General information for g5828.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as E3 ubiquitin-protein ligase MIB2.
Parent gene
- The parent gene g5828 is located on chr_2: 12103796..12112762 (+ 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 | g5828 | g5828.t1 | isoform | g5828.t1 | 12100417 | 12112762 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon1 | 12100417 | 12100474 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS1 | 12100417 | 12100474 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon2 | 12108656 | 12108758 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS2 | 12108656 | 12108758 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon3 | 12108821 | 12109057 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS3 | 12108821 | 12109057 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon4 | 12109155 | 12109235 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS4 | 12109155 | 12109235 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon5 | 12109539 | 12109678 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS5 | 12109539 | 12109678 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon6 | 12109783 | 12110059 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS6 | 12109783 | 12110059 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon7 | 12110118 | 12110567 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS7 | 12110118 | 12110567 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon8 | 12110629 | 12110960 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS8 | 12110629 | 12110960 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon9 | 12111019 | 12111161 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS9 | 12111019 | 12111161 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon10 | 12111221 | 12112650 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS10 | 12111221 | 12112650 |
| chr_2 | g5828 | g5828.t1 | exon | g5828.t1.exon11 | 12112723 | 12112762 |
| chr_2 | g5828 | g5828.t1 | cds | g5828.t1.CDS11 | 12112723 | 12112762 |
| chr_2 | g5828 | g5828.t1 | TTS | g5828.t1 | 12113756 | 12113756 |
| chr_2 | g5828 | g5828.t1 | TSS | g5828.t1 | NA | NA |
Sequences
>g5828.t1 Gene=g5828 Length=3291
ATGATTGCGCCTGGAATACGTGTCGTGCGTGGACCTGATTGGATTTGGCAGAATCAAGAC
GGAGGTGAAGGTCACGTTGGAACACTTTGTGAAGTTGGCCGGTCAGGTTCCACACATTCA
CCAGAGAAAACAGTTGTTGTTAATTGGGACTCGGGTCATCGAACAAATTATCGTGTAGGC
TATCAATGTCAGTATGATCTTATAGTTGTTGACAACGCTCAAATTGGCGTGCGTCATCCA
AATATAATTTGTGACGGTTGTAAAAAAGCAGGAATTGCTGGAATTCTCTTCCGCTGTGCA
GAATGTGCCAATTTTGATTTATGTGCTCATTGCTATGGAAATGATGTTCACAATTTAGAG
CATTCCTTTGTGCGCTATCAGACGGCAAACTCTGTTGGTGTTCGTGTACCTCCACGTGCT
GGCTCAGTTCGTATACAACTCAAAGGAATTTTCGTTAACGCAAAAGTTGTTCGTGGACCC
GATTGGGAGTGGGGTCAACAAGATGGTGGCGAAGGCAAGACAGGTCGAGTGATGGAAATT
CGTGGATGGGACAATGAATCATGTCGAAGTGTTGCGAATGTTTCATGGGCATCTGGTTCC
