General information for g534.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin-protein ligase E3C.
Parent gene
- The parent gene g534 is located on chr_3: 3967847..3968996 (+ 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 | g534 | g534.t1 | TSS | g534.t1 | 3965392 | 3965392 |
| chr_3 | g534 | g534.t1 | isoform | g534.t1 | 3965428 | 3968996 |
| chr_3 | g534 | g534.t1 | exon | g534.t1.exon1 | 3965428 | 3965597 |
| chr_3 | g534 | g534.t1 | cds | g534.t1.CDS1 | 3965428 | 3965597 |
| chr_3 | g534 | g534.t1 | exon | g534.t1.exon2 | 3965659 | 3965809 |
| chr_3 | g534 | g534.t1 | cds | g534.t1.CDS2 | 3965659 | 3965809 |
| chr_3 | g534 | g534.t1 | exon | g534.t1.exon3 | 3965867 | 3966939 |
| chr_3 | g534 | g534.t1 | cds | g534.t1.CDS3 | 3965867 | 3966939 |
| chr_3 | g534 | g534.t1 | exon | g534.t1.exon4 | 3966997 | 3967118 |
| chr_3 | g534 | g534.t1 | cds | g534.t1.CDS4 | 3966997 | 3967118 |
| chr_3 | g534 | g534.t1 | exon | g534.t1.exon5 | 3967177 | 3968996 |
| chr_3 | g534 | g534.t1 | cds | g534.t1.CDS5 | 3967177 | 3968996 |
| chr_3 | g534 | g534.t1 | TTS | g534.t1 | 3969124 | 3969124 |
Sequences
>g534.t1 Gene=g534 Length=3336
ATGTTTAATTTTGACGGAAATTTTCGTCGTTTGCCAGTTCAATCGCTTGGAGGATCATCT
ATAGAAACAGATCGTAGTCGTTTAATCAAAAAAGCACAAGATGAGCGTAAGAAACGGGAA
GAATTGAGAAAAAAGGAAATTTCCTGCATTACAATTCAAAAGTGGATTAGGAGTTTTCAT
CAACGACAGGCTGTCAAACGACGAGAACGACTTAATTATGAAAGTTATATAAAAACGAAT
GGCTTAAAGAATATTCAAGATCTTGAATTTTTGCTAAAACGACTGCTGTATTACTATGAC
TTGAATGATAGTGATAAACTTATTACATTATGCCAATTTATAATCAAAAATGTTGGCATA
CTATTTGAAATAATCCTTCAAAACAATAATAGTTTTATTAAACAAAAATTACAATGGCAA
TTTCGCATACAAAAACTATTGACTCTATGTCTTAAACAAATATTTGTGTCACCATCAACA
TCAATAGCAATCCCAATGAGAACAATTGAAATTTTCACTTCTTTTGAATCAATAAGAAAT
TTTGCACCGGCTGGCATTAATGAGAATGACCTCATGAAATTCTCACGTCAAATTTTCTCT
TACATGATTGATCAAAATTACTATGAAAATGTACGAAAGATGTTGAATGAGAAAATTGCT
GAAAATACGTACGATGAAATCACAACTGTGCCGCGCACTGAAATCTCAAAAGTAATTCTG
TCAATGATTGAACGACCATTAAAATTGGTAAATTGTACCACTGGAGATGAAAAGCTCGAC
TCAAAGATTCTTACTGCATTCACAAACGATATTCTCGCCAAAGACTCAAATTCAACAATC
ATCAATTTTATAATTCCATCATTAGCAAAAAGTAAAGATTTTCCATTCATGAAATTTCTC
AATTTCCTATATTCAATTCAAATAAAACGAACAACAAACAATACTTTTAATGAACGGAAT
GACTCAAATGTTATTTTCAACGGGTTTCTTTTATATGCAATTTTGCATCTGGATGAGAAT
TTTCTCAAACAAATTATAACTCAAGGATGTTTGCAACAATATTTGATTGTAATTGGCAGT
ATGATAAATTGCATATCAAAATTACCAAAAGCAAATGACAAATATATTAAGTTTAGTAAT
