General information for g3898.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin-like modifier-activating enzyme 1.
Parent gene
- The parent gene g3898 is located on chr_3: 28704954..28706269 (+ 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 | g3898 | g3898.t1 | TSS | g3898.t1 | 28702074 | 28702074 |
| chr_3 | g3898 | g3898.t1 | isoform | g3898.t1 | 28702095 | 28705915 |
| chr_3 | g3898 | g3898.t1 | exon | g3898.t1.exon1 | 28702095 | 28702946 |
| chr_3 | g3898 | g3898.t1 | cds | g3898.t1.CDS1 | 28702095 | 28702946 |
| chr_3 | g3898 | g3898.t1 | exon | g3898.t1.exon2 | 28703274 | 28704581 |
| chr_3 | g3898 | g3898.t1 | cds | g3898.t1.CDS2 | 28703274 | 28704581 |
| chr_3 | g3898 | g3898.t1 | exon | g3898.t1.exon3 | 28704648 | 28704956 |
| chr_3 | g3898 | g3898.t1 | cds | g3898.t1.CDS3 | 28704648 | 28704956 |
| chr_3 | g3898 | g3898.t1 | exon | g3898.t1.exon4 | 28705014 | 28705277 |
| chr_3 | g3898 | g3898.t1 | cds | g3898.t1.CDS4 | 28705014 | 28705277 |
| chr_3 | g3898 | g3898.t1 | exon | g3898.t1.exon5 | 28705342 | 28705439 |
| chr_3 | g3898 | g3898.t1 | cds | g3898.t1.CDS5 | 28705342 | 28705439 |
| chr_3 | g3898 | g3898.t1 | exon | g3898.t1.exon6 | 28705498 | 28705915 |
| chr_3 | g3898 | g3898.t1 | cds | g3898.t1.CDS6 | 28705498 | 28705915 |
| chr_3 | g3898 | g3898.t1 | TTS | g3898.t1 | 28706435 | 28706435 |
Sequences
>g3898.t1 Gene=g3898 Length=3249
ATGTCCAAAGAAACTACAAATTTTTCTTCACCTGTCGCAAAGAAGAGAAAATTAGAGAGT
GAAATCGAGGATAATTCAGTTGCTAACAACTTTGGTACTACGCAACACTCCAAGAATTCG
ACGGGTGAATTGGAAAATAGTAAAAATCATTCAATAAATCAGCAACAGCAGCAACAACAA
CAAAATTTCTCAAATAAAAAAACAATGGCGAATGGAAATAATGAAGAAAAAGGGCACAAA
GAGATCGATGAGGCACTTTATAGCCGTCAATTATATGTGCTTGGACACGAGGCAATGAGA
AGAATGGCGGCCTCTGATGTCTTAATCTCTGGAATCAATGGATTGGGAGTTGAAATTGCT
AAAAATGTTATATTGGCTGGTGTAAAAAGTGTAACACTACATGACCAGCAAATTTGCTCA
TTGGCGGATCTTTCATCACAATTCTATTTGAGTGAATCATCAATTGGAACAAATCGTGCC
GAAGCTAGTTGTTCTCATTTAGCCGAGTTGAATCAATATGTTCCAACAACTGCCTATATT
GGCGATTTAGATGAGGAATTCTTGAAAAAATTCAGTGTTATAGTTTACACCGAGAACAAT
GAGGAAGAGCAGAAACGTCTTTCAAATATTGCTCGTAAACTTAACATCAAATTAATATTA
GCAATGACAAGAGGTTTATTTGGACAAATTTTCTGTGACTTTGGACCCGAATTTGTAGTT
TACGATGTAAATGGAGCCAGTCCTCTGTCAGCTATGATCGCAGGCATTTCGAAAGATCAA
