General information for g7345.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribosome biogenesis protein bms1.
Parent gene
- The parent gene g7345 is located on chr_2: 23172882..23174055 (+ 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 | g7345 | g7345.t1 | TSS | g7345.t1 | 23170385 | 23170385 |
| chr_2 | g7345 | g7345.t1 | isoform | g7345.t1 | 23170455 | 23174055 |
| chr_2 | g7345 | g7345.t1 | exon | g7345.t1.exon1 | 23170455 | 23170512 |
| chr_2 | g7345 | g7345.t1 | cds | g7345.t1.CDS1 | 23170455 | 23170512 |
| chr_2 | g7345 | g7345.t1 | exon | g7345.t1.exon2 | 23170571 | 23170771 |
| chr_2 | g7345 | g7345.t1 | cds | g7345.t1.CDS2 | 23170571 | 23170771 |
| chr_2 | g7345 | g7345.t1 | exon | g7345.t1.exon3 | 23170835 | 23174055 |
| chr_2 | g7345 | g7345.t1 | cds | g7345.t1.CDS3 | 23170835 | 23174055 |
| chr_2 | g7345 | g7345.t1 | TTS | g7345.t1 | 23174123 | 23174123 |
Sequences
>g7345.t1 Gene=g7345 Length=3480
ATGGGTGATGATGCAAATTTTATGGACAAAAAGAAACCACATAAAGCTAAGCATTCAGGT
GTGAAAGCAAAAAAGAAAGATGAGAAGAAAAGAAAACAATTTCCTACGGATAAGCAGAAG
AATCCAAAAGCTTTTGCAATTACTTCTGCTCGAAGTGCTGCAGATCGTTTTCATCGAAAA
CAAGATCTGAGAACGAAAAAGCATCATATTCCTTTGGTTGACCAAACTTCAGTCGATGAA
CCGCCGCCAATAGTTATTGGTGTTGTAGGCCCAGCGAAAGTAGGAAAAACAACTCTTATA
AATAATCTGATTAGAAATTTCACTAGAACGAATGTAACTTCAATCAATGGACCAGTTACA
ATTGTTGTTTCAAAGAAACGAAGAATTACACTAATAGAATGTAACAATGATATCAACTCA
ATGATTGATATTGCAAAATGTGCTGATTTGATTTTGTTAATGTGTGATGCCAGTTTTGGC
TTTGAAATGGAAATCTTTGAATTTTTAAATATTGCACAAGTACATGGAATGCCGAAAATT
ATGGGAGTACTGACACATTTAGACGCTTTTAAGAACGCCAAAGCATTACAAAAACGTAAG
AAATTACTTAAACATCGGTTTTGGACTGAAGTCTATCAAGGAGCAAAATTATTCTATTTA
TCCGGTATTCAACATGGTGAATATTTGCGAAATGAAATTAAAAACTTAGGCAGATTTATT
CATGTAATGAAGTTTAGACCTCTTACATGGCGTGGTCAACATAGTTACATTTTAGCTGAT
CGTATGGAAGATATTACAAATCAAGAAACGATTCGTCTTAATCCAAAATGTGATCGAAAT
GTCGTTTTATATGGCTATGTTCGTGGTATTCCATTGAAAAAAGATTCATCAGTTCATATA
GCTGGATATGGCGACACGAAAATTGATGAGTTGCAAGCACTTGCTGATCCTTGTCCAATG
GCTTCTAAAGAGAAGAAAAGAAACCTTTTAGAAAAAGAGCGATTGCTTTATGCTCCGATG
TCTGGTGTTGGTGGAATAGTTTATGATAAAGATGCAGTTTATATTGAACTACAAGGCTCA
CATAGTCATACAAAAGAAAATAGTGAACAGTCAAAACTTGTCAAAGAAATTATTGAAAAG
AAAGAAACTTTTGATCAACAAATTAAAAATCAAGAATTTCGTTTGTTCTCTGATGGAGAT
GTTATTAAATCAAAAGATTTTCAAGAAAAGAATAATGAGAGTGAAAGTGAAGAAGAAAAT
TTGTCTGAAAATGATGACGATGATGAGGACTCAGGAATGGATTCAGAACCTGAAAATTAT
AATGAAAGTGGATGGAATCCAAATGAGGATGATCAAGAAGATGAAGCTGAAAGCAATGTA
GACGAATCCGATGAAGAATATCAAGAAATTAATGAAAATAATGACAACAATAGTGATGAA
