General information for g8890.t2
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.t2 | isoform | g8890.t2 | 33711003 | 33714514 |
| chr_2 | g8890 | g8890.t2 | exon | g8890.t2.exon1 | 33711003 | 33711023 |
| chr_2 | g8890 | g8890.t2 | cds | g8890.t2.CDS1 | 33711003 | 33711023 |
| chr_2 | g8890 | g8890.t2 | exon | g8890.t2.exon2 | 33711104 | 33711173 |
| chr_2 | g8890 | g8890.t2 | cds | g8890.t2.CDS2 | 33711104 | 33711173 |
| chr_2 | g8890 | g8890.t2 | exon | g8890.t2.exon3 | 33711620 | 33713118 |
| chr_2 | g8890 | g8890.t2 | cds | g8890.t2.CDS3 | 33711620 | 33713118 |
| chr_2 | g8890 | g8890.t2 | exon | g8890.t2.exon4 | 33713180 | 33713507 |
| chr_2 | g8890 | g8890.t2 | cds | g8890.t2.CDS4 | 33713180 | 33713507 |
| chr_2 | g8890 | g8890.t2 | exon | g8890.t2.exon5 | 33714081 | 33714251 |
| chr_2 | g8890 | g8890.t2 | cds | g8890.t2.CDS5 | 33714081 | 33714251 |
| chr_2 | g8890 | g8890.t2 | exon | g8890.t2.exon6 | 33714342 | 33714514 |
| chr_2 | g8890 | g8890.t2 | cds | g8890.t2.CDS6 | 33714342 | 33714514 |
| chr_2 | g8890 | g8890.t2 | TSS | g8890.t2 | NA | NA |
| chr_2 | g8890 | g8890.t2 | TTS | g8890.t2 | NA | NA |
Sequences
>g8890.t2 Gene=g8890 Length=2262
ATGAGTCCAACAACACTTGAGGCACAAGGTCTACTCATTCAACAACATAATACGAATAAT
CCCTCGTCAGATGCAGGCAAAAAAATTACAGGAATTCTCGCAAAAGTTAAAGAAGGTGCG
GAACAAGTAGGAACAAAAATACAAGCAAAAGTCGAAACTGTCGTAAAGCAGATAAATGAA
ACTGGCAAAGAATCGTCTGATGGCATCAAAAGAATTACGCCTAGAATGGAGGCGACACAT
GTAATGGAAGTTGCGCAACTTTTACTATCTTTGATTCATTCATGGGGACTTGATCCTCAT
CTTGATAAAGTTTGTGAATCACAGTTGGGTTTGCTTCGTCCAATGGTGCCAATATCTTTT
GGTGTTTTGTCTAAAGGAGGCTACATGTCTTTACTCTTACCAACATGGCAAAATACAATC
AAACAAGAGACTGTTCAGAAATTGCTTCAAAGTAGTGATATGCAATTGTCAAAAGCATTA
CCAGAAAATCTTTTACGACAAGAGGCTTTGACAAAACTTTTTACTGCACGTTTACATTGG
GAATTGAGCACAACAATAACATCAAATCATCTTTTGGGAATGGTTGCCATGTCAAATACA
TTAATGTCAATGAAAATGGCAACATTCGTACCAGAATCAGAACGAGCAAGAAAACTTATG
AAGCAAGCGACAAAAAATAACGTTGCTTGGGCAAGTGATGATGATCATGAAGAGCAATTG
ATTACAGAGCAGCAAGCACAAATAAAACAAGGATGGAGTTTATTATCGACACATCATTGC
TTTTTATTGCCAGATAAAATTGATGCCATGGAACCAAAGAACTTTAAGCGTCCTCAAGTT
GAATTAATGGCACGTCGTTGGCAACATCATTGCATTGAAATTCGTGAAGCAGCTCAACAG
ATGTTACTTGGCGAACTCGGTCGTATGGGAAAGAAAGGAAGAAAGCAACTTGTTGAAAAT
TGGGCACAGTATTTGCCACAATATACTCATACTGAACCAATTGTTCAGCAAACACAACCT
TCTAGTCCAGGCTCAACTAGTCCCTCTGCATTATCGCCGTCTGCTGCACAACAACAACAA
GCAGAAGCAGAAGAAGAAGTTGAAGAGGAGGAAGAAGTTGTTCGACAAAAACCTTCAAGT
TTAGCTGAATTGAAAAGAAAGCAATCGACAGCTGTTATCATTTTGGGTGTAATTGGAGCA
GAATTTGGTCAAGATATTTCAATTGAAACTGGTGCAAACGGAAAGAAACCAACAACAGAG
CAGCAACAAAGAAGAAAAAGTTCAATTGTTGAAGGTTTTGGCATTGGAAATAATAACTTG