GAGGGTGTAGTTACTTGCTTAGATGAAACACGTCATGGATTCGAAGACGGAGATTATGTG
ACATTTACGGAGGTTCAAGGAATGACACAGCTAAATGGATGTAATCCAATGAAAATCAAG
GTTCTTGGACCTTATACTTTCAGTATTGGTGACACAACCGGCTTTGATGATTACATTCGT
GGTGGTCTTGCAATTCAAGTGAAGATGCCGAAAACTGTTTCATTTAAACCATTGGAAGAA
GCTGAAAAAAGTCCCGAGTTTATTCTTTCTGATTATGCAAAATTCGATCATCCACAAAAT
ATCAATATTGCATTTACCGCCTTGTCACGTTTCAATACTAAATTCAGTCGCAATCCTCGG
CCGTGGAACGCTGAAGATGCTGCTGAATTCCTCTCATTGTGTAAAGAACGTGCAAAAGAA
TTGAATGTCGATGAGCTTAAAGAAGAATTGTTGTTGATCTTTGCTAAAATTTCAAGCGGC
GATCTCTGTCCAATTAATGCAGTAATTGGTGGTATGAGTGCTCAAGAAGTAATGAAAGCA
TGCAGTGGAAAGTTTATGCCAATAATGCAATTCTTCAGTTTTGATGCAATCGAATGTTTA
CCAGAAGATCTCAGTGTCTTGACTGAAAGTGAATGTCAACCAAATGGATCTCGATATGAT
TCACAAATTGCAATTTTTGGAAAAACCTTTCAAGAAAAACTGAGTGCATTAAAGTACTTC
ATTGTTGGTGCAGGAGCTATCGGTTGTGAGTTGCTCAAAAATTTTGGAATGATGGGTGTT
GGTGCTGGACAAAATGGTGAACTTATTATTACGGATATGGATCTTATTGAAAAATCCAAT
TTGAATCGTCAATTTTTGTTCCGGCCTCATGATGTTCAATCACCAAAATCACGTGTTGCT
GCAGCCGCTGTTAAACGAATGAATCCACACATTAACATCACTTATCATGAAAATCGTGTA
GGAGCACAGACTGAAAACATTTATGATGATGATTTCTTTGAACGATTAAACGGTGTCGCT
AATGCTTTAGATAATATTGAAGCTCGCAATTATATGGATCGTCGTTGCGTATATTATCGT
TTGCCTCTTCTTGAATCTGGGACTTTAGGAACAATGGGAAATGTTCAAGTTGTAGTGCCG
TTCTTAACTGAATCATACAGCTCAAGCCAAGATCCACCGGAAAAAAGTATTCCAATCTGT
ACTCTCAAGAATTTCCCAAATGCCATTGAACATACATTGCAGTGGGCTCGCGATATGTTC
GAAGGTGTCTTCACTCAATCACCTTTTAATGCATCAGAGTACATTCGTGATATTACATTC
ATTGAACGTACTTTAAAATTGCCTGGAGTTCAGCCTCTTGAAACAATGGAATCGGTCAAG
CGTGCTTTGATCGATGAACGTCCTCAGAATTTTGCTGATTGCGTAAAATGGGCACGTTTT
CACTTTGAGGAAAACTTTGTAAATCAAATTAAGCAATTGCTATTTAATTTTCCACCTGAT
CAGCAAACATCTACCGGGCAACCTTTTTGGTCAGGTCCAAAACGTTGCCCTGTTCCTATG
GTGTTTAATGCTGACGATGAACTTCATCTTGACTATATTGTAGCTGCAGCTAATTTGAAA
GCTGAGGTATATGGTGTTAGTCAAAATCGTAATCGAAACGAAATTCGTGAATTGGTTCTT
CAAGTTGACGTTCCTGTTTTTACTCCTAAATCAGGTGTAAAAATTGCAGAAAATGATGCT
GCATTACAAGCGCAGCAAGATAACAACTCATTCGATCAATATCGTGTTGATAACATTGTC
GAAGAATTAAAATCACTGGGAAAACCGAACTTTTCTATTACGCCACTTGAGTTCGAAAAA
GACGATGATTCTAATTTTCATATGGATTTTATTGTTGCTGCATCAAATCTTCGTGCCGCT
AATTATAGTATTCCACCGGCTGACAAGCATAAGTCGAAGCTTATTGCAGGAAAAATTATT
CCAGCTATTGCAACAACAACGTCTCTTGTCTCAGGATGTGTTTCTTTAGAGTTGATTAAA
TTGACTCAAGATTTTAAGAAGCTTGATCGTTACAAGAACGGATTTATTAATATCGCATTA
CCATTAGTTGCATTTACTGATCCCATTCATGCAAAAGAGCAAGAATATAATGGCAACAAA
TGGACTTTATGGGATCGTTTTGAAGTTAAAGGTGAAATGACACTGCAAGAATTCCTCGAT
