General information for g5506.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Synaptogenesis protein syg-1.
Parent gene
- The parent gene g5506 is located on chr_2: 9954850..9962064 (+ 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 | g5506 | g5506.t1 | TSS | g5506.t1 | 9954428 | 9954428 |
| chr_2 | g5506 | g5506.t1 | isoform | g5506.t1 | 9954850 | 9962064 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon1 | 9954850 | 9954954 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS1 | 9954850 | 9954954 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon2 | 9955210 | 9955357 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS2 | 9955210 | 9955357 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon3 | 9956944 | 9957074 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS3 | 9956944 | 9957074 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon4 | 9958549 | 9958708 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS4 | 9958549 | 9958708 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon5 | 9958974 | 9959073 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS5 | 9958974 | 9959073 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon6 | 9959160 | 9959271 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS6 | 9959160 | 9959271 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon7 | 9959486 | 9959567 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS7 | 9959486 | 9959567 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon8 | 9959696 | 9959837 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS8 | 9959696 | 9959837 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon9 | 9959982 | 9960166 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS9 | 9959982 | 9960166 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon10 | 9960228 | 9960493 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS10 | 9960228 | 9960493 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon11 | 9960629 | 9960767 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS11 | 9960629 | 9960767 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon12 | 9960881 | 9960939 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS12 | 9960881 | 9960939 |
| chr_2 | g5506 | g5506.t1 | exon | g5506.t1.exon13 | 9961954 | 9962064 |
| chr_2 | g5506 | g5506.t1 | cds | g5506.t1.CDS13 | 9961954 | 9962064 |
| chr_2 | g5506 | g5506.t1 | TTS | g5506.t1 | NA | NA |
Sequences
>g5506.t1 Gene=g5506 Length=1740
ATGGTTGCTGATCGAAGATATGAGATTATCTGTGAGAGTTCTGGATCAAGACCAAACGCA
ATCATTACCTGGTACAAGGGAAAAAGACAACTAAGAAGAACGAAGGATGAGATTTTGAAT
AATACCACAAAATCGGAATTAAGCTTTTCACCTACTGTAGAGGATGATGGAAAATTTATG
GTGTGTCGAGCGGAGAATCCCGTGTCCTCGACGAGTCTTTTTCTCGAAGCAACATATAAA
CTAAGCGTTGTCTATCCGCCGCTTGTGACTTTACAACTCGGTTCGACTCTTACAAATGAT
GATATCAAGGAGGGAGACGATGTTTATTTCGAATGTCATGTCGAAGCGAATCCAAGATTT
ACAAAACTCTCATGGCTTCATAATGGTATTCATTTAACGCACAATGCATCGGCTCGTATA
ATTAGATCCAATCAAAGTCTGGTGCTACAGAAAGTTACCCGAAATTCATCTGGAAATTAC
GCCTGCAGTGCTTTGAATTCAGAAGGTGAAACTGTAAGCAATCAGCTTCCTTTAAGGGTC
AAATATGCCCCAGTCTGTGCCACCGACAAAGTAGTCCTAATTGGTGCTGCCAAGGATGAA
AGTGTAGAAATAATTTGTGATATTCATGCCGACCCGCCGGCAAGAAAGTTTCGATGGAAA
TTTAATAATTCGGGTGAAGTCTTGTTTCTTGACTCGGAGCGTTTCAGTAAAAATGGTACA
CGAAGCATTCTCTTATATACACCCGTTACAGAACAGGACTTTGGAACGTTGTCTTGCTGG
GCGATAAATGAGATTGGCGAACAATCTGTTAGTTGCTTATTTCAAGTTGTTCTGGCAGTC
ACTCCATCACCTGTCACAAACTGCAGTGTTAGTAATTACACGAGAGAAGTAGCAGAGATC
CAATGTACATCGGGTTATGATGGCGGTATCCAGCAGCGTTTTGTACTTGAAATGATATCA
AGAAAGACTAAAGCAATCAAATACAACTTCACTAACGCTGATGAGCCATTTTTCGTGTTG