GAGGAAATTCTTGGAAGCAATTGGAAAGAAGGAGTTGCTGATCGAGCTCGTGATGCTTAT
TTAGAAAGAAAATCAAATAATCAAAGTCTAATGAAACTTGTTTATGGCAAATATGATCAA
AAAGGATTGCAATCAAATCTTAATAACAATGAAGGTGAATCAGATGATGAGATAGGCGGT
CTTTTTAAGAGTGTTTCAAAAAAGCAATCACAATTGCAGCAAGAAAAACAACAAAAAGAT
GAAGACGATAGTCCATTTTTCGAAAGCTATGGTGATGGCATAAGAAATTGGTTGTCTGAT
GAAAACAAAAAATTATTAGCTAATCATTTCGTGACTGGTAAATGGAAAAGTTCAGAAGAT
GCAGAGCAGTTATTGGAACTTGACGATATGAGTGACAATGATAGTGAAGTTTATGGTGAT
TTTGAAGACTTAGAAACTGGTGAGAAATTTGAAGGAAAAGAATCAATGAATGATAAGAAT
GCAACAGATGACGAGGTAACAAAAGATGAAAAATCGCAATCACGCAAAAGATGTCGAGTT
GAAGAAATGAATATGACACGAGCTGAATTGATGGCAAAGAAAATGAAATTGAAAGCAAAA
TTTGATGCTGAATATGACAATCCTGAACTTAAAGACTCACATCATATTGAAGGTGATGAA
GCATTTTATGAAAAATGGAAAGCTGAGGCAGAAAAACAAGCTGAAATCAATCGAAAAGAA
TTTTCTGGTCTCGATGAAGATGTTAGAAATGAAATTGAAGGTTTTCGAGCTGGTCTTTAT
GTTAGAATGTGTTTTAAGCAAGTTCCATGTGAATTTGTCACTAACTTTGATCCTTCTTAT
CCAATTTTAATTGGTGCCTTAAATATGAATGAAGAGAATGTTGGATATGTTAGTGGTGAA
GTCAAAAAGCATCGCTGGTACAGAAAACTTTTAAAAACTGGTGATCCTTTAATAATCTCA
CTTGGCTGGCGACGTTTTCAAACTGTTCCAATTTATGCAAAACGAGAAGATGATTTAAAG
CATCGATATTTGAAATATACACCTAATCATGTTGCATGTCATATGAGTTTTTATGGTCCT
ATTACTCCACAAGGTACAGGTTTTTTCGCAGTTCAAACAATTTCAAATAATGTTAAAGAG
CTTAAAAGAATTGGCTTTCGAATTGCTGCTACTGGTTCTATTAAAGAAGTTGACAAATCA
ACAACAATTCTCAAAAAGTTAAAACTTGTTGGTACACCAATTAAAATTTTTCAAAAATCT
GCATTCATCACTGGTATGTTTAACAGTGAATTAGAAGTATCGAAATTCGCTGGTGCAAAG
ATTAAAACCGTGTCAGGAATTAGAGGTCAAATTAAAAAATCAATTAGTTCAATTAGAGCA
GACAATTCTGGTAAGCATTTGAGTGTGGAACCAGGAACATACCGTGCAACGTTTGAAGAT
AAAATTAAAATAAGTGATATTGTATTCTGCCGAACTTGGTTTAAAGTTGATGTGCCACAA
TTTTATGCTCCAATTACAAATATGCTTTTGCCACAAGAAAAGAAATCACAATGGGAAGGA
ATGAAGACACTTGGACAACTAAAACGTGAACGTAACATAAAAGCAGAAGTTGATGAAGAT
CATTTGTACAAACCAATCGAAAGACCACCACCTAGTTTCAAGCCACTTGTGATTCCAGCA
TCACTTCAAAAAGCTCTTCCTTATAAAGATAAACCGAAGAAAGGTCCACTTAATCCTAAA
CAAAAGTTTGAAGAGACACGAGTAGCTGTTGTGCATTCACCGCATGAACAAAAAGTCGCA
AAAATGATGAACATGTTGAAGACAAATTATATAGCAAAGAAAAACAAGCAAAAAGAACGT
TCAAATGCAAAATATATCGAGAAAATCAAAGCTAAACAGAAGGAAGAAATTAATCGTATG
CAACGTGAGAAAGAAGTGAAAAGGAAAATTTTTAAAGCTTTATCAAAAATTCAATCAAAA
GAAGAAAAAGGTGAGAAGACAACAGGTGGTAAAAAGAAGCATTTTAAAAAGAAAAACTAA
>g7345.t1 Gene=g7345 Length=1159
MGDDANFMDKKKPHKAKHSGVKAKKKDEKKRKQFPTDKQKNPKAFAITSARSAADRFHRK
QDLRTKKHHIPLVDQTSVDEPPPIVIGVVGPAKVGKTTLINNLIRNFTRTNVTSINGPVT
IVVSKKRRITLIECNNDINSMIDIAKCADLILLMCDASFGFEMEIFEFLNIAQVHGMPKI
MGVLTHLDAFKNAKALQKRKKLLKHRFWTEVYQGAKLFYLSGIQHGEYLRNEIKNLGRFI