TATTTCTTAAACGTACATAAGCTGGAAATAACAATGTTATCTCAAGGTGTGGGAATGCTT
TATTCATTTTTTCAACCAAAGGCAAAACGTGACGAAAGAATGCCTTTAAAAATGACTGAA
ATTGTCCGTCAAGTAACAAAACGTAAGATTGCTCCACACGAACGAGCTTTGGTATTTGAA
ATTTGCTGTAATGATGAAACTGGTGAAGACTGTGAGGTCCCTTATGTACGTTACACGTTG
CCGCGTTAA
>g3898.t1 Gene=g3898 Length=1082
MSKETTNFSSPVAKKRKLESEIEDNSVANNFGTTQHSKNSTGELENSKNHSINQQQQQQQ
QNFSNKKTMANGNNEEKGHKEIDEALYSRQLYVLGHEAMRRMAASDVLISGINGLGVEIA
KNVILAGVKSVTLHDQQICSLADLSSQFYLSESSIGTNRAEASCSHLAELNQYVPTTAYI
GDLDEEFLKKFSVIVYTENNEEEQKRLSNIARKLNIKLILAMTRGLFGQIFCDFGPEFVV
YDVNGASPLSAMIAGISKDQEGVVTCLDETRHGFEDGDYVTFTEVQGMTQLNGCNPMKIK
VLGPYTFSIGDTTGFDDYIRGGLAIQVKMPKTVSFKPLEEAEKSPEFILSDYAKFDHPQN
INIAFTALSRFNTKFSRNPRPWNAEDAAEFLSLCKERAKELNVDELKEELLLIFAKISSG
DLCPINAVIGGMSAQEVMKACSGKFMPIMQFFSFDAIECLPEDLSVLTESECQPNGSRYD
SQIAIFGKTFQEKLSALKYFIVGAGAIGCELLKNFGMMGVGAGQNGELIITDMDLIEKSN
LNRQFLFRPHDVQSPKSRVAAAAVKRMNPHINITYHENRVGAQTENIYDDDFFERLNGVA
NALDNIEARNYMDRRCVYYRLPLLESGTLGTMGNVQVVVPFLTESYSSSQDPPEKSIPIC
TLKNFPNAIEHTLQWARDMFEGVFTQSPFNASEYIRDITFIERTLKLPGVQPLETMESVK
RALIDERPQNFADCVKWARFHFEENFVNQIKQLLFNFPPDQQTSTGQPFWSGPKRCPVPM
VFNADDELHLDYIVAAANLKAEVYGVSQNRNRNEIRELVLQVDVPVFTPKSGVKIAENDA
ALQAQQDNNSFDQYRVDNIVEELKSLGKPNFSITPLEFEKDDDSNFHMDFIVAASNLRAA
NYSIPPADKHKSKLIAGKIIPAIATTTSLVSGCVSLELIKLTQDFKKLDRYKNGFINIAL
PLVAFTDPIHAKEQEYNGNKWTLWDRFEVKGEMTLQEFLDYFLNVHKLEITMLSQGVGML
YSFFQPKAKRDERMPLKMTEIVRQVTKRKIAPHERALVFEICCNDETGEDCEVPYVRYTL
PR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g3898.t1 | CDD | cd01491 | Ube1_repeat1 | 86 | 463 | 3.72825E-156 |
| 23 | g3898.t1 | CDD | cd01490 | Ube1_repeat2 | 498 | 1034 | 0.0 |
| 19 | g3898.t1 | Gene3D | G3DSA:3.50.50.80 | - | 79 | 195 | 8.8E-43 |
| 18 | g3898.t1 | Gene3D | G3DSA:3.40.50.12550 | - | 207 | 490 | 1.2E-113 |
| 17 | g3898.t1 | Gene3D | G3DSA:2.40.30.180 | - | 247 | 327 | 1.2E-113 |
| 16 | g3898.t1 | Gene3D | G3DSA:3.40.50.720 | - | 497 | 972 | 2.3E-208 |
| 20 | g3898.t1 | Gene3D | G3DSA:1.10.10.2660 | - | 651 | 920 | 2.3E-208 |
| 21 | g3898.t1 | Gene3D | G3DSA:3.10.290.60 | - | 986 | 1080 | 1.7E-39 |
| 28 | g3898.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 64 | - |
| 27 | g3898.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 24 | 64 | - |
