General information for g2469.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein sel-1 homolog 1.
Parent gene
- The parent gene g2469 is located on chr_3: 18122733..18123802 (+ 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_3 | g2469 | g2469.t1 | TSS | g2469.t1 | 18119581 | 18119581 |
| chr_3 | g2469 | g2469.t1 | isoform | g2469.t1 | 18119758 | 18122733 |
| chr_3 | g2469 | g2469.t1 | exon | g2469.t1.exon1 | 18119758 | 18120208 |
| chr_3 | g2469 | g2469.t1 | cds | g2469.t1.CDS1 | 18119758 | 18120208 |
| chr_3 | g2469 | g2469.t1 | exon | g2469.t1.exon2 | 18120266 | 18121023 |
| chr_3 | g2469 | g2469.t1 | cds | g2469.t1.CDS2 | 18120266 | 18121023 |
| chr_3 | g2469 | g2469.t1 | exon | g2469.t1.exon3 | 18121591 | 18122733 |
| chr_3 | g2469 | g2469.t1 | cds | g2469.t1.CDS3 | 18121591 | 18122733 |
| chr_3 | g2469 | g2469.t1 | TTS | g2469.t1 | 18122933 | 18122933 |
Sequences
>g2469.t1 Gene=g2469 Length=2352
ATGAAATTCAATTTTGTAATTTTCCTATTAGTAATTGTTGCCATAAATTGTGCATTTGGT
AATTCAGAGCAACAAGAATCCGATTTAAAAGAGCAATCTAAACAATATGAACGCAAATCT
GCCAAAGGACTTGACGAAGATGAATCAAGTGAACAAGAAGAGAATACAGTTAATCATCAG
CAAACAACATCCAGTGAAGAATTAGACGAAGATCAATTTATCAAAATAATTGCTGATGAT
TTAAATCTTCCAAGTAGTGGAATCAAAATAGTTAAAGCGCCAGACCTCTCGAAAGATAAT
GAAGGCAAAAAGATTACGGACTCACTTGCAATGATGATTGAAAATCAAGAAAAATGGATA
CAAAAAATCGAAGAAGAGCTTGAAGAAATAAATAAAAATGAATCAACAGAAGAGAAACAA
GAGAAAGAAAAGACGGCAGAAGAAATTGAAGCTGATAACTTTTATGAACAAGCTTTAAAA
ATTCTCAATAAAACTAAAGCATCAAATAGAGCTGAAGGATTTTCTCTACTTCATAAAGCT
GCTGAAAAGGGTCACAAATTGGCTAAAGTTAATATTGCATGGGCTCATTTGCTAGGGAAT
CCTCTTGAGCTAAAAATTGAAACTGCTAAAGCAATTTTCGAAGAGTTAGCAGAATTAGGA
ATGGCTGAAGCTCATATGGGCCTTGGTTTTATGTATTCAACAGGAATTGGTTATAATGTT
TCTCAATCAAAAGCACTTGTTCATTATACTGTTGCTGCTATTGGAGATAATGCTTTTGCA
CAAATGGCTCTTGGTTATCGATATTGGGCAGGTGTTACTGTGGCAAACAGCTGTGAAAAG
GCTTTAGACTTTTATCGTAAAGTAGCAACAAAAGTTGCTTCGGAAGTCAAATTCTCGGGC
GGACCTGCAATTCATCGTGTAAGACTATTGGATGAAGTTGAAAATGCTGGTTTGAGTTCT
GGAGTTTTAGACAATGATTTGATTGATTATTATGAACTACTTGCTAACAAAGGCGATATT
CAAGCTCAAGTAGGTTTGGGACAATTACATTATCAAGGCGGACGAGGAATCCCACTTGAT
CATAAGAAAGCATTGTCTTATTTTCTACCAGCTGCAAATGCTGGAAATGCTGTAGCAATG
GGCTTCTTAGGTAAAATCTATCTTGAAGGAAGTGAACATATTAAAGCTGATAACGAAACT
GCATTTAAGTATTTCAAAAAAGCAGCAGAGTTAGGAAATCCGGTTGGTCAAAGTGGTCTT
GGTATTATGTATTTACAAGGAAAAGGTGTAACAAAAGATACAGATCAAGCACTCAAATAT
TTTACGCTTGCTGCAGATCAAGGATGGGTTGATGGTCAATTACAACTTGGGAATATGTAT
TATGGTGGAATCGGTGTGAAAAGAGATTTTAAACTTGCGAGTAAATACTTTAATCTTGCA
TCGCAGTCCGGGCATGTTTTAGCGTTTTACAACCTCGCTCAAATGCATAGTACTGGTGTT
