General information for g5300.t1
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.t1 | TSS | g5300.t1 | 8579693 | 8579693 |
| chr_2 | g5300 | g5300.t1 | isoform | g5300.t1 | 8579816 | 8587690 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon1 | 8579816 | 8579922 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS1 | 8579816 | 8579922 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon2 | 8580088 | 8580273 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS2 | 8580088 | 8580273 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon3 | 8580336 | 8580389 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS3 | 8580336 | 8580389 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon4 | 8580566 | 8580625 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS4 | 8580566 | 8580625 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon5 | 8580679 | 8580747 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS5 | 8580679 | 8580747 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon6 | 8580933 | 8581004 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS6 | 8580933 | 8581004 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon7 | 8581066 | 8581137 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS7 | 8581066 | 8581137 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon8 | 8581192 | 8581283 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS8 | 8581192 | 8581283 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon9 | 8583701 | 8583889 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS9 | 8583701 | 8583889 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon10 | 8583949 | 8584001 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS10 | 8583949 | 8584001 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon11 | 8584068 | 8584118 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS11 | 8584068 | 8584118 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon12 | 8584189 | 8584244 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS12 | 8584189 | 8584244 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon13 | 8584313 | 8584338 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS13 | 8584313 | 8584338 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon14 | 8584465 | 8584566 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS14 | 8584465 | 8584566 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon15 | 8584628 | 8584703 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS15 | 8584628 | 8584703 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon16 | 8585033 | 8585142 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS16 | 8585033 | 8585142 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon17 | 8585752 | 8585853 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS17 | 8585752 | 8585853 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon18 | 8585927 | 8586132 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS18 | 8585927 | 8586132 |
| chr_2 | g5300 | g5300.t1 | exon | g5300.t1.exon19 | 8587634 | 8587690 |
| chr_2 | g5300 | g5300.t1 | cds | g5300.t1.CDS19 | 8587634 | 8587690 |
| chr_2 | g5300 | g5300.t1 | TTS | g5300.t1 | NA | NA |
Sequences
>g5300.t1 Gene=g5300 Length=1740
ATGATAAATTTAAAGTGGATTTATTTGACATTGGCACTATGTGTGCATCTTTTTAGTGTC
ACTTTATCACAAGATTTTGTGTTTCCCGAAAGTGATGAAAATAATGACCCCTTTCAAAGT
ATTCGAAGCAATTGGCAAATTAAAACTCCATCAAACGTTCTCGATAAAGGTGTGAAATCT
GTAAAAACCTTTTTCTCAACCTCATCGAGATCGTCTGACCAGCAACCCGTTCAAGAACCA
TTGGCAACACGAATCCTAACGTATCAATCTGGCTCAGGTTCTTCGGCACAAGCTAATTCT
GGATCAATGAATTTTGGAAGTGGAATGAGTGGCAGTGGTTCATCTGCAAATGCTGGATCG
ATGAGTTTTGGTAGTGGCGGTGGTATGGGTGGAAGTGGATCATCAGCAAATGCCGGTTCA