TATGAAGAAGATGAAGATGGAATGAATGACAGTGATGATGAAGATAACGAAAGTGAACCT
GATGAAGAAATGCAACCACAATTTGAAAGACTGATTTTGATCAAAATTATACATCAGCTT
AATACAGAAAATCGTGTAAATGCCATTGTTAGGAATATTGACTCCATTTTACATCTACCG
AATGTAATTCATAGTGTTTGTGTTATTGCACATAATCTAATGATTTTTAATCGAGCAGCA
ATCAATGAATATAGACTGTTAGATTTATTGGCATTCAAACCTGAATTCATAAGAACACTT
TGGTATATTTTACTTACAACAAAATCAGAAAAGAATAATCTCTGTATAAGCATTTTATCA
AAAGGAATTACAATTCCTCCCAATGAAAGCTTCCTTGTAATTCCAATTTTGGCATCATTT
TGTGCACTTTTTGGAAGACTTTTATCTACATTGCATGATGGAGAGTTCTTTTATTGCAAT
TTTGATACAAATCAGCAATCATCTATTGAAATGACATCTTCATCAAATGTTGAACCAATA
AGAAATAATGTTATGCCATTTCATATAAAGGACATCATTCATATGTGCTTGACACTCAAA
GAACTTTCAATTGGACTGGTTGAACTTGCATTCCCTGAAAGTAGATCAGCAATTCGTGAT
CATTATAGAAATATTCTCTTAGGAAGTGACGATGATGTTCGAAATAATGCAAGAATGAAT
CAGGAGAAAACAATTTGGTCTCAACTTCTTCGAGTTTGTGTTTCACTTCTTCGTCAATTG
CATACACGTGATTTGAGATGTGAATTTGCACCAGCAGAAAATTGGATTGCGCCAACTCTT
AATATTCCATTAGATAGGCCAACAGACTTGCAATTTTCAGCAAGAAGACGTGGACCAAGA
CCCTTCCAACCGATTAGAGATTTCACAAGAAAAGACCTTGAAGAAGGCCCACCAATTTCA
ACAAAGCAAATTCGATCAATAACAATATTGAAAGAAATTCCTTTTGTGGTTCCATTTAAC
AAGCGATTTGAAGTTTTACAAGGACTTTTAGCTGCAGAGAAATTAAGGAGTCAAGGAGAT
ATGCAAGGATTTCTGCAAGGACCACAAACTCATTTGACTGTGCGAAGAACACATTTGTAT
GAAGATGCATTTGATAAATTATCACCTGAAAATGAACCAAATCTAAGGACGAGATGGCGA
GTTCAGATGGTTAATGAACAAGGACTTGAAGAGGCTGGTATTGATGGTGGTGGTATTTTT
AGAGAATTTCTCAGTGAATTAATTAAAACAGCATTCGATCCTAATCGTGGATTTTTCATA
CTAACAAAGGATAACATGTTATATCCAAATCCAAGTGCTAGTGTGATACAAGAAAACTAT
AAGAAACATTACTATTTTATTGGTCGAATGCTAGGCAAAGCATTGTTTGAGAATCTTCTC
GTTGAGCTTCCATTAGCTGAATTTTTCTTATCAAAATTGGCTGGACGTCATGCAGACATA
ATTGACATTCATCAATTAATTTCACTAGATCCCGATATGCACAAAAATTTAATGAAATTA
AAAAGCTACAACGAAAATGATTTCAAAGACCTTGGATTAGATTTCACTGTTGTTTGTGAT
GATTTGGGTGATACAAGAGTTGTTGAATTAAAACCTGATGGCGCTAATATAACTGTGAAT
TCAAGTAATTGGATTGAATATATTCAAGTTATGGCAGATTTCAAACTTAATCGACAAATT
CATGAGCAATGTTTAGCATTTAGACAAGGTTTAGCCAACGTACTTCCAATCTCATGGCTT
TACATGTTCAACACTAAAGAACTTCAAGTGTTGATTTCTGGTGCAGAAATTCCTGTAGAT
GTTGATGATTTAATGGCACATACGAGATATGGAGGTGATTATACACCAGAACATGAAACA
ATAAAAATGTTTTGGAATGTCGTTAAAAGTTTTGATGACTTAGAGAAACGACAATTGTTA
AAATTTGTCACAAGTTGCTCACGACCTCCCTTACTCGGTTTTAAAGATCTCGATCCACCA
TTCTGCATACAAAATTCAGGGGATGATAGTGATCGATTGGCAAGTGCATCAACTTGCATG
AATTTACTTAAATTACCCACCTATTCTGATGAAAACACTATGCGAGAGAAATTACTTTAT
TCCATAAATAGTGGCGTTGGTTTCGAATTGAGTTAA
>g534.t1 Gene=g534 Length=1111
MFNFDGNFRRLPVQSLGGSSIETDRSRLIKKAQDERKKREELRKKEISCITIQKWIRSFH
