General information for g12807.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Netrin-A.
Parent gene
- The parent gene g12807 is located on chr_1: 26334231..26335394 (- 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 | g12807 | g12807.t1 | isoform | g12807.t1 | 26334231 | 26335394 |
| chr_1 | g12807 | g12807.t1 | exon | g12807.t1.exon1 | 26334231 | 26335394 |
| chr_1 | g12807 | g12807.t1 | cds | g12807.t1.CDS1 | 26334231 | 26335394 |
| chr_1 | g12807 | g12807.t1 | TSS | g12807.t1 | NA | NA |
| chr_1 | g12807 | g12807.t1 | TTS | g12807.t1 | NA | NA |
Sequences
>g12807.t1 Gene=g12807 Length=1164
ATGTATCGAATTGTTTTTATTTGCGGCTTCTTGCTTGCAGTAGCAAAAACTTCGTCATCG
GCAGCTCACAACAATCGAATCAACTTACGCAGTTTTATACCTCAGCAGCTGCAAATTGAT
CCATGTTATGACGAAGATAGACCAATGCGCTGCATGCCAGACTTTGTAAATGCTGCATTT
GGCAGGACCATTGAGGCCTCGTCCACTTGTGGAATGAATGGGCCTGAAAAGTACTGTGAT
GCTGATGGCAAATGTCATATTTGCAATATCAACGACTCATCAAAGAATTTCAGTGCTGCT
GCACTTTCTGATATTCACAATATGCAAAATTTAACTTGCTGGCGTTCTGAGCCGCGACCA
ATGACAAACACGAATTTTGGATTTGACAATACTCCTGATAATGTGACATTAACGTTGTCA
TTTGGTAAAAAGTTTGAGCTAACTTATGTTAGCTTGCTATTTTGTCCTGGTGCCATTAAA
CCTGATTCTATGGCTATTTATAAGAGTGCCGATTATGGTAAAACATGGCAGCCATTTCAA
TTTTATAGTTCACAATGCAAAAAACTCTACGGTAGAACATCAAAGCTACAGATAACAAAA
CGAAATGAACAAGAACCACGCTGCTTGGATCATAATCGATTTGCAACTGATGGTATGAGT
GGTATTCAGGGATCAAGAATTGCATTTAGCACTCTGGAAGGTCGACCATCAGCTAATGAG
TTTGATACATCTGCAATATTGCAGGATTGGGTTACAGCTACCGACATTCGAGTCATTTTT
CATCGCCTGCAGAGTCCATTAGCAGCTCAGCAAATGAAAGCGAGAATGAAGAGTGAAATT
ATTTCATCATCCAAGGAAACAGCTTCTACACTGTCTCCAAACTCATTATTGTCGGCTGGT
ACTGGCACCTATGCACTATCTGACTTCTCTGTTGGCGGTCGATGCAAGTGCAATGGACAT
GCATCGCGTTGTATTAAAAACACCGATGGATTGCTGGAATGTGAATGCAAGCACAATACA
GCGGGACGCGACTGCGAAAAATGCAAACCATTCTATTTCGATAGACCGTGGGCACGAGCG
ACTGTGCAGAATGCAAACGAATGCAAAGGTGAGTTCTACTTTAAACTAATACTTACTATT
CAAGGCATTGACACTTTAGATTGA
>g12807.t1 Gene=g12807 Length=387
MYRIVFICGFLLAVAKTSSSAAHNNRINLRSFIPQQLQIDPCYDEDRPMRCMPDFVNAAF
GRTIEASSTCGMNGPEKYCDADGKCHICNINDSSKNFSAAALSDIHNMQNLTCWRSEPRP
MTNTNFGFDNTPDNVTLTLSFGKKFELTYVSLLFCPGAIKPDSMAIYKSADYGKTWQPFQ
FYSSQCKKLYGRTSKLQITKRNEQEPRCLDHNRFATDGMSGIQGSRIAFSTLEGRPSANE
FDTSAILQDWVTATDIRVIFHRLQSPLAAQQMKARMKSEIISSSKETASTLSPNSLLSAG
TGTYALSDFSVGGRCKCNGHASRCIKNTDGLLECECKHNTAGRDCEKCKPFYFDRPWARA
TVQNANECKGEFYFKLILTIQGIDTLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g12807.t1 | CDD | cd00055 | EGF_Lam | 314 | 359 | 7.18511E-12 |
| 8 | g12807.t1 | Gene3D | G3DSA:2.60.120.1490 | - | 26 | 336 | 2.9E-87 |
| 9 | g12807.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 337 | 371 | 2.5E-8 |
| 3 | g12807.t1 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 39 | 369 | 1.9E-92 |
| 4 | g12807.t1 | PANTHER | PTHR10574:SF365 | NETRIN-A-RELATED | 39 | 369 | 1.9E-92 |
| 1 | g12807.t1 | Pfam | PF00055 | Laminin N-terminal (Domain VI) | 51 | 313 | 1.8E-63 |
| 2 | g12807.t1 | Pfam | PF00053 | Laminin EGF domain | 315 | 368 | 1.0E-8 |
| 11 | g12807.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 12 | g12807.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 13 | g12807.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 14 | g12807.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 21 | - |
| 10 | g12807.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 387 | - |
| 17 | g12807.t1 | ProSitePatterns | PS01248 | Laminin-type EGF-like (LE) domain signature. | 334 | 368 | - |
| 21 | g12807.t1 | ProSiteProfiles | PS51117 | Laminin N-terminal domain profile. | 47 | 314 | 45.492 |
| 20 | g12807.t1 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 315 | 370 | 12.026 |
| 19 | g12807.t1 | SMART | SM00136 | LamNT_2 | 45 | 313 | 6.2E-88 |
| 18 | g12807.t1 | SMART | SM00180 | lamegf_3 | 315 | 368 | 4.3E-9 |
| 5 | g12807.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 315 | 367 | 3.91E-10 |
| 7 | g12807.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 16 | g12807.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 6 | g12807.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 21 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K06843 (netrin 1)
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.