AAAAGTTTTTATCAACCAAGTGCAATTTTTTCTTATGGTGGAAGTGGATCTTCTGCAAAT
TCAGGTTCAATGAATTATGGTTTTTCACCAGCAAATTTACAGTCAGTGGGAGGAAGCAGT
TCATCAGCTAACGCTGGCTCATCGAGTTTCAATTTCCAACCTGGTGTAATGCAGTCATAT
GGTGGAAGTGGTTCATCCGCAAATGCTGGATCAATGAGTTTTGGCAGTGGTTTACAATCA
GGTGGCAGTGGATCATTTTCACAAGCAGGCTCATCATCATTCTCAATGAGTGGCAAACAA
TGCACACAAAGACCACAACCACCCGCAAATGCAGGAATGAAATGTTCACAATCGGCATGT
CAGATTACATGCTTAGCTGACTATAAATTTCCAAATGGTGAAATGACCATGACACTCGAA
TGCAACAATGGCCGTTGGCTCGTGAAAAGCCTCGAACTTAACGAGATGCCGCCTTGTGAA
CCAATATGTCTACCTAAGTGTTTAAATAACGGAATTTGTGTAGCACCTGGACAGTGTAAA
TGTCCTGAAAACTATATGGGTCCAACATGTCAAATGAAGAAAGAGCTATGTCTCGCATCA
CCACCGCTCCCGGCAAATTCAAAGCGAAGCTGTACATCATCCTTGTGCACTGTAACATGC
ATGAAAGGCTACAAGTTTCCTGATGCATCGCTTTCCATGAATCTTTTATGCAAAAGCGGC
AAATGGGTGCCTGAAAAGCAAGGAATTCAACTTATACCAGATTGCGAACCTGTTTGTGAT
TCTCCATGTCTTAATGGAGGAACTTGCTTATCGTACAATGTGTGTCAATGTACAGCAAAT
TATAGAGGTGCTCAATGTCAGTACAGCATAGAACGTTGCTTGCCAAAAAAGCTCAACTTT
AACGGTGCTTACAACTGCACAAGCACGGGAGATTTCATTAGTTGCAAACTTTACTGTCCG
AAAGGAATAAGTTTTGACTTTGAGCCAGCATCAGTTTACACATGCAGCTATGCAGTGGGT
GAATTTATGCCGAAACAAGTTCCCACATGTGTTTATGGAGAAGGAATGCAAGTAGTTCAA
TTGGCACCAACTGGAAAAATTGAATATTCTCAAACAAATGGAACACTTAAAAAACAGTCA
AGTGGTAAGAAAATTATTAAGCAAGAGATTGACTATGATGACGGAGATGAGGAAGAAGAA
ATTGAAGAGACCATCATAAAAAAGACGAAAGTTATCAAGAAGAAAAAAAAGACAAAAAAT
ATCGTTGAAGAAGAAGACGAAGAATTTTTCCAACACCAGGAGTTTATCAGCTTTATTTGA
>g5300.t1 Gene=g5300 Length=579
MINLKWIYLTLALCVHLFSVTLSQDFVFPESDENNDPFQSIRSNWQIKTPSNVLDKGVKS
VKTFFSTSSRSSDQQPVQEPLATRILTYQSGSGSSAQANSGSMNFGSGMSGSGSSANAGS
MSFGSGGGMGGSGSSANAGSKSFYQPSAIFSYGGSGSSANSGSMNYGFSPANLQSVGGSS
SSANAGSSSFNFQPGVMQSYGGSGSSANAGSMSFGSGLQSGGSGSFSQAGSSSFSMSGKQ
CTQRPQPPANAGMKCSQSACQITCLADYKFPNGEMTMTLECNNGRWLVKSLELNEMPPCE
PICLPKCLNNGICVAPGQCKCPENYMGPTCQMKKELCLASPPLPANSKRSCTSSLCTVTC
MKGYKFPDASLSMNLLCKSGKWVPEKQGIQLIPDCEPVCDSPCLNGGTCLSYNVCQCTAN
YRGAQCQYSIERCLPKKLNFNGAYNCTSTGDFISCKLYCPKGISFDFEPASVYTCSYAVG
EFMPKQVPTCVYGEGMQVVQLAPTGKIEYSQTNGTLKKQSSGKKIIKQEIDYDDGDEEEE
IEETIIKKTKVIKKKKKTKNIVEEEDEEFFQHQEFISFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5300.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 229 | 336 | 1.4E-7 |
| 7 | g5300.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 339 | 432 | 2.8E-8 |
| 3 | g5300.t1 | PANTHER | PTHR14949 | EGF-LIKE-DOMAIN, MULTIPLE 7, 8 | 227 | 365 | 6.4E-16 |
| 2 | g5300.t1 | PANTHER | PTHR14949 | EGF-LIKE-DOMAIN, MULTIPLE 7, 8 | 392 | 471 | 6.4E-16 |
| 1 | g5300.t1 | Pfam | PF07974 | EGF-like domain | 306 | 330 | 8.4E-5 |
| 10 | g5300.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 11 | g5300.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 12 | g5300.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 13 | g5300.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 9 | g5300.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 579 | - |
| 16 | g5300.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 319 | 330 | - |
| 15 | g5300.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 415 | 426 | - |
| 20 | g5300.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 300 | 331 | 10.534 |
| 19 | g5300.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 396 | 427 | 11.806 |
| 18 | g5300.t1 | SMART | SM00181 | egf_5 | 298 | 331 | 0.017 |
| 17 | g5300.t1 | SMART | SM00181 | egf_5 | 394 | 427 | 15.0 |
| 5 | g5300.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 296 | 341 | 2.05E-6 |
| 4 | g5300.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 392 | 435 | 1.84E-7 |
| 6 | g5300.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 14 | g5300.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5300/g5300.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5300.t1.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.
