General information for g3146.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3146 is located on chr_3: 23195307..23196647 (- 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_3 | g3146 | g3146.t1 | TTS | g3146.t1 | 23193306 | 23193306 |
| chr_3 | g3146 | g3146.t1 | isoform | g3146.t1 | 23193526 | 23196647 |
| chr_3 | g3146 | g3146.t1 | exon | g3146.t1.exon1 | 23193526 | 23193570 |
| chr_3 | g3146 | g3146.t1 | cds | g3146.t1.CDS1 | 23193526 | 23193570 |
| chr_3 | g3146 | g3146.t1 | exon | g3146.t1.exon2 | 23193632 | 23196060 |
| chr_3 | g3146 | g3146.t1 | cds | g3146.t1.CDS2 | 23193632 | 23196060 |
| chr_3 | g3146 | g3146.t1 | exon | g3146.t1.exon3 | 23196141 | 23196279 |
| chr_3 | g3146 | g3146.t1 | cds | g3146.t1.CDS3 | 23196141 | 23196279 |
| chr_3 | g3146 | g3146.t1 | exon | g3146.t1.exon4 | 23196588 | 23196647 |
| chr_3 | g3146 | g3146.t1 | cds | g3146.t1.CDS4 | 23196588 | 23196647 |
| chr_3 | g3146 | g3146.t1 | TSS | g3146.t1 | 23196756 | 23196756 |
Sequences
>g3146.t1 Gene=g3146 Length=2673
ATGACCGATGTTGTCAATAGAAACAGTGCCGATGAAAGCGAAGAAAAGCAACGAACGATG
AGCTTAACAGAAAACTCGCCAACATCGGGTGGAATTGAGTCTGAATATGATACGGCGAGT
ACAAATTCAAGATCTGATAATGAAAGAGATGAATATGAAGACAGCGAAGAGGACAGTATG
GATGAGGAAGAAGCTACTGATGATGAAGATGAACCGCAAGATGATGAAAGAGAATCAGGT
GATGACGATGATGAAAATCAAGAAGAGCAAGAAAGTGAAGGTGGAACAAAGAAAAAAGTC
GATCATGATGAAGATCGAAGTAATCCACAATATATCCCAAAAAAGGGAACATTTTATGAA
CATGATGATCGTACAGCTGAAGACCTTGATGCAAATGAACCAGTAGAAAATTTGGAAAAT
GCAAATAATAGCACAGAAGGTTTAGCCGGTACTGGAAAAGTTTTATCAACACAAAATCAA
AAAGTCACACCGAAACAGGTAAAGAAAAAAGAGGCAGATCGTTGGACTCATGATCGTTTT
AATGAATATGAGCAAGCACCGAAATCAAAAGCAGAATTGGTCTCAGCCTATGGCTATGAT
ATCAGAAATGAAGATTGCCCACCAAGACCACGTCGTCAAAGACGCTATGGTCGTCATCAA
TCAAAATACTCGAGAAATTGGGAAGATGAAGAAGCTTATAAAAAGCAACAGTCGAGTGCA
AAACCACCAAGGCGTGTTCCTAAACCAGAAGATTTTCCAGCACTCGGTTCAACTCCTCGT
CCTACTTCATCATCAAAATCTCGCATTTCGCGATCTCGTCGTAATCATCAACAAGATGAA
AATGATCCACAATCATCACAGCAGCAACAACAACAACAGAATTATCGATCGCCAATAAGA
AATTCTCGTGAGCAAAGGTCACATCGTGAAGATCGTGGATCACGTGGTGATGGAAGAAAT
CAACGTTATAATAATGACAACAGCAACAATAACAATGCAAGACATGTCAAAGGCAAAAAG
AATATCAATTTCAATCACAATATTGAGTTCAAGAACCAAAATCGTAAAAATATTAATTAT
GAATCGACACAAACAAAGAATAATAATGTGCTGAATCAACAAATGCAATCGTCATCACAT
CAGCATCATAGTCAATCATCGTCACATGCGAGTTCACATCATCAACAATCACAGCAACAA
CAACATCAGCAACATCAATCGAATCAACGTTATAATAATAATGAAGCACCGCTGCCAACT
TTAAGCTTCACTAACAGCAAAATGAATAATGCAACAAATAATTCGAGCGCAACGCCGACA
TCGTCGAGGACAATTTTAAATTTTGACAATTCATCGGGCAATTATGGTCGCGGCAGTCGC
GAAAAAGAGGTCAATAGTCATAATATGCAACAATCATCATCAGCAATGTCACCGAATAAA
AATATTCAACAACAATATGCTGATCATCAAATGGATCAAATGAAACTCATGGAAAAGAGC
TATCAGGGCAAAGCGACAAATTTGAATTTGAATCAAGTGCCATCACAGCAGCAACAAATT
CAACAGCAACAGCCAATTAATAATATGCAAGATGCTTCGATGATGAATAGCTCAGAAATG
AGCCGATCAAAAAGATATTCAAGTCTTCGTCAGAGATCAAATATTAATGAAGGACCACCG
CAGCAACAGACTGCTCAACAGCAACAACAGCAGCAGTCAGTTCAAAATCAAGCACCCCAG
CCACAGCAATATCATCCTCAATATCATCCACAGCAAGAAATTGATCCATCACAGCATGTA
CAGAATGTGATGACAACACAACAGCCTACTCAAACTTACTTGTCTCAACCGCAGCCGAAT
GCTCAACAACAACAGCCTCCTCCGCCACAGAATCAACAGCAAACGACTACAAATGTTCAG
CAACAAGCAGCAGCAGCTCAAAAATATCAAGCTGCTTATTATGCTGCAAATCCTGCAAGT
GAATATGCAGTAGCTCAACAGCAAGCATTAATGCAAGCAGCAATGGTTGAAAAATATCAA
TATCAACAGCAAACTTCACCTGCTCAATACTTGCCGCCTCCACAACAAACCCAACAAATT
TATATGCCTACACAGACGCAGCCGACACAGCAACAACAAATTTTGAATTATGTCTCGACA