ACTAATGTTTATAGATTAGGTCATAAAGGTAACGTTGATTTAAAATACGTTGTGCCAGCT
GTGGGCGGTTATTATTACAAGGATCACATGCCTGTGTTAGGGCAACGTGACGAACAGCAG
CCCGTCATTCAGGCTACACGACCAATTTTCTATGTTGGTGATCGTGTGCGTGTATGTTTG
GATAAAGAAAGTCTTATGAGGCTGCAATCGGGTCATGGTGGTTGGAATCCAAGAATGGCT
GAATTTCTCAGCAAAATTGGAACTGTTCATCGGATTACTGAAAAAGGTGATATTAGAGTA
CAATATGAAGGATGTTCAAATCGATGGACATTTCATCCAGCAGCACTTGTAAAAGTTTTT
AGTTTCCATGTTGGTGATTTAGTTACAATCATCAATGATGCATGCAAAGTGCAACAGTTT
CAGAAAAATCATGGTGAATGGGTTGAAACAATGAGAAATGCATTAGGAAAAACTTGTAAA
ATTGTCAAAATTTATGCTGATGGAGATTTAAGAGTGACACAACTTGATGATGGTGTTGCA
TGGACATTAAATCCAAAATGTGTGAAACTTGAACGTTCACCAATGGCTTCAGCGGCTGAA
AGATCAAATAGCATGATGGATTTGAGTCATCAACGAACGGATCATGTGCTAATGCCATTG
CAAGGACTGTCTGGAACATCATCTGCTGATAAACTTGTTAGAGAAGCTGCACAGGGAAAA
TTGGAATATGTTCAACATTATTTAGGTGCAAATCCTGATCAAGTTGATGTTATGAGTGGT
GGCAAAACTTGCTTGCAAGTTGCAGCACATCAAGGACATAAAGCACTGGTTGAATATTTG
TTATCAGTTGGAGCAAATGTCAATGTTGTTGATAAAGAAGGCGATTCTGTTCTCCATTAT
GCTGCCTTTGGCAATCAACCAGAAATTATGAAAATTCTTCTACAACATGGCGCAAATATT
AATGTGCTTAATGCAAGTCATTGCACAGCTCTACACATTTCTGCACATAAAAAACCGCCA
CATTGTGTACGAGTTTTATTGGAATTTAATGCTGATGTAAATTTGCAAGATTCTTATGGC
GATTCAGCACTTCATGATGCAATTGGAAAAGAAAATTCTGAAGTTGTCGAGCTTTTATGT
AATGTCCAGTCATTGGATTTGACTATAAGAAATAAAAGAGGCTTCAATTGTCTTCATCAT
GCTTCATTAAAAGGCAATGTTTTTGCTGCACGTAGAATTCTTCAATTAGCACGTCAACTA
GTTGATGTAAAAAAAGATGATGGATTTTCAGCATTGCATCTGGCAGCATTAAATGGTCAT
AGTCAAGTTTGTGAAGTGCTAGTTAAAGAAGGACAAGCCGATATTGATATTCGTAATGAT
AGACGACAAACACCATTTTTGTTAGCAGTTAGTCAAGGTCATGCGGCTGCAGTTGAAAAA
TTAGTCGAACTAGGTTGCGATATTTTAGCTAAAGATGAAGATGGTGATAATGCCATGCAT
TTGACCATTATTAAAAAGGCAAATCTTGTGCAAGAAGTTCCACAGCAAGAAGCACCAAAG
ATTTTTGAAATTTATCAGCACTTGAGTCACATTCAAGAGCATCGACTGATGTATACTTTG
CTATGCTATTTGGCACAAGAAGGTTGTAAAATAGAACCAAATTATAAAGGTGCAAGAATT
TTCGATTGGATTCCAGAACCTGAAATTCGTGACCTGATTTTGAGTTATGAAAAGAAAAGA
ACTGCAGTCATTGCCAATAATGCAAGTGGTAGTAATGATTGCAATCAATCTCGTGACATG
ACAGAGCTGTATAATAATATTGAAATGATGAATCTCACATCACAAGACTCATCAACACTT
AGCACAATTGAGCAAGACAATAGTGGTGGAAGTTCAAGTATGGCCAATTGTAATACAATA
AGCACAACAGCAAATAATTCAAATCCGCCAACACCAGCAAGAAGAAATCGTGTTGCAGTT
GCTAGCAATAATAATAACAACAATAATACCAGAGATGTACCAACACCACCACCAACTTCT
TCAGCTGCAACAACATCAACTGAAGATGAGAAAAAATTAAATGTTGAAAGCAGAAATCTT
CCAAGAAATCATACAACATCACCACCATTACCGCATGCAGAGCCAACAACTTCTTCCAAT
ACAATTGTCGACACATCGTCGAGTTCGCCAAATCGCAATACAAGCCAATCACCACCACTT
CCAATGTCATCAAAACACATTAGTCGTAAACAACAGCAAAAAACTTATCCAACACCGCAG
CCTTTTAATGGCAAACCACAACTGCAAGCACCACATGAATGTAAAGTATGCAATGAATAT
TTCTTATTGGTAACTTTTGATCCTTGCGGACATCAAATTTGCTGCGAAGAATGCAGTTGG
CGCATGAAAAAGTGTCTCGAATGCCAAACAGTCATTGACAAGCGTTATGCTATGAATGGT
AAAATGTTGCTTCCAAAAGAAACACAACGACAACCCTCAGCCGATCGATTGCGCTATTTA
GAGCATAAAATATTAGAAATTGAAGAAACACATTCGTGTGGAATTTGCATGGAAAGAAGA
AGAAATGTTGCATTTTTATGTGGACATAGTGCATGCTCAAAATGTGCTGAGACACTTAAA
ACGTGTCATATGTGTCGAAAAACTATTGCCAAAAAGATTAATTTATATTAA
>g5828.t1 Gene=g5828 Length=1096