QRQAVKRRERLNYESYIKTNGLKNIQDLEFLLKRLLYYYDLNDSDKLITLCQFIIKNVGI
LFEIILQNNNSFIKQKLQWQFRIQKLLTLCLKQIFVSPSTSIAIPMRTIEIFTSFESIRN
FAPAGINENDLMKFSRQIFSYMIDQNYYENVRKMLNEKIAENTYDEITTVPRTEISKVIL
SMIERPLKLVNCTTGDEKLDSKILTAFTNDILAKDSNSTIINFIIPSLAKSKDFPFMKFL
NFLYSIQIKRTTNNTFNERNDSNVIFNGFLLYAILHLDENFLKQIITQGCLQQYLIVIGS
MINCISKLPKANDKYIKFSNYEEDEDGMNDSDDEDNESEPDEEMQPQFERLILIKIIHQL
NTENRVNAIVRNIDSILHLPNVIHSVCVIAHNLMIFNRAAINEYRLLDLLAFKPEFIRTL
WYILLTTKSEKNNLCISILSKGITIPPNESFLVIPILASFCALFGRLLSTLHDGEFFYCN
FDTNQQSSIEMTSSSNVEPIRNNVMPFHIKDIIHMCLTLKELSIGLVELAFPESRSAIRD
HYRNILLGSDDDVRNNARMNQEKTIWSQLLRVCVSLLRQLHTRDLRCEFAPAENWIAPTL
NIPLDRPTDLQFSARRRGPRPFQPIRDFTRKDLEEGPPISTKQIRSITILKEIPFVVPFN
KRFEVLQGLLAAEKLRSQGDMQGFLQGPQTHLTVRRTHLYEDAFDKLSPENEPNLRTRWR
VQMVNEQGLEEAGIDGGGIFREFLSELIKTAFDPNRGFFILTKDNMLYPNPSASVIQENY
KKHYYFIGRMLGKALFENLLVELPLAEFFLSKLAGRHADIIDIHQLISLDPDMHKNLMKL
KSYNENDFKDLGLDFTVVCDDLGDTRVVELKPDGANITVNSSNWIEYIQVMADFKLNRQI
HEQCLAFRQGLANVLPISWLYMFNTKELQVLISGAEIPVDVDDLMAHTRYGGDYTPEHET
IKMFWNVVKSFDDLEKRQLLKFVTSCSRPPLLGFKDLDPPFCIQNSGDDSDRLASASTCM
NLLKLPTYSDENTMREKLLYSINSGVGFELS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g534.t1 | CDD | cd00078 | HECTc | 751 | 1109 | 2.01006E-136 |
| 8 | g534.t1 | Coils | Coil | Coil | 25 | 45 | - |
| 5 | g534.t1 | Gene3D | G3DSA:3.90.1750.10 | Hect | 752 | 994 | 7.6E-73 |
| 6 | g534.t1 | Gene3D | G3DSA:3.30.2160.10 | Hect | 876 | 959 | 7.6E-73 |
| 7 | g534.t1 | Gene3D | G3DSA:3.30.2410.10 | Hect | 997 | 1111 | 8.8E-39 |
| 2 | g534.t1 | PANTHER | PTHR45700:SF2 | UBIQUITIN-PROTEIN LIGASE E3C | 2 | 1111 | 9.2E-256 |
| 3 | g534.t1 | PANTHER | PTHR45700 | UBIQUITIN-PROTEIN LIGASE E3C | 2 | 1111 | 9.2E-256 |
| 1 | g534.t1 | Pfam | PF00632 | HECT-domain (ubiquitin-transferase) | 806 | 1111 | 4.1E-92 |
| 11 | g534.t1 | ProSiteProfiles | PS50237 | HECT domain profile. | 771 | 1111 | 87.197 |
| 10 | g534.t1 | SMART | SM00119 | hect_3 | 769 | 1111 | 7.1E-135 |
| 4 | g534.t1 | SUPERFAMILY | SSF56204 | Hect, E3 ligase catalytic domain | 747 | 1105 | 4.19E-108 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g534/g534.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g534.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004842 | ubiquitin-protein transferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10589 (ubiquitin-protein ligase E3 C)
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.