GGAATGATGCGCTCATGTCCAACTGCTGTTGAACTATTCAAGAATGTTGCAGAACGTGGA
AAATGGGGCGAACGATTAATGATTGCTTATCAGGATTATCGAGTATATAAATATGATGAG
GCTTTTATGCAATATGCTCTTCTCGCTGAACTCGGATATGAAGTTGCACAATCAAATACA
GCGTGGCTTTTAGACAGAAATGAAATCAAACTTTTTAACAATCGACAAGAGGAATTGATA
AGAGCGTTACAACAATGGGGAAGAGCAGCAGGTCAAGGATATTCTGCAGCTCAAGTAAAA
CTCGGTGATTATCATTATTATGGTCTCGGAACTGGCGTTGTTGACTATGAAACTGCAGCA
TCTCACTATAGAACTGCATCAGAACAACAGCATAATGCACAAGCTATGTTTAATTTAGCA
TATATGCATGAGCAAGGATTAGGGATGAAAAAAGACATGCATCTTGCTAAACGATTTTAT
GATTTAGCTGCAGAAACAAATGCTGATGCAAAAATTCCTGTTGCTTTAGCATTACTCAAA
CTACAAGTTCTTTATAAACTCGATTCATTTTTAAATCGTGAAGATAACTTTTTCAAAGTA
CTTGGGCTTGATGAAAATTTCGCATCAAATTGGGATTTATATTTAATTACAATTATCACA
ATACTATTGGGCATGATTATTTATTCAAGAAGACCTCCGCCTGAAGCACCAGCTTCTCAG
GTACAGCAGCAACAGCAACAACAACAAACAAGCAGTAATAATGATTCAAATAGTAGTAAT
AATACTAATGATGAACAACAACCATCAAACGATAGTCAGCAGCAAAATAATAGCAACACA
AGTGTACAATAA
>g2469.t1 Gene=g2469 Length=783
MKFNFVIFLLVIVAINCAFGNSEQQESDLKEQSKQYERKSAKGLDEDESSEQEENTVNHQ
QTTSSEELDEDQFIKIIADDLNLPSSGIKIVKAPDLSKDNEGKKITDSLAMMIENQEKWI
QKIEEELEEINKNESTEEKQEKEKTAEEIEADNFYEQALKILNKTKASNRAEGFSLLHKA
AEKGHKLAKVNIAWAHLLGNPLELKIETAKAIFEELAELGMAEAHMGLGFMYSTGIGYNV
SQSKALVHYTVAAIGDNAFAQMALGYRYWAGVTVANSCEKALDFYRKVATKVASEVKFSG
GPAIHRVRLLDEVENAGLSSGVLDNDLIDYYELLANKGDIQAQVGLGQLHYQGGRGIPLD
HKKALSYFLPAANAGNAVAMGFLGKIYLEGSEHIKADNETAFKYFKKAAELGNPVGQSGL
GIMYLQGKGVTKDTDQALKYFTLAADQGWVDGQLQLGNMYYGGIGVKRDFKLASKYFNLA
SQSGHVLAFYNLAQMHSTGVGMMRSCPTAVELFKNVAERGKWGERLMIAYQDYRVYKYDE
AFMQYALLAELGYEVAQSNTAWLLDRNEIKLFNNRQEELIRALQQWGRAAGQGYSAAQVK
LGDYHYYGLGTGVVDYETAASHYRTASEQQHNAQAMFNLAYMHEQGLGMKKDMHLAKRFY
DLAAETNADAKIPVALALLKLQVLYKLDSFLNREDNFFKVLGLDENFASNWDLYLITIIT
ILLGMIIYSRRPPPEAPASQVQQQQQQQQTSSNNDSNSSNNTNDEQQPSNDSQQQNNSNT
SVQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g2469.t1 | Coils | Coil | Coil | 22 | 42 | - |
| 21 | g2469.t1 | Coils | Coil | Coil | 113 | 152 | - |
| 19 | g2469.t1 | Gene3D | G3DSA:1.25.40.10 | - | 19 | 315 | 1.0E-26 |
| 18 | g2469.t1 | Gene3D | G3DSA:1.25.40.10 | - | 326 | 779 | 2.9E-81 |
| 41 | g2469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 24 | 69 | - |
| 43 | g2469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 27 | 46 | - |
| 42 | g2469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 734 | 783 | - |
| 40 | g2469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 736 | 783 | - |
| 11 | g2469.t1 | PANTHER | PTHR11102:SF70 | PROTEIN SEL-1 HOMOLOG 1 | 116 | 740 | 2.3E-241 |
| 12 | g2469.t1 | PANTHER | PTHR11102 | SEL-1-LIKE PROTEIN | 116 | 740 | 2.3E-241 |
