General information for g17570.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17570 is located on chr_4: 13936701..13937988 (+ 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_4 | g17570 | g17570.t1 | isoform | g17570.t1 | 13936701 | 13937988 |
| chr_4 | g17570 | g17570.t1 | exon | g17570.t1.exon1 | 13936701 | 13936762 |
| chr_4 | g17570 | g17570.t1 | cds | g17570.t1.CDS1 | 13936701 | 13936762 |
| chr_4 | g17570 | g17570.t1 | exon | g17570.t1.exon2 | 13936904 | 13936973 |
| chr_4 | g17570 | g17570.t1 | cds | g17570.t1.CDS2 | 13936904 | 13936973 |
| chr_4 | g17570 | g17570.t1 | exon | g17570.t1.exon3 | 13937084 | 13937282 |
| chr_4 | g17570 | g17570.t1 | cds | g17570.t1.CDS3 | 13937084 | 13937282 |
| chr_4 | g17570 | g17570.t1 | exon | g17570.t1.exon4 | 13937345 | 13937386 |
| chr_4 | g17570 | g17570.t1 | cds | g17570.t1.CDS4 | 13937345 | 13937386 |
| chr_4 | g17570 | g17570.t1 | exon | g17570.t1.exon5 | 13937450 | 13937782 |
| chr_4 | g17570 | g17570.t1 | cds | g17570.t1.CDS5 | 13937450 | 13937782 |
| chr_4 | g17570 | g17570.t1 | exon | g17570.t1.exon6 | 13937846 | 13937988 |
| chr_4 | g17570 | g17570.t1 | cds | g17570.t1.CDS6 | 13937846 | 13937988 |
| chr_4 | g17570 | g17570.t1 | TTS | g17570.t1 | 13938035 | 13938035 |
| chr_4 | g17570 | g17570.t1 | TSS | g17570.t1 | NA | NA |
Sequences
>g17570.t1 Gene=g17570 Length=849
ATGAATAAAAATGTTCTGTATTTTTTGCCTAAATTTATGCTATTAATTGGCAATACGAAT
ATTTTTCGAATAGACAACAATGATCATGTTATAGATGTAAATCGTGGAAATGTAAAATTT
GAATATGATCAGGTGCACATCATTTGTCCCTATTATGAGGCTGGTACAAATGAAAATGAG
ACAGAAAAATATATTATTTACAATGTTTCTAAAGTCGAGTACGAGACTTGCCGCATAACA
AATCCAAATCCACGAATAATAGCGATATGTGATAAGCCATTTAGCGTAACTCTTGTAACA
ATCTCATTCCGACCATTCACTCCACAGCCAGGTGGGCTTGAATTTAAACCTGGCAATGAT
TACTATTTTATATCAACATCATCTGGTGAGGATTTACATCGACGAATAGGTGGTCGTTGT
ACAACAGACAATACAAAAGTGATATTCAAAGTGTTTGGTGGTGATGAAAGTCATAAAACA
ACAGCAGTTCCAGCTAAAAATGACAAACCCTCACCAACAGATCAAAACAGTCACGATGAT
TCAAGTGACAATACAAATAATGAAAGTGAAGAGTTAAATAAGATAAATTATAATAATGAT
CATTTTGGTCATAGTTTCCATCCAACACAACGTCCATTTTTCGTGAATAGCAACAACAAT
GTTAACAATGATAATTTTAATAATAATAAGTCGACAAAAAAGACTAATGAACATGATAGC
CGTCAAAATGAAGTAGTTAAAAATGAAGAGCTAACGTACAATAATGCTTCTTCAAGATCA
AATTACGCCTCAAGTGCCGCCCTAAACTTTCTTATTATCATTCTCATGCGAAATGGACGA
AGCACGTGA
>g17570.t1 Gene=g17570 Length=282
MNKNVLYFLPKFMLLIGNTNIFRIDNNDHVIDVNRGNVKFEYDQVHIICPYYEAGTNENE
TEKYIIYNVSKVEYETCRITNPNPRIIAICDKPFSVTLVTISFRPFTPQPGGLEFKPGND
YYFISTSSGEDLHRRIGGRCTTDNTKVIFKVFGGDESHKTTAVPAKNDKPSPTDQNSHDD
SSDNTNNESEELNKINYNNDHFGHSFHPTQRPFFVNSNNNVNNDNFNNNKSTKKTNEHDS
RQNEVVKNEELTYNNASSRSNYASSAALNFLIIILMRNGRST
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g17570.t1 | CDD | cd02675 | Ephrin_ectodomain | 18 | 151 | 3.22892E-51 |
| 9 | g17570.t1 | Gene3D | G3DSA:2.60.40.420 | - | 15 | 152 | 4.5E-41 |
| 11 | g17570.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 159 | 188 | - |
| 12 | g17570.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 172 | 187 | - |
| 2 | g17570.t1 | PANTHER | PTHR11304 | EPHRIN | 18 | 260 | 9.2E-69 |
| 3 | g17570.t1 | PANTHER | PTHR11304:SF29 | EPHRIN | 18 | 260 | 9.2E-69 |
| 5 | g17570.t1 | PRINTS | PR01347 | Ephrin signature | 36 | 53 | 4.1E-7 |
| 4 | g17570.t1 | PRINTS | PR01347 | Ephrin signature | 62 | 77 | 4.1E-7 |
| 7 | g17570.t1 | PRINTS | PR01347 | Ephrin signature | 98 | 110 | 4.1E-7 |
| 6 | g17570.t1 | PRINTS | PR01347 | Ephrin signature | 111 | 122 | 4.1E-7 |
| 1 | g17570.t1 | Pfam | PF00812 | Ephrin | 21 | 151 | 5.3E-36 |
| 13 | g17570.t1 | ProSiteProfiles | PS51551 | Ephrin receptor-binding (ephrin RBD) domain profile. | 10 | 151 | 34.539 |
| 8 | g17570.t1 | SUPERFAMILY | SSF49503 | Cupredoxins | 18 | 153 | 1.82E-29 |
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:0016020 | membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K05463 (ephrin-B)
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.
