKEVREKKTNKENIAETQNNAA
NIKNIISNGKDDDKCLIDLDDGPQLNYLYSKERNREYFKTTWVNFE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5065.t2 | Coils | Coil | Coil | 219 | 239 | - |
| 6 | g5065.t2 | Gene3D | G3DSA:2.30.29.30 | - | 46 | 220 | 4.2E-33 |
| 2 | g5065.t2 | PANTHER | PTHR11232:SF35 | LOW DENSITY LIPOPROTEIN RECEPTOR ADAPTER PROTEIN 1 | 1 | 277 | 1.4E-42 |
| 3 | g5065.t2 | PANTHER | PTHR11232 | PHOSPHOTYROSINE INTERACTION DOMAIN-CONTAINING FAMILY MEMBER | 1 | 277 | 1.4E-42 |
| 1 | g5065.t2 | Pfam | PF00640 | Phosphotyrosine interaction domain (PTB/PID) | 50 | 215 | 1.3E-13 |
| 8 | g5065.t2 | ProSiteProfiles | PS01179 | Phosphotyrosine interaction domain (PID) profile. | 50 | 221 | 15.215 |
| 5 | g5065.t2 | SMART | SM00462 | PTB_9 | 45 | 219 | 8.7E-13 |
| 4 | g5065.t2 | SUPERFAMILY | SSF50729 | PH domain-like | 37 | 216 | 1.85E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5065/g5065.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5065.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12474 (low density lipoprotein receptor adapter protein 1)
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.