| 3 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 167 | 185 | 13.0 |
| 6 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 222 | 253 | 2.5 |
| 5 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 258 | 287 | 2.2 |
| 10 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 341 | 376 | 0.0021 |
| 2 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 378 | 413 | 1.6E-6 |
| 1 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 416 | 448 | 5.1E-7 |
| 8 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 452 | 485 | 0.0029 |
| 7 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 490 | 520 | 79.0 |
| 9 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 595 | 631 | 0.0034 |
| 4 | g2469.t1 | Pfam | PF08238 | Sel1 repeat | 633 | 665 | 7.8E-6 |
| 24 | g2469.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 25 | g2469.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 26 | g2469.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 28 | g2469.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 23 | g2469.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 710 | - |
| 27 | g2469.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 711 | 728 | - |
| 22 | g2469.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 729 | 783 | - |
| 32 | g2469.t1 | SMART | SM00671 | sel1 | 186 | 221 | 160.0 |
| 34 | g2469.t1 | SMART | SM00671 | sel1 | 222 | 257 | 0.05 |
| 30 | g2469.t1 | SMART | SM00671 | sel1 | 258 | 293 | 0.0018 |
| 37 | g2469.t1 | SMART | SM00671 | sel1 | 340 | 376 | 1.7E-6 |
| 33 | g2469.t1 | SMART | SM00671 | sel1 | 377 | 413 | 2.5E-8 |
| 36 | g2469.t1 | SMART | SM00671 | sel1 | 414 | 449 | 1.0E-10 |
| 38 | g2469.t1 | SMART | SM00671 | sel1 | 450 | 485 | 6.6E-9 |
| 31 | g2469.t1 | SMART | SM00671 | sel1 | 486 | 521 | 0.019 |
| 39 | g2469.t1 | SMART | SM00671 | sel1 | 595 | 631 | 3.6E-5 |
| 35 | g2469.t1 | SMART | SM00671 | sel1 | 633 | 668 | 8.8E-8 |
| 15 | g2469.t1 | SUPERFAMILY | SSF81901 | HCP-like | 167 | 289 | 1.22E-20 |
| 14 | g2469.t1 | SUPERFAMILY | SSF81901 | HCP-like | 360 | 563 | 4.38E-42 |
| 13 | g2469.t1 | SUPERFAMILY | SSF81901 | HCP-like | 534 | 668 | 3.01E-21 |
| 17 | g2469.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 29 | g2469.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 16 | g2469.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 20 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14026 (SEL1 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.
