General information for g8890.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as WD repeat-containing protein 7.
Parent gene
- The parent gene g8890 is located on chr_2: 33711620..33714514 (+ 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 | g8890 | g8890.t1 | isoform | g8890.t1 | 33711003 | 33714514 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon1 | 33711003 | 33711023 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS1 | 33711003 | 33711023 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon2 | 33711104 | 33711173 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS2 | 33711104 | 33711173 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon3 | 33711349 | 33711417 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS3 | 33711349 | 33711417 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon4 | 33711620 | 33713118 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS4 | 33711620 | 33713118 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon5 | 33713180 | 33713507 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS5 | 33713180 | 33713507 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon6 | 33714081 | 33714251 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS6 | 33714081 | 33714251 |
| chr_2 | g8890 | g8890.t1 | exon | g8890.t1.exon7 | 33714342 | 33714514 |
| chr_2 | g8890 | g8890.t1 | cds | g8890.t1.CDS7 | 33714342 | 33714514 |
| chr_2 | g8890 | g8890.t1 | TSS | g8890.t1 | NA | NA |
| chr_2 | g8890 | g8890.t1 | TTS | g8890.t1 | NA | NA |
Sequences
>g8890.t1 Gene=g8890 Length=2331
ATGAGTCCAACAACACTTGAGGCACAAGGTCTACTCATTCAACAACATAATACGAATAAT
CCCTCGTCAGATGCAGGCAAAAAAATTACAGATTTTCTTGGAAAAGTAAAGAATAAGACA
GGAGATCTTGAGAAAATTCTGAAGGAAAAAGATAAACATGGAATTCTCGCAAAAGTTAAA
GAAGGTGCGGAACAAGTAGGAACAAAAATACAAGCAAAAGTCGAAACTGTCGTAAAGCAG
ATAAATGAAACTGGCAAAGAATCGTCTGATGGCATCAAAAGAATTACGCCTAGAATGGAG
GCGACACATGTAATGGAAGTTGCGCAACTTTTACTATCTTTGATTCATTCATGGGGACTT
GATCCTCATCTTGATAAAGTTTGTGAATCACAGTTGGGTTTGCTTCGTCCAATGGTGCCA
ATATCTTTTGGTGTTTTGTCTAAAGGAGGCTACATGTCTTTACTCTTACCAACATGGCAA
AATACAATCAAACAAGAGACTGTTCAGAAATTGCTTCAAAGTAGTGATATGCAATTGTCA
AAAGCATTACCAGAAAATCTTTTACGACAAGAGGCTTTGACAAAACTTTTTACTGCACGT
TTACATTGGGAATTGAGCACAACAATAACATCAAATCATCTTTTGGGAATGGTTGCCATG
TCAAATACATTAATGTCAATGAAAATGGCAACATTCGTACCAGAATCAGAACGAGCAAGA
AAACTTATGAAGCAAGCGACAAAAAATAACGTTGCTTGGGCAAGTGATGATGATCATGAA
GAGCAATTGATTACAGAGCAGCAAGCACAAATAAAACAAGGATGGAGTTTATTATCGACA
CATCATTGCTTTTTATTGCCAGATAAAATTGATGCCATGGAACCAAAGAACTTTAAGCGT
CCTCAAGTTGAATTAATGGCACGTCGTTGGCAACATCATTGCATTGAAATTCGTGAAGCA
GCTCAACAGATGTTACTTGGCGAACTCGGTCGTATGGGAAAGAAAGGAAGAAAGCAACTT
GTTGAAAATTGGGCACAGTATTTGCCACAATATACTCATACTGAACCAATTGTTCAGCAA
ACACAACCTTCTAGTCCAGGCTCAACTAGTCCCTCTGCATTATCGCCGTCTGCTGCACAA
CAACAACAAGCAGAAGCAGAAGAAGAAGTTGAAGAGGAGGAAGAAGTTGTTCGACAAAAA