MIAPGIRVVRGPDWIWQNQDGGEGHVGTLCEVGRSGSTHSPEKTVVVNWDSGHRTNYRVG
YQCQYDLIVVDNAQIGVRHPNIICDGCKKAGIAGILFRCAECANFDLCAHCYGNDVHNLE
HSFVRYQTANSVGVRVPPRAGSVRIQLKGIFVNAKVVRGPDWEWGQQDGGEGKTGRVMEI
RGWDNESCRSVANVSWASGSTNVYRLGHKGNVDLKYVVPAVGGYYYKDHMPVLGQRDEQQ
PVIQATRPIFYVGDRVRVCLDKESLMRLQSGHGGWNPRMAEFLSKIGTVHRITEKGDIRV
QYEGCSNRWTFHPAALVKVFSFHVGDLVTIINDACKVQQFQKNHGEWVETMRNALGKTCK
IVKIYADGDLRVTQLDDGVAWTLNPKCVKLERSPMASAAERSNSMMDLSHQRTDHVLMPL
QGLSGTSSADKLVREAAQGKLEYVQHYLGANPDQVDVMSGGKTCLQVAAHQGHKALVEYL
LSVGANVNVVDKEGDSVLHYAAFGNQPEIMKILLQHGANINVLNASHCTALHISAHKKPP
HCVRVLLEFNADVNLQDSYGDSALHDAIGKENSEVVELLCNVQSLDLTIRNKRGFNCLHH
ASLKGNVFAARRILQLARQLVDVKKDDGFSALHLAALNGHSQVCEVLVKEGQADIDIRND
RRQTPFLLAVSQGHAAAVEKLVELGCDILAKDEDGDNAMHLTIIKKANLVQEVPQQEAPK
IFEIYQHLSHIQEHRLMYTLLCYLAQEGCKIEPNYKGARIFDWIPEPEIRDLILSYEKKR
TAVIANNASGSNDCNQSRDMTELYNNIEMMNLTSQDSSTLSTIEQDNSGGSSSMANCNTI
STTANNSNPPTPARRNRVAVASNNNNNNNTRDVPTPPPTSSAATTSTEDEKKLNVESRNL
PRNHTTSPPLPHAEPTTSSNTIVDTSSSSPNRNTSQSPPLPMSSKHISRKQQQKTYPTPQ
PFNGKPQLQAPHECKVCNEYFLLVTFDPCGHQICCEECSWRMKKCLECQTVIDKRYAMNG
KMLLPKETQRQPSADRLRYLEHKILEIEETHSCGICMERRRNVAFLCGHSACSKCAETLK
TCHMCRKTIAKKINLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g5828.t1 | CDD | cd16726 | RING1-HC_MIB2 | 973 | 1009 | 3.83799E-16 |
| 26 | g5828.t1 | CDD | cd16520 | RING-HC_MIBs_like | 1052 | 1089 | 2.11938E-18 |
| 21 | g5828.t1 | Gene3D | G3DSA:2.30.30.920 | - | 1 | 73 | 7.6E-23 |
| 22 | g5828.t1 | Gene3D | G3DSA:3.30.60.90 | - | 74 | 129 | 5.8E-13 |
| 20 | g5828.t1 | Gene3D | G3DSA:2.30.30.920 | - | 139 | 222 | 1.4E-22 |
| 19 | g5828.t1 | Gene3D | G3DSA:1.25.40.20 | - | 420 | 584 | 1.9E-41 |
| 18 | g5828.t1 | Gene3D | G3DSA:1.25.40.20 | - | 585 | 752 | 2.3E-27 |
| 24 | g5828.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 946 | 1018 | 4.2E-9 |
| 23 | g5828.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 1034 | 1096 | 1.1E-13 |
| 37 | g5828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 862 | 964 | - |
| 38 | g5828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 862 | 888 | - |
| 39 | g5828.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 899 | 964 | - |
| 11 | g5828.t1 | PANTHER | PTHR24202 | - | 3 | 1091 | 4.3E-283 |
| 12 | g5828.t1 | PRINTS | PR01415 | Ankyrin repeat signature | 461 | 476 | 5.0E-5 |
| 13 | g5828.t1 | PRINTS | PR01415 | Ankyrin repeat signature | 509 | 523 | 5.0E-5 |
| 2 | g5828.t1 | Pfam | PF06701 | Mib_herc2 | 5 | 71 | 1.4E-23 |
| 5 | g5828.t1 | Pfam | PF00569 | Zinc finger, ZZ type | 79 | 114 | 1.5E-7 |
| 1 | g5828.t1 | Pfam | PF06701 | Mib_herc2 | 154 | 217 | 2.3E-23 |
| 4 | g5828.t1 | Pfam | PF18346 | Mind bomb SH3 repeat domain | 250 | 316 | 1.8E-23 |
| 3 | g5828.t1 | Pfam | PF18346 | Mind bomb SH3 repeat domain | 322 | 388 | 2.9E-19 |
| 8 | g5828.t1 | Pfam | PF12796 | Ankyrin repeats (3 copies) | 436 | 522 | 1.9E-13 |