| 7 | g3898.t1 | PANTHER | PTHR10953:SF195 | UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 1 | 69 | 1073 | 0.0 |
| 8 | g3898.t1 | PANTHER | PTHR10953 | UBIQUITIN-ACTIVATING ENZYME E1 | 69 | 1073 | 0.0 |
| 11 | g3898.t1 | PRINTS | PR01849 | Ubiquitin-activating enzyme E1 signature | 108 | 132 | 9.3E-66 |
| 13 | g3898.t1 | PRINTS | PR01849 | Ubiquitin-activating enzyme E1 signature | 221 | 248 | 9.3E-66 |
| 12 | g3898.t1 | PRINTS | PR01849 | Ubiquitin-activating enzyme E1 signature | 526 | 549 | 9.3E-66 |
| 9 | g3898.t1 | PRINTS | PR01849 | Ubiquitin-activating enzyme E1 signature | 573 | 598 | 9.3E-66 |
| 10 | g3898.t1 | PRINTS | PR01849 | Ubiquitin-activating enzyme E1 signature | 726 | 753 | 9.3E-66 |
| 4 | g3898.t1 | Pfam | PF00899 | ThiF family | 87 | 471 | 5.7E-32 |
| 1 | g3898.t1 | Pfam | PF16190 | Ubiquitin-activating enzyme E1 FCCH domain | 259 | 329 | 3.8E-34 |
| 3 | g3898.t1 | Pfam | PF16191 | Ubiquitin-activating enzyme E1 four-helix bundle | 330 | 396 | 6.0E-21 |
| 5 | g3898.t1 | Pfam | PF00899 | ThiF family | 479 | 974 | 1.8E-69 |
| 6 | g3898.t1 | Pfam | PF10585 | Ubiquitin-activating enzyme active site | 666 | 913 | 1.9E-91 |
| 2 | g3898.t1 | Pfam | PF09358 | Ubiquitin fold domain | 984 | 1076 | 2.8E-35 |
| 25 | g3898.t1 | ProSitePatterns | PS00536 | Ubiquitin-activating enzyme signature 1. | 439 | 447 | - |
| 24 | g3898.t1 | ProSitePatterns | PS00865 | Ubiquitin-activating enzyme active site. | 658 | 666 | - |
| 26 | g3898.t1 | SMART | SM00985 | UBA_e1_C_a_2 | 951 | 1076 | 3.5E-70 |
| 14 | g3898.t1 | SUPERFAMILY | SSF69572 | Activating enzymes of the ubiquitin-like proteins | 81 | 462 | 7.46E-107 |
| 15 | g3898.t1 | SUPERFAMILY | SSF69572 | Activating enzymes of the ubiquitin-like proteins | 473 | 969 | 1.96E-136 |
| 29 | g3898.t1 | TIGRFAM | TIGR01408 | Ube1: ubiquitin-activating enzyme E1 | 81 | 1079 | 0.0 |
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:0008641 | ubiquitin-like modifier activating enzyme activity | MF |
| GO:0006464 | cellular protein modification process | BP |
KEGG
Orthology
- This transcript has been annotated with K03178 (ubiquitin-activating enzyme E1)
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.