CCTTCAAGTTTAGCTGAATTGAAAAGAAAGCAATCGACAGCTGTTATCATTTTGGGTGTA
ATTGGAGCAGAATTTGGTCAAGATATTTCAATTGAAACTGGTGCAAACGGAAAGAAACCA
ACAACAGAGCAGCAACAAAGAAGAAAAAGTTCAATTGTTGAAGGTTTTGGCATTGGAAAT
AATAACTTGGCACGTCTTACTGCAATGGCATTGACACATCTTTTGCTTGCTCCACCAACA
CCTAAATTACCAGCATATACACAATTAAGACGTGCTGCAATTGATCTTATTGGAAGAGGA
TTTACAGTTTGGGAGCCTTATTTGGATGTCAGTAAAGTTCTATTAGGACTTTTAGAAATT
TCATGTGATTCATCTCGTTTGGTCCCAAGTCTTACATATAAATTGCCATTAACACCACAA
GCTGATGCATGTCGAACAGCTAGACATGCACTTCGATTGATTGCAACAGCAAGACCAGCT
GCATTTATTACAACAATGGCGAGAGAAGTTGCAAGATATAATACATTACAGCAAAATTCA
CAAGCATTAAGTGTACCATTAACACAGTCAGTTTTGCATCGTGCAAAGAAAGAAATTTTA
CAATGCGTTGAAATGTTAATTGAAAAAATGCAATCCGATATGGCAGCATTGCTAGTTGAA
GTAACTGATATCACATTACATTGCTTGGATATGTCCGACTTGAAAAATCGTTCACTGAAT
GAAGTTTGTCCATCAATATGCAAATTCAACCAAGTATCACATTGCTCATCAACAAGAAGA
ATTGCAGTTGGTGCAAGCAACGGTCATATGGCAATTTATGAACTTCGACAAAATAAATGT
CAAATGATTCCAGCACATTCACAACCCATAACAGCGTTGGCATTTAGTCCCGATGGAAAA
TATTTGGTCAGTTATTCATGTAGCGAAAATCGATTATCGTTTTGGCAAACAAGCACTGGC
ATGTTTGGACTTGGTCAAAGTCAAACACGATGCATAAAAGGATATTCAACAGCACCTATC
CCAGATATTGCACGTTTAAATCCAATGCGATTGGGAAAACTAATATGGATAAATAATCGA
ACTGTTACTCTTATGTTAGCTGATGGTTCTGAGACACGTTTCAATGTTTAA
>g8890.t1 Gene=g8890 Length=776
MSPTTLEAQGLLIQQHNTNNPSSDAGKKITDFLGKVKNKTGDLEKILKEKDKHGILAKVK
EGAEQVGTKIQAKVETVVKQINETGKESSDGIKRITPRMEATHVMEVAQLLLSLIHSWGL
DPHLDKVCESQLGLLRPMVPISFGVLSKGGYMSLLLPTWQNTIKQETVQKLLQSSDMQLS
KALPENLLRQEALTKLFTARLHWELSTTITSNHLLGMVAMSNTLMSMKMATFVPESERAR
KLMKQATKNNVAWASDDDHEEQLITEQQAQIKQGWSLLSTHHCFLLPDKIDAMEPKNFKR
PQVELMARRWQHHCIEIREAAQQMLLGELGRMGKKGRKQLVENWAQYLPQYTHTEPIVQQ
TQPSSPGSTSPSALSPSAAQQQQAEAEEEVEEEEEVVRQKPSSLAELKRKQSTAVIILGV
IGAEFGQDISIETGANGKKPTTEQQQRRKSSIVEGFGIGNNNLARLTAMALTHLLLAPPT
PKLPAYTQLRRAAIDLIGRGFTVWEPYLDVSKVLLGLLEISCDSSRLVPSLTYKLPLTPQ
ADACRTARHALRLIATARPAAFITTMAREVARYNTLQQNSQALSVPLTQSVLHRAKKEIL
QCVEMLIEKMQSDMAALLVEVTDITLHCLDMSDLKNRSLNEVCPSICKFNQVSHCSSTRR
IAVGASNGHMAIYELRQNKCQMIPAHSQPITALAFSPDGKYLVSYSCSENRLSFWQTSTG
MFGLGQSQTRCIKGYSTAPIPDIARLNPMRLGKLIWINNRTVTLMLADGSETRFNV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8890.t1 | Coils | Coil | Coil | 379 | 399 | - |
| 7 | g8890.t1 | Gene3D | G3DSA:2.130.10.10 | - | 588 | 734 | 1.8E-12 |
| 5 | g8890.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 358 | 384 | - |
| 6 | g8890.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 358 | 404 | - |
| 1 | g8890.t1 | PANTHER | PTHR44099 | RABCONNECTIN-3B, ISOFORM A | 24 | 775 | 2.6E-188 |
| 2 | g8890.t1 | PANTHER | PTHR44099:SF4 | RABCONNECTIN-3B, ISOFORM A | 24 | 775 | 2.6E-188 |
| 4 | g8890.t1 | SMART | SM00320 | WD40_4 | 676 | 716 | 0.0019 |
| 3 | g8890.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 647 | 720 | 1.45E-12 |
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 transcript has been annotated with K24738 (rabconnectin-3b)
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.