GATATGCTTGAGTTAATTAACGCTAAGCTAATTGAAGAGAATGACTCGGTGTTCATTGTT
GTTTACGCTGTTAATCAGAAGGGTAGTAGCATAGGTGTTATCATTCGTGATTTAGAACTC
GGTGCTGTTCAGAAATTAGATAGAGTAGATAACTTAATTGTTGTTGCTGGCTCGCAAGAT
ACGCTTCCATATTTTATCGGAATAATTGCAACAATTCTCATCGTGTTTATTTTTATCGCT
TTTAAAATAATTTCGGTTTGTTGGACACAAGACTCATCCTCAAAACGAACTTCTACTGCG
CCCACAACAGTAACAACGTCAATAACACATAATGAACAAAATGGAGCGACAAAATTGACA
AATCATTCAAATAATTTGTTGATAATTAGCAGTTATAACGGTGGCATTAAGAATGGAATT
AACAATAATGTTGGTCAGGCAATCACAACATTTACATCACCTACGAGTAGTCTCAAGAGC
AACAAGCCACAAATACTCGATGATGATGTAGATAGAGATCCAGACGTTATTCCTCCTTAT
CACCAATATGGCTCATCGATTTCGACTACAGAAGAACCATATAGCTATAAATCTTTTCAG
CAGCAAGACGCATTTCACCTTATAAGCACAAGTATGCTTTCGAGACAGGCTGCGAGATCG
ATAAATGAGGAAATTAAAGAGCGCCTCATGAACGCAAAAGTTCCGGAGAGTTGCGTTTAA
>g5506.t1 Gene=g5506 Length=579
MVADRRYEIICESSGSRPNAIITWYKGKRQLRRTKDEILNNTTKSELSFSPTVEDDGKFM
VCRAENPVSSTSLFLEATYKLSVVYPPLVTLQLGSTLTNDDIKEGDDVYFECHVEANPRF
TKLSWLHNGIHLTHNASARIIRSNQSLVLQKVTRNSSGNYACSALNSEGETVSNQLPLRV
KYAPVCATDKVVLIGAAKDESVEIICDIHADPPARKFRWKFNNSGEVLFLDSERFSKNGT
RSILLYTPVTEQDFGTLSCWAINEIGEQSVSCLFQVVLAVTPSPVTNCSVSNYTREVAEI
QCTSGYDGGIQQRFVLEMISRKTKAIKYNFTNADEPFFVLDMLELINAKLIEENDSVFIV
VYAVNQKGSSIGVIIRDLELGAVQKLDRVDNLIVVAGSQDTLPYFIGIIATILIVFIFIA
FKIISVCWTQDSSSKRTSTAPTTVTTSITHNEQNGATKLTNHSNNLLIISSYNGGIKNGI
NNNVGQAITTFTSPTSSLKSNKPQILDDDVDRDPDVIPPYHQYGSSISTTEEPYSYKSFQ
QQDAFHLISTSMLSRQAARSINEEIKERLMNAKVPESCV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5506.t1 | CDD | cd00096 | Ig | 108 | 173 | 4.80151E-8 |
| 13 | g5506.t1 | CDD | cd00096 | Ig | 202 | 272 | 5.1042E-6 |
| 9 | g5506.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 89 | 1.4E-16 |
| 7 | g5506.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 92 | 182 | 3.4E-17 |
| 8 | g5506.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 183 | 277 | 5.1E-11 |
| 3 | g5506.t1 | PANTHER | PTHR23278 | SIDESTEP PROTEIN | 2 | 443 | 7.6E-134 |
| 1 | g5506.t1 | Pfam | PF08205 | CD80-like C2-set immunoglobulin domain | 6 | 70 | 3.3E-7 |
| 2 | g5506.t1 | Pfam | PF13927 | Immunoglobulin domain | 86 | 166 | 1.2E-11 |
| 11 | g5506.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 403 | - |
| 12 | g5506.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 404 | 428 | - |
| 10 | g5506.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 429 | 579 | - |
| 23 | g5506.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 1 | 82 | 9.119 |
| 21 | g5506.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 86 | 173 | 13.058 |
| 22 | g5506.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 177 | 271 | 8.538 |
| 19 | g5506.t1 | SMART | SM00408 | igc2_5 | 2 | 69 | 0.91 |
| 17 | g5506.t1 | SMART | SM00409 | IG_3c | 97 | 181 | 1.2E-5 |
| 18 | g5506.t1 | SMART | SM00408 | igc2_5 | 103 | 169 | 1.6E-9 |
| 16 | g5506.t1 | SMART | SM00409 | IG_3c | 191 | 277 | 13.0 |
| 20 | g5506.t1 | SMART | SM00408 | igc2_5 | 197 | 266 | 3.3 |
| 5 | g5506.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 3 | 87 | 9.25E-13 |
| 6 | g5506.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 83 | 185 | 4.3E-17 |
| 4 | g5506.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 199 | 281 | 4.28E-11 |
| 15 | g5506.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 404 | 426 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5506/g5506.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5506.t1.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 K06467 (CD22 antigen)
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. There were no conditions that were differentially expressed