ATTCAACCACAAGGACCAACTGCAGGCTATCCACAATATACAAATTATCAAAATTTTAAT
ATTCAAGGTCCACAACCTGCAGCAAGTGCTCCACAGCCTCAGGCACCACCACCTGCTCAA
ACAACTCCCATCTATCAGACACAAAGTGGACTGACTTATTATCCTAATCAACAAATACAA
ACAACTCATCAGCCACGAATAATTCAGCCTCAACGACGTCCAAATCCAATTCCGATACTC
GCGCCACCTGATCATAAAGCAAAAAATAGCTCGGCTGTGAATGACGATATTGATAAAAAT
ATTGATGGCGATAAAGGTACAAGTAGTGCAGAAAATATCGATCATATTTTGGATAATATG
TTTGTGCAGCGTCCAATGACAAATGTTGTGTCATTAAAAGATCCAACAACTGTAACGACA
ATGTCTAGTGATGATAAAAATGATGATCAAATCAATGATGGCATGAATTCAATGTCAATA
AATGATGATAAGAAGGGCGATGGCAGTAAATAA
>g3146.t1 Gene=g3146 Length=890
MTDVVNRNSADESEEKQRTMSLTENSPTSGGIESEYDTASTNSRSDNERDEYEDSEEDSM
DEEEATDDEDEPQDDERESGDDDDENQEEQESEGGTKKKVDHDEDRSNPQYIPKKGTFYE
HDDRTAEDLDANEPVENLENANNSTEGLAGTGKVLSTQNQKVTPKQVKKKEADRWTHDRF
NEYEQAPKSKAELVSAYGYDIRNEDCPPRPRRQRRYGRHQSKYSRNWEDEEAYKKQQSSA
KPPRRVPKPEDFPALGSTPRPTSSSKSRISRSRRNHQQDENDPQSSQQQQQQQNYRSPIR
NSREQRSHREDRGSRGDGRNQRYNNDNSNNNNARHVKGKKNINFNHNIEFKNQNRKNINY
ESTQTKNNNVLNQQMQSSSHQHHSQSSSHASSHHQQSQQQQHQQHQSNQRYNNNEAPLPT
LSFTNSKMNNATNNSSATPTSSRTILNFDNSSGNYGRGSREKEVNSHNMQQSSSAMSPNK
NIQQQYADHQMDQMKLMEKSYQGKATNLNLNQVPSQQQQIQQQQPINNMQDASMMNSSEM
SRSKRYSSLRQRSNINEGPPQQQTAQQQQQQQSVQNQAPQPQQYHPQYHPQQEIDPSQHV
QNVMTTQQPTQTYLSQPQPNAQQQQPPPPQNQQQTTTNVQQQAAAAQKYQAAYYAANPAS
EYAVAQQQALMQAAMVEKYQYQQQTSPAQYLPPPQQTQQIYMPTQTQPTQQQQILNYVST
IQPQGPTAGYPQYTNYQNFNIQGPQPAASAPQPQAPPPAQTTPIYQTQSGLTYYPNQQIQ
TTHQPRIIQPQRRPNPIPILAPPDHKAKNSSAVNDDIDKNIDGDKGTSSAENIDHILDNM
FVQRPMTNVVSLKDPTTVTTMSSDDKNDDQINDGMNSMSINDDKKGDGSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 356 | - |
| 13 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 20 | 41 | - |
| 9 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 50 | 90 | - |
| 8 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 91 | 131 | - |
| 10 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 136 | 163 | - |
| 16 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 164 | 186 | - |
| 11 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 221 | 248 | - |
| 18 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 281 | 300 | - |
| 14 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 301 | 319 | - |
| 17 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 338 | - |
| 12 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 373 | 410 | - |
| 6 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 453 | 480 | - |
| 4 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 556 | 587 | - |
| 5 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 613 | 641 | - |
| 7 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 627 | 641 | - |
| 15 | g3146.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 853 | 890 | - |
| 2 | g3146.t1 | PANTHER | PTHR13434 | PROTEIN CASC3 | 11 | 685 | 1.7E-45 |
| 1 | g3146.t1 | Pfam | PF09405 | CASC3/Barentsz eIF4AIII binding | 73 | 205 | 3.5E-24 |
| 3 | g3146.t1 | SMART | SM01044 | Btz_2 | 74 | 206 | 7.6E-37 |
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:0006397 | mRNA processing | BP |
| GO:0003723 | RNA binding | MF |
| GO:0035145 | exon-exon junction complex | CC |
KEGG
Orthology
- This transcript has been annotated with K14323 (protein CASC3)
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.