GCACGTCTTACTGCAATGGCATTGACACATCTTTTGCTTGCTCCACCAACACCTAAATTA
CCAGCATATACACAATTAAGACGTGCTGCAATTGATCTTATTGGAAGAGGATTTACAGTT
TGGGAGCCTTATTTGGATGTCAGTAAAGTTCTATTAGGACTTTTAGAAATTTCATGTGAT
TCATCTCGTTTGGTCCCAAGTCTTACATATAAATTGCCATTAACACCACAAGCTGATGCA
TGTCGAACAGCTAGACATGCACTTCGATTGATTGCAACAGCAAGACCAGCTGCATTTATT
ACAACAATGGCGAGAGAAGTTGCAAGATATAATACATTACAGCAAAATTCACAAGCATTA
AGTGTACCATTAACACAGTCAGTTTTGCATCGTGCAAAGAAAGAAATTTTACAATGCGTT
GAAATGTTAATTGAAAAAATGCAATCCGATATGGCAGCATTGCTAGTTGAAGTAACTGAT
ATCACATTACATTGCTTGGATATGTCCGACTTGAAAAATCGTTCACTGAATGAAGTTTGT
CCATCAATATGCAAATTCAACCAAGTATCACATTGCTCATCAACAAGAAGAATTGCAGTT
GGTGCAAGCAACGGTCATATGGCAATTTATGAACTTCGACAAAATAAATGTCAAATGATT
CCAGCACATTCACAACCCATAACAGCGTTGGCATTTAGTCCCGATGGAAAATATTTGGTC
AGTTATTCATGTAGCGAAAATCGATTATCGTTTTGGCAAACAAGCACTGGCATGTTTGGA
CTTGGTCAAAGTCAAACACGATGCATAAAAGGATATTCAACAGCACCTATCCCAGATATT
GCACGTTTAAATCCAATGCGATTGGGAAAACTAATATGGATAAATAATCGAACTGTTACT
CTTATGTTAGCTGATGGTTCTGAGACACGTTTCAATGTTTAA
>g8890.t2 Gene=g8890 Length=753
MSPTTLEAQGLLIQQHNTNNPSSDAGKKITGILAKVKEGAEQVGTKIQAKVETVVKQINE
TGKESSDGIKRITPRMEATHVMEVAQLLLSLIHSWGLDPHLDKVCESQLGLLRPMVPISF
GVLSKGGYMSLLLPTWQNTIKQETVQKLLQSSDMQLSKALPENLLRQEALTKLFTARLHW
ELSTTITSNHLLGMVAMSNTLMSMKMATFVPESERARKLMKQATKNNVAWASDDDHEEQL
ITEQQAQIKQGWSLLSTHHCFLLPDKIDAMEPKNFKRPQVELMARRWQHHCIEIREAAQQ
MLLGELGRMGKKGRKQLVENWAQYLPQYTHTEPIVQQTQPSSPGSTSPSALSPSAAQQQQ
AEAEEEVEEEEEVVRQKPSSLAELKRKQSTAVIILGVIGAEFGQDISIETGANGKKPTTE
QQQRRKSSIVEGFGIGNNNLARLTAMALTHLLLAPPTPKLPAYTQLRRAAIDLIGRGFTV
WEPYLDVSKVLLGLLEISCDSSRLVPSLTYKLPLTPQADACRTARHALRLIATARPAAFI
TTMAREVARYNTLQQNSQALSVPLTQSVLHRAKKEILQCVEMLIEKMQSDMAALLVEVTD
ITLHCLDMSDLKNRSLNEVCPSICKFNQVSHCSSTRRIAVGASNGHMAIYELRQNKCQMI
PAHSQPITALAFSPDGKYLVSYSCSENRLSFWQTSTGMFGLGQSQTRCIKGYSTAPIPDI
ARLNPMRLGKLIWINNRTVTLMLADGSETRFNV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8890.t2 | Coils | Coil | Coil | 356 | 376 | - |
| 7 | g8890.t2 | Gene3D | G3DSA:2.130.10.10 | - | 565 | 711 | 1.8E-12 |
| 5 | g8890.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 335 | 381 | - |
| 6 | g8890.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 335 | 361 | - |
| 1 | g8890.t2 | PANTHER | PTHR44099 | RABCONNECTIN-3B, ISOFORM A | 16 | 752 | 4.3E-188 |
| 2 | g8890.t2 | PANTHER | PTHR44099:SF4 | RABCONNECTIN-3B, ISOFORM A | 16 | 752 | 4.3E-188 |
| 4 | g8890.t2 | SMART | SM00320 | WD40_4 | 653 | 693 | 0.0019 |
| 3 | g8890.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 624 | 697 | 1.4E-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.
