General information for g5300.t3
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.t3 | TSS | g5300.t3 | 8579693 | 8579693 |
| chr_2 | g5300 | g5300.t3 | isoform | g5300.t3 | 8580568 | 8586132 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon1 | 8580568 | 8580625 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS1 | 8580579 | 8580625 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon2 | 8580679 | 8580747 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS2 | 8580679 | 8580747 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon3 | 8580933 | 8581004 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS3 | 8580933 | 8581004 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon4 | 8581066 | 8581137 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS4 | 8581066 | 8581137 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon5 | 8581192 | 8581283 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS5 | 8581192 | 8581283 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon6 | 8583701 | 8583889 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS6 | 8583701 | 8583889 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon7 | 8583949 | 8584001 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS7 | 8583949 | 8584001 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon8 | 8584068 | 8584118 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS8 | 8584068 | 8584118 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon9 | 8584189 | 8584244 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS9 | 8584189 | 8584244 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon10 | 8584313 | 8584338 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS10 | 8584313 | 8584338 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon11 | 8584465 | 8584566 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS11 | 8584465 | 8584566 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon12 | 8584628 | 8584703 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS12 | 8584628 | 8584703 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon13 | 8585033 | 8585142 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS13 | 8585033 | 8585142 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon14 | 8585752 | 8585853 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS14 | 8585752 | 8585853 |
| chr_2 | g5300 | g5300.t3 | exon | g5300.t3.exon15 | 8585927 | 8586132 |
| chr_2 | g5300 | g5300.t3 | cds | g5300.t3.CDS15 | 8585927 | 8586132 |
| chr_2 | g5300 | g5300.t3 | TTS | g5300.t3 | 8586110 | 8586110 |
Sequences
>g5300.t3 Gene=g5300 Length=1334
ATGCTGGATCGATGAGTTTTGGTAGTGGCGGTGGTATGGGTGGAAGTGGATCATCAGCAA
ATGCCGGTTCAAAAAGTTTTTATCAACCAAGTGCAATTTTTTCTTATGGTGGAAGTGGAT
CTTCTGCAAATTCAGGTTCAATGAATTATGGTTTTTCACCAGCAAATTTACAGTCAGTGG
GAGGAAGCAGTTCATCAGCTAACGCTGGCTCATCGAGTTTCAATTTCCAACCTGGTGTAA
TGCAGTCATATGGTGGAAGTGGTTCATCCGCAAATGCTGGATCAATGAGTTTTGGCAGTG
GTTTACAATCAGGTGGCAGTGGATCATTTTCACAAGCAGGCTCATCATCATTCTCAATGA
GTGGCAAACAATGCACACAAAGACCACAACCACCCGCAAATGCAGGAATGAAATGTTCAC
AATCGGCATGTCAGATTACATGCTTAGCTGACTATAAATTTCCAAATGGTGAAATGACCA
TGACACTCGAATGCAACAATGGCCGTTGGCTCGTGAAAAGCCTCGAACTTAACGAGATGC
CGCCTTGTGAACCAATATGTCTACCTAAGTGTTTAAATAACGGAATTTGTGTAGCACCTG
GACAGTGTAAATGTCCTGAAAACTATATGGGTCCAACATGTCAAATGAAGAAAGAGCTAT
GTCTCGCATCACCACCGCTCCCGGCAAATTCAAAGCGAAGCTGTACATCATCCTTGTGCA
CTGTAACATGCATGAAAGGCTACAAGTTTCCTGATGCATCGCTTTCCATGAATCTTTTAT
GCAAAAGCGGCAAATGGGTGCCTGAAAAGCAAGGAATTCAACTTATACCAGATTGCGAAC
CTGTTTGTGATTCTCCATGTCTTAATGGAGGAACTTGCTTATCGTACAATGTGTGTCAAT
GTACAGCAAATTATAGAGGTGCTCAATGTCAGTACAGCATAGAACGTTGCTTGCCAAAAA
AGCTCAACTTTAACGGTGCTTACAACTGCACAAGCACGGGAGATTTCATTAGTTGCAAAC
TTTACTGTCCGAAAGGAATAAGTTTTGACTTTGAGCCAGCATCAGTTTACACATGCAGCT
ATGCAGTGGGTGAATTTATGCCGAAACAAGTTCCCACATGTGTTTATGGAGAAGGAATGC
AAGTAGTTCAATTGGCACCAACTGGAAAAATTGAATATTCTCAAACAAATGGAACACTTA
AAAAACAGTCAAGTGGTAAGAAAATTATTAAGCAAGAGATTGACTATGATGACGGAGATG
AGGAAGAAGAAATTGAAGAGACCATCATAAAAAAGACGAAAGTTATCAAGAAGAAAAAAA
AGACAAAAAATATC
>g5300.t3 Gene=g5300 Length=441
MSFGSGGGMGGSGSSANAGSKSFYQPSAIFSYGGSGSSANSGSMNYGFSPANLQSVGGSS
SSANAGSSSFNFQPGVMQSYGGSGSSANAGSMSFGSGLQSGGSGSFSQAGSSSFSMSGKQ
CTQRPQPPANAGMKCSQSACQITCLADYKFPNGEMTMTLECNNGRWLVKSLELNEMPPCE
PICLPKCLNNGICVAPGQCKCPENYMGPTCQMKKELCLASPPLPANSKRSCTSSLCTVTC
MKGYKFPDASLSMNLLCKSGKWVPEKQGIQLIPDCEPVCDSPCLNGGTCLSYNVCQCTAN
YRGAQCQYSIERCLPKKLNFNGAYNCTSTGDFISCKLYCPKGISFDFEPASVYTCSYAVG
EFMPKQVPTCVYGEGMQVVQLAPTGKIEYSQTNGTLKKQSSGKKIIKQEIDYDDGDEEEE
IEETIIKKTKVIKKKKKTKNI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5300.t3 | Gene3D | G3DSA:2.10.25.10 | Laminin | 110 | 216 | 1.0E-7 |
| 10 | g5300.t3 | Gene3D | G3DSA:2.10.25.10 | Laminin | 219 | 312 | 7.6E-8 |
| 3 | g5300.t3 | PANTHER | PTHR14949 | EGF-LIKE-DOMAIN, MULTIPLE 7, 8 | 107 | 245 | 2.3E-15 |
| 2 | g5300.t3 | PANTHER | PTHR14949 | EGF-LIKE-DOMAIN, MULTIPLE 7, 8 | 272 | 351 | 2.3E-15 |
| 1 | g5300.t3 | Pfam | PF07974 | EGF-like domain | 186 | 210 | 6.0E-5 |
| 8 | g5300.t3 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 199 | 210 | - |
| 9 | g5300.t3 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 295 | 306 | - |
| 13 | g5300.t3 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 180 | 211 | 10.534 |
| 12 | g5300.t3 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 276 | 307 | 11.806 |
| 6 | g5300.t3 | SMART | SM00181 | egf_5 | 178 | 211 | 0.017 |
| 7 | g5300.t3 | SMART | SM00181 | egf_5 | 274 | 307 | 15.0 |
| 4 | g5300.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 176 | 221 | 1.4E-6 |
| 5 | g5300.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 272 | 316 | 1.28E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5300/g5300.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5300.t3.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.
