General information for g12813.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Netrin-A.
Parent gene
- The parent gene g12813 is located on chr_1: 26371717..26393637 (- 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 | g12813 | g12813.t1 | isoform | g12813.t1 | 26371717 | 26393637 |
| chr_1 | g12813 | g12813.t1 | exon | g12813.t1.exon1 | 26371717 | 26371844 |
| chr_1 | g12813 | g12813.t1 | cds | g12813.t1.CDS1 | 26371717 | 26371844 |
| chr_1 | g12813 | g12813.t1 | exon | g12813.t1.exon2 | 26374370 | 26374462 |
| chr_1 | g12813 | g12813.t1 | cds | g12813.t1.CDS2 | 26374370 | 26374462 |
| chr_1 | g12813 | g12813.t1 | exon | g12813.t1.exon3 | 26374544 | 26374693 |
| chr_1 | g12813 | g12813.t1 | cds | g12813.t1.CDS3 | 26374544 | 26374693 |
| chr_1 | g12813 | g12813.t1 | exon | g12813.t1.exon4 | 26383827 | 26384015 |
| chr_1 | g12813 | g12813.t1 | cds | g12813.t1.CDS4 | 26383827 | 26384015 |
| chr_1 | g12813 | g12813.t1 | exon | g12813.t1.exon5 | 26392314 | 26393637 |
| chr_1 | g12813 | g12813.t1 | cds | g12813.t1.CDS5 | 26392314 | 26393637 |
| chr_1 | g12813 | g12813.t1 | TSS | g12813.t1 | 26394099 | 26394099 |
| chr_1 | g12813 | g12813.t1 | TTS | g12813.t1 | NA | NA |
Sequences
>g12813.t1 Gene=g12813 Length=1884
ATGTTTAGTGTAAAATTCTTGATTTATGCAAATATTATAACTTGTTCACTGTTGCATGCA
GCTTCATTTGAATCATTTAAAAAGTCATCGCAATTTTCAATTCCACTAAAGTCATCTTTC
GATCCATGTTATGATGAGGATCGACCTACCCGCTGTTTGCCAGACTTTGTAAATGCCGCA
TATGGAAGAACTATTGAGGCATCATCGACTTGTGGCGAAAGTGGACCAGTCAAGGTCTGC
GATGGTGCAGAAAATTATAAAAATGAATCTCCAGTGTGCAATATCTGTGATGATTCGAAT
CCAAAGCGAAGATATGCTGCATCTGCACTATCAGACTTAAATAATAGTCAAAACATTACA
TGTTGGCGTTCAGAGCCAGCACCAGCACCGACAAGTATTGACGCACCGCCCGATAATGTG
ACATTGACATTATCATTGGGCAAAAAGTTTGAATTGACTTATGTGAGCTTGGTATTTTGT
CCACGTTCGATTAAGCCCGATTCACTGGCCATTTACAAAAGCACAGACTATGGTAAAACG
TGGCAACCATTTCAGTATTATAGCACGCAATGTCGTCGTTTTTATGGACGTCCTAATCGT
GCGAGCATAACGAAAAATAATGAACAAGAGGCATTGTGTACGGATGGACATATGTACAAC
AAAGATACAACGACTTTGCAGGGTTCACGTATTGCATTTAGTACACTTGAAGGACGACCA
TCAGCTTCGGAATTTGATACATCGACAATTTTACAAGACTGGGTAACAGCGACAGACATT
CGAGTAATTTTCCATCGACTTCAATTGCCACAACTTCCACAACAATTTGATGACAGCGAG
CATCAAAGTGGCGATGATAATAGCGATATTGAAGACGACGATGACGATGCAATTGAAGAG
GATGAGATTGATGATGATATTGTTTACACAGAAACATCAAGCATGAAATCGATTAAAACA
ACATTGCCAAAATATAGCACAAAAGATACTGACAACGCATATGATGACAATCAACTTGAC
ATGTCATCAAAAACATTGACAACGGCCTCATATAATATTAAAATCAATGGCAATGTCAAA
AATGATAATGGACAAGTGATGACAAAGGCGACATTAATGCAACACTATGCTCTTTCGGAT
TTTTCCGTTGGCGGTCGATGCAAATGCAATGGTCATGCATCACGCTGCGTGCAAGGTGCT
GACGGTCAACTTGAATGCGAATGTAAACACAATACAGCGGGTAGAGATTGTGAAAAGTGT
AAATTGTTCTATTTTGATCGACCATGGGCACGAGCTACGCCACGAGATGCAAATGAATGC
AGAGCTTGCGAATGCAATGGACATGCCAGACAATGCCGCTTCAATATGGAGTTGTATAAA
CTATCTGGTCGCGTTTCGGGTGGAGTTTGCATTGGTTGTCGACATGCAACAACAGGACGA
CATTGCCATTATTGCAGGGAAGGATTTTATCGTGATCCAACGAAGCCAATAACACATAAA
AAGGCATGCAAACCTTGTGACTGTCATCCAATCGGTTCATCGGGAAGAACATGCAATCAT
ACATCAGGACAATGCACTTGCAAGGATGGCGTAACTGGGTTAACATGCAATCGTTGTGCT
CGAGGCTATCAGCAAAGTCGTTCACATATTGCTCCATGCATTAAAATCCCGAGAGTTGTT
AGCGCAATGATGACGCAAAATGAGGAACCAAATGAGGATCCATCTTATGAACGATATCAA
TCGAGTGAACAGCAAGAATGCGGACAATGTCGCGTAAATTCAAAAAAGTTGAGCCTAAAC
AAATTTTGCAAGCGTGATTATGGTGAGTTTCATTTTCATGAGAAAAGTCCTTATCGATTT
AGAAACAGACCGCGCGAGTGGTAA
>g12813.t1 Gene=g12813 Length=627
MFSVKFLIYANIITCSLLHAASFESFKKSSQFSIPLKSSFDPCYDEDRPTRCLPDFVNAA
YGRTIEASSTCGESGPVKVCDGAENYKNESPVCNICDDSNPKRRYAASALSDLNNSQNIT
CWRSEPAPAPTSIDAPPDNVTLTLSLGKKFELTYVSLVFCPRSIKPDSLAIYKSTDYGKT
