General information for g12805.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Netrin-B.
Parent gene
- The parent gene g12805 is located on chr_1: 26319293..26326459 (- 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_1 | g12805 | g12805.t1 | TTS | g12805.t1 | 26316176 | 26316176 |
| chr_1 | g12805 | g12805.t1 | isoform | g12805.t1 | 26316578 | 26322958 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon1 | 26316578 | 26316710 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS1 | 26316578 | 26316710 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon2 | 26316788 | 26316977 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS2 | 26316788 | 26316977 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon3 | 26317874 | 26317936 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS3 | 26317874 | 26317936 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon4 | 26319293 | 26319388 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS4 | 26319293 | 26319388 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon5 | 26319736 | 26319885 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS5 | 26319736 | 26319885 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon6 | 26321502 | 26321690 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS6 | 26321502 | 26321690 |
| chr_1 | g12805 | g12805.t1 | exon | g12805.t1.exon7 | 26322922 | 26322958 |
| chr_1 | g12805 | g12805.t1 | cds | g12805.t1.CDS7 | 26322922 | 26322958 |
| chr_1 | g12805 | g12805.t1 | TSS | g12805.t1 | NA | NA |
Sequences
>g12805.t1 Gene=g12805 Length=858
ATGGCTTTAATTGCATTATTTATGAGACTACAACGAACTTGCAATTGCAATGGACACGCT
AGACGATGTCGCTTCAATGTAGAACTGTACAAGTTGTCGGGCCGTGTTTCGGGTGGTGTA
TGCGTGGACTGTCGACATGATACAACTGGACGCTATTGTCACTACTGTAAAGAAGGCTTT
TACCGGGATCCATCTAAAGCAATTACACATAAAAAGGCATGCAAACCTTGTGCCTGTCAC
GCAATTGGATCAACGGGCAAATCATGTAACAATACGACCGGTCAATGTGCATGCAAAGAG
GGTGTGACCGGACTGACATGTAATCGATGCGCTCGCGGCTATCAGCAGAGTCGATCCCAT
ATTGCACCATGTATTAAAATTCCACGTGTTATTCACATGAATATGCCACAAAACACTGCA
CCAGAGAGCTATTATAATGACCAAACTGAAATGAAACCAAAATCACGAGAAGATTGCAAA
TGTAAAATTGAAGCACAACGATTGAATAGCAAGAAATTCTGCAAAAGAGATTATGCGATT
CTAGCAAAAGTCGTTGGCAAGCCGGGACGACGTGATGATGAGACCCGTTACAATATCATT
ATCAACCATGTATACAAGAATAGTGAAGGACGCAATCCAATCTCAGCTAGAAACAACAAG
AAGGTTCAGCTAGTCTTGCCCGCAGCAGCGAGCAACTGTCGATGTCCAAACTTGGAAATT
AACAAATCGTACTACATACTCGGAATGCACTCAAAGCATGGTAGAAATGAGCTTGAGATT
ACCAAGAAATCGATTGTCATCGAGTGGCGTGAGGACTTTAAGGGACGTTTTGAAAAGTTC
CGCAATGAATGCTACTAA
>g12805.t1 Gene=g12805 Length=285
MALIALFMRLQRTCNCNGHARRCRFNVELYKLSGRVSGGVCVDCRHDTTGRYCHYCKEGF
YRDPSKAITHKKACKPCACHAIGSTGKSCNNTTGQCACKEGVTGLTCNRCARGYQQSRSH
IAPCIKIPRVIHMNMPQNTAPESYYNDQTEMKPKSREDCKCKIEAQRLNSKKFCKRDYAI
LAKVVGKPGRRDDETRYNIIINHVYKNSEGRNPISARNNKKVQLVLPAAASNCRCPNLEI
NKSYYILGMHSKHGRNELEITKKSIVIEWREDFKGRFEKFRNECY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g12805.t1 | CDD | cd00055 | EGF_Lam | 14 | 67 | 6.07861E-5 |
| 13 | g12805.t1 | CDD | cd00055 | EGF_Lam | 76 | 124 | 5.55425E-12 |
| 10 | g12805.t1 | Gene3D | G3DSA:2.170.300.10 | - | 8 | 68 | 2.5E-16 |
| 9 | g12805.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 75 | 124 | 7.2E-10 |
| 11 | g12805.t1 | Gene3D | G3DSA:2.40.50.120 | - | 153 | 285 | 7.9E-18 |
| 4 | g12805.t1 | PANTHER | PTHR10574:SF383 | NETRIN 5 | 13 | 281 | 1.3E-64 |
| 5 | g12805.t1 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 13 | 281 | 1.3E-64 |
| 1 | g12805.t1 | Pfam | PF00053 | Laminin EGF domain | 14 | 74 | 2.7E-8 |
| 2 | g12805.t1 | Pfam | PF00053 | Laminin EGF domain | 77 | 119 | 1.6E-9 |
| 3 | g12805.t1 | Pfam | PF01759 | UNC-6/NTR/C345C module | 171 | 281 | 3.9E-18 |
| 14 | g12805.t1 | ProSitePatterns | PS01248 | Laminin-type EGF-like (LE) domain signature. | 41 | 77 | - |
| 15 | g12805.t1 | ProSitePatterns | PS01248 | Laminin-type EGF-like (LE) domain signature. | 96 | 124 | - |
| 20 | g12805.t1 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 14 | 76 | 11.835 |
| 21 | g12805.t1 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 77 | 126 | 20.461 |
| 19 | g12805.t1 | ProSiteProfiles | PS50189 | NTR domain profile. | 159 | 285 | 17.165 |
| 17 | g12805.t1 | SMART | SM00180 | lamegf_3 | 14 | 74 | 2.0E-6 |
| 18 | g12805.t1 | SMART | SM00180 | lamegf_3 | 77 | 124 | 3.9E-11 |
| 16 | g12805.t1 | SMART | SM00643 | c345c | 170 | 283 | 2.8E-11 |
| 8 | g12805.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 14 | 67 | 3.35E-10 |
| 7 | g12805.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 77 | 118 | 1.56E-7 |
| 6 | g12805.t1 | SUPERFAMILY | SSF50242 | TIMP-like | 157 | 282 | 2.98E-21 |
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 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.
