General information for g5300.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5300 is located on chr_2: 8580679..8587690 (+ 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 | g5300 | g5300.t5 | TSS | g5300.t5 | 8579693 | 8579693 |
| chr_2 | g5300 | g5300.t5 | isoform | g5300.t5 | 8580679 | 8586132 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon1 | 8580679 | 8580747 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon2 | 8580933 | 8581004 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS1 | 8580946 | 8581004 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon3 | 8581066 | 8581137 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS2 | 8581066 | 8581137 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon4 | 8581192 | 8581283 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS3 | 8581192 | 8581283 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon5 | 8583701 | 8583889 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS4 | 8583701 | 8583889 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon6 | 8583949 | 8584001 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS5 | 8583949 | 8584001 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon7 | 8584068 | 8584118 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS6 | 8584068 | 8584118 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon8 | 8584189 | 8584244 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS7 | 8584189 | 8584244 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon9 | 8584313 | 8584338 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS8 | 8584313 | 8584338 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon10 | 8584465 | 8584566 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS9 | 8584465 | 8584566 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon11 | 8584628 | 8584703 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS10 | 8584628 | 8584703 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon12 | 8585033 | 8585142 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS11 | 8585033 | 8585142 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon13 | 8585752 | 8585853 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS12 | 8585752 | 8585853 |
| chr_2 | g5300 | g5300.t5 | exon | g5300.t5.exon14 | 8585927 | 8586132 |
| chr_2 | g5300 | g5300.t5 | cds | g5300.t5.CDS13 | 8585927 | 8586132 |
| chr_2 | g5300 | g5300.t5 | TTS | g5300.t5 | 8586110 | 8586110 |
Sequences
>g5300.t5 Gene=g5300 Length=1276
AAATGCCGGTTCAAAAAGTTTTTATCAACCAAGTGCAATTTTTTCTTATGGTGGAAGTGG
ATCTTCTGCAAATTCAGGTTCAATGAATTATGGTTTTTCACCAGCAAATTTACAGTCAGT
GGGAGGAAGCAGTTCATCAGCTAACGCTGGCTCATCGAGTTTCAATTTCCAACCTGGTGT
AATGCAGTCATATGGTGGAAGTGGTTCATCCGCAAATGCTGGATCAATGAGTTTTGGCAG
TGGTTTACAATCAGGTGGCAGTGGATCATTTTCACAAGCAGGCTCATCATCATTCTCAAT
GAGTGGCAAACAATGCACACAAAGACCACAACCACCCGCAAATGCAGGAATGAAATGTTC
ACAATCGGCATGTCAGATTACATGCTTAGCTGACTATAAATTTCCAAATGGTGAAATGAC
CATGACACTCGAATGCAACAATGGCCGTTGGCTCGTGAAAAGCCTCGAACTTAACGAGAT
GCCGCCTTGTGAACCAATATGTCTACCTAAGTGTTTAAATAACGGAATTTGTGTAGCACC
TGGACAGTGTAAATGTCCTGAAAACTATATGGGTCCAACATGTCAAATGAAGAAAGAGCT
ATGTCTCGCATCACCACCGCTCCCGGCAAATTCAAAGCGAAGCTGTACATCATCCTTGTG
CACTGTAACATGCATGAAAGGCTACAAGTTTCCTGATGCATCGCTTTCCATGAATCTTTT
ATGCAAAAGCGGCAAATGGGTGCCTGAAAAGCAAGGAATTCAACTTATACCAGATTGCGA
ACCTGTTTGTGATTCTCCATGTCTTAATGGAGGAACTTGCTTATCGTACAATGTGTGTCA
ATGTACAGCAAATTATAGAGGTGCTCAATGTCAGTACAGCATAGAACGTTGCTTGCCAAA
AAAGCTCAACTTTAACGGTGCTTACAACTGCACAAGCACGGGAGATTTCATTAGTTGCAA
ACTTTACTGTCCGAAAGGAATAAGTTTTGACTTTGAGCCAGCATCAGTTTACACATGCAG
CTATGCAGTGGGTGAATTTATGCCGAAACAAGTTCCCACATGTGTTTATGGAGAAGGAAT
GCAAGTAGTTCAATTGGCACCAACTGGAAAAATTGAATATTCTCAAACAAATGGAACACT
TAAAAAACAGTCAAGTGGTAAGAAAATTATTAAGCAAGAGATTGACTATGATGACGGAGA
TGAGGAAGAAGAAATTGAAGAGACCATCATAAAAAAGACGAAAGTTATCAAGAAGAAAAA
AAAGACAAAAAATATC
>g5300.t5 Gene=g5300 Length=398
MNYGFSPANLQSVGGSSSSANAGSSSFNFQPGVMQSYGGSGSSANAGSMSFGSGLQSGGS
GSFSQAGSSSFSMSGKQCTQRPQPPANAGMKCSQSACQITCLADYKFPNGEMTMTLECNN
GRWLVKSLELNEMPPCEPICLPKCLNNGICVAPGQCKCPENYMGPTCQMKKELCLASPPL
PANSKRSCTSSLCTVTCMKGYKFPDASLSMNLLCKSGKWVPEKQGIQLIPDCEPVCDSPC
LNGGTCLSYNVCQCTANYRGAQCQYSIERCLPKKLNFNGAYNCTSTGDFISCKLYCPKGI
SFDFEPASVYTCSYAVGEFMPKQVPTCVYGEGMQVVQLAPTGKIEYSQTNGTLKKQSSGK
KIIKQEIDYDDGDEEEEIEETIIKKTKVIKKKKKTKNI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5300.t5 | Gene3D | G3DSA:2.10.25.10 | Laminin | 67 | 174 | 1.6E-7 |
| 10 | g5300.t5 | Gene3D | G3DSA:2.10.25.10 | Laminin | 176 | 269 | 9.8E-8 |
| 2 | g5300.t5 | PANTHER | PTHR14949 | EGF-LIKE-DOMAIN, MULTIPLE 7, 8 | 65 | 202 | 1.0E-15 |
| 3 | g5300.t5 | PANTHER | PTHR14949 | EGF-LIKE-DOMAIN, MULTIPLE 7, 8 | 229 | 308 | 1.0E-15 |
| 1 | g5300.t5 | Pfam | PF07974 | EGF-like domain | 143 | 167 | 5.3E-5 |
| 8 | g5300.t5 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 156 | 167 | - |
| 9 | g5300.t5 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 252 | 263 | - |
| 12 | g5300.t5 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 137 | 168 | 10.534 |
| 13 | g5300.t5 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 233 | 264 | 11.806 |
| 7 | g5300.t5 | SMART | SM00181 | egf_5 | 135 | 168 | 0.017 |
| 6 | g5300.t5 | SMART | SM00181 | egf_5 | 231 | 264 | 15.0 |
| 4 | g5300.t5 | SUPERFAMILY | SSF57196 | EGF/Laminin | 133 | 178 | 1.74E-6 |
| 5 | g5300.t5 | SUPERFAMILY | SSF57196 | EGF/Laminin | 229 | 273 | 1.12E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5300/g5300.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5300.t5.fa.iupred3.txt does not exist
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.