| 6 | g5828.t1 | Pfam | PF12796 | Ankyrin repeats (3 copies) | 528 | 589 | 1.8E-7 |
| 7 | g5828.t1 | Pfam | PF12796 | Ankyrin repeats (3 copies) | 598 | 692 | 3.2E-10 |
| 10 | g5828.t1 | Pfam | PF13920 | Zinc finger, C3HC4 type (RING finger) | 972 | 1014 | 1.8E-6 |
| 9 | g5828.t1 | Pfam | PF13920 | Zinc finger, C3HC4 type (RING finger) | 1051 | 1090 | 2.2E-7 |
| 43 | g5828.t1 | ProSiteProfiles | PS51416 | MIB/HERC2 domain profile. | 1 | 73 | 31.345 |
| 44 | g5828.t1 | ProSiteProfiles | PS50135 | Zinc finger ZZ-type profile. | 78 | 125 | 12.421 |
| 42 | g5828.t1 | ProSiteProfiles | PS51416 | MIB/HERC2 domain profile. | 142 | 220 | 32.968 |
| 40 | g5828.t1 | ProSiteProfiles | PS50297 | Ankyrin repeat region circular profile. | 449 | 703 | 58.44 |
| 45 | g5828.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 460 | 492 | 12.876 |
| 49 | g5828.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 493 | 525 | 13.544 |
| 47 | g5828.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 526 | 558 | 9.778 |
| 48 | g5828.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 627 | 651 | 10.286 |
| 46 | g5828.t1 | ProSiteProfiles | PS50088 | Ankyrin repeat profile. | 661 | 693 | 9.698 |
| 41 | g5828.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 1053 | 1086 | 10.04 |
| 34 | g5828.t1 | SMART | SM00291 | zz_5 | 78 | 123 | 7.6E-9 |
| 30 | g5828.t1 | SMART | SM00248 | ANK_2a | 460 | 489 | 1.9E-4 |
| 28 | g5828.t1 | SMART | SM00248 | ANK_2a | 493 | 522 | 1.5E-6 |
| 29 | g5828.t1 | SMART | SM00248 | ANK_2a | 526 | 555 | 0.016 |
| 33 | g5828.t1 | SMART | SM00248 | ANK_2a | 559 | 589 | 6.0 |
| 32 | g5828.t1 | SMART | SM00248 | ANK_2a | 593 | 623 | 150.0 |
| 31 | g5828.t1 | SMART | SM00248 | ANK_2a | 627 | 657 | 1.7E-4 |
| 27 | g5828.t1 | SMART | SM00248 | ANK_2a | 661 | 690 | 0.79 |
| 36 | g5828.t1 | SMART | SM00184 | ring_2 | 974 | 1008 | 0.26 |
| 35 | g5828.t1 | SMART | SM00184 | ring_2 | 1053 | 1085 | 0.0078 |
| 17 | g5828.t1 | SUPERFAMILY | SSF159034 | Mib/herc2 domain-like | 2 | 72 | 1.09E-20 |
| 15 | g5828.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 59 | 140 | 9.89E-22 |
| 16 | g5828.t1 | SUPERFAMILY | SSF159034 | Mib/herc2 domain-like | 145 | 217 | 2.09E-20 |
| 14 | g5828.t1 | SUPERFAMILY | SSF48403 | Ankyrin repeat | 432 | 705 | 9.05E-64 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5828/g5828.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5828.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046872 | metal ion binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0016567 | protein ubiquitination | BP |
| GO:0008270 | zinc ion binding | MF |
| GO:0004842 | ubiquitin-protein transferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10645 (E3 ubiquitin-protein ligase mind-bomb)
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.