WQPFQYYSTQCRRFYGRPNRASITKNNEQEALCTDGHMYNKDTTTLQGSRIAFSTLEGRP
SASEFDTSTILQDWVTATDIRVIFHRLQLPQLPQQFDDSEHQSGDDNSDIEDDDDDAIEE
DEIDDDIVYTETSSMKSIKTTLPKYSTKDTDNAYDDNQLDMSSKTLTTASYNIKINGNVK
NDNGQVMTKATLMQHYALSDFSVGGRCKCNGHASRCVQGADGQLECECKHNTAGRDCEKC
KLFYFDRPWARATPRDANECRACECNGHARQCRFNMELYKLSGRVSGGVCIGCRHATTGR
HCHYCREGFYRDPTKPITHKKACKPCDCHPIGSSGRTCNHTSGQCTCKDGVTGLTCNRCA
RGYQQSRSHIAPCIKIPRVVSAMMTQNEEPNEDPSYERYQSSEQQECGQCRVNSKKLSLN
KFCKRDYGEFHFHEKSPYRFRNRPREW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g12813.t1 | CDD | cd00055 | EGF_Lam | 386 | 431 | 1.25607E-9 |
| 23 | g12813.t1 | CDD | cd00055 | EGF_Lam | 442 | 496 | 5.03822E-6 |
| 21 | g12813.t1 | CDD | cd00055 | EGF_Lam | 505 | 553 | 7.65184E-13 |
| 12 | g12813.t1 | Gene3D | G3DSA:2.60.120.1490 | - | 28 | 287 | 3.2E-77 |
| 13 | g12813.t1 | Gene3D | G3DSA:2.60.120.1490 | - | 288 | 408 | 2.7E-14 |
| 15 | g12813.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 410 | 506 | 3.1E-23 |
| 14 | g12813.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 507 | 553 | 5.4E-10 |
| 31 | g12813.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 273 | 294 | - |
| 5 | g12813.t1 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 40 | 601 | 9.1E-143 |
| 6 | g12813.t1 | PANTHER | PTHR10574:SF365 | NETRIN-A-RELATED | 40 | 601 | 9.1E-143 |
| 1 | g12813.t1 | Pfam | PF00055 | Laminin N-terminal (Domain VI) | 52 | 283 | 8.4E-67 |
| 3 | g12813.t1 | Pfam | PF00053 | Laminin EGF domain | 387 | 435 | 4.6E-8 |
| 4 | g12813.t1 | Pfam | PF00053 | Laminin EGF domain | 443 | 503 | 4.3E-8 |
| 2 | g12813.t1 | Pfam | PF00053 | Laminin EGF domain | 506 | 548 | 4.5E-9 |
| 17 | g12813.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 18 | g12813.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 19 | g12813.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 15 | - |
| 20 | g12813.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 16 | g12813.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 627 | - |
| 29 | g12813.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 406 | 417 | - |
| 30 | g12813.t1 | ProSitePatterns | PS01248 | Laminin-type EGF-like (LE) domain signature. | 525 | 553 | - |
| 35 | g12813.t1 | ProSiteProfiles | PS51117 | Laminin N-terminal domain profile. | 48 | 386 | 46.379 |
| 34 | g12813.t1 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 387 | 442 | 11.892 |
| 33 | g12813.t1 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 443 | 505 | 11.873 |
| 32 | g12813.t1 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 506 | 555 | 22.613 |
| 28 | g12813.t1 | SMART | SM00136 | LamNT_2 | 46 | 305 | 2.2E-95 |
| 25 | g12813.t1 | SMART | SM00180 | lamegf_3 | 387 | 440 | 1.4E-8 |
| 27 | g12813.t1 | SMART | SM00180 | lamegf_3 | 443 | 503 | 2.5E-7 |
| 26 | g12813.t1 | SMART | SM00180 | lamegf_3 | 506 | 553 | 1.3E-10 |
| 8 | g12813.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 387 | 445 | 1.84E-10 |
| 9 | g12813.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 443 | 498 | 1.0E-9 |
| 7 | g12813.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 506 | 546 | 2.06E-7 |
| 11 | g12813.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 24 | g12813.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 10 | g12813.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
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. There were no conditions that were differentially expressed