HVMKFRPLTWRGQHSYILADRMEDITNQETIRLNPKCDRNVVLYGYVRGIPLKKDSSVHI
AGYGDTKIDELQALADPCPMASKEKKRNLLEKERLLYAPMSGVGGIVYDKDAVYIELQGS
HSHTKENSEQSKLVKEIIEKKETFDQQIKNQEFRLFSDGDVIKSKDFQEKNNESESEEEN
LSENDDDDEDSGMDSEPENYNESGWNPNEDDQEDEAESNVDESDEEYQEINENNDNNSDE
EEILGSNWKEGVADRARDAYLERKSNNQSLMKLVYGKYDQKGLQSNLNNNEGESDDEIGG
LFKSVSKKQSQLQQEKQQKDEDDSPFFESYGDGIRNWLSDENKKLLANHFVTGKWKSSED
AEQLLELDDMSDNDSEVYGDFEDLETGEKFEGKESMNDKNATDDEVTKDEKSQSRKRCRV
EEMNMTRAELMAKKMKLKAKFDAEYDNPELKDSHHIEGDEAFYEKWKAEAEKQAEINRKE
FSGLDEDVRNEIEGFRAGLYVRMCFKQVPCEFVTNFDPSYPILIGALNMNEENVGYVSGE
VKKHRWYRKLLKTGDPLIISLGWRRFQTVPIYAKREDDLKHRYLKYTPNHVACHMSFYGP
ITPQGTGFFAVQTISNNVKELKRIGFRIAATGSIKEVDKSTTILKKLKLVGTPIKIFQKS
AFITGMFNSELEVSKFAGAKIKTVSGIRGQIKKSISSIRADNSGKHLSVEPGTYRATFED
KIKISDIVFCRTWFKVDVPQFYAPITNMLLPQEKKSQWEGMKTLGQLKRERNIKAEVDED
HLYKPIERPPPSFKPLVIPASLQKALPYKDKPKKGPLNPKQKFEETRVAVVHSPHEQKVA
KMMNMLKTNYIAKKNKQKERSNAKYIEKIKAKQKEEINRMQREKEVKRKIFKALSKIQSK
EEKGEKTTGGKKKHFKKKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g7345.t1 | CDD | cd01882 | BMS1 | 44 | 275 | 8.00315E-143 |
| 8 | g7345.t1 | Coils | Coil | Coil | 404 | 424 | - |
| 10 | g7345.t1 | Coils | Coil | Coil | 453 | 480 | - |
| 9 | g7345.t1 | Coils | Coil | Coil | 660 | 680 | - |
| 7 | g7345.t1 | Coils | Coil | Coil | 1095 | 1130 | - |
| 6 | g7345.t1 | Gene3D | G3DSA:3.40.50.300 | - | 83 | 246 | 1.5E-15 |
| 21 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 74 | - |
| 20 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 12 | 29 | - |
| 17 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 404 | 489 | - |
| 16 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 418 | 436 | - |
| 19 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 447 | 479 | - |
| 15 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 524 | 568 | - |
| 18 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 553 | 568 | - |
| 22 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 624 | 657 | - |
| 14 | g7345.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1136 | 1159 | - |
| 3 | g7345.t1 | PANTHER | PTHR12858 | RIBOSOME BIOGENESIS PROTEIN | 9 | 1143 | 0.0 |
| 4 | g7345.t1 | PANTHER | PTHR12858:SF2 | RIBOSOME BIOGENESIS PROTEIN BMS1 HOMOLOG | 9 | 1143 | 0.0 |
| 1 | g7345.t1 | Pfam | PF08142 | AARP2CN (NUC121) domain | 232 | 317 | 2.1E-30 |
| 2 | g7345.t1 | Pfam | PF04950 | 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal | 662 | 977 | 5.1E-84 |
| 23 | g7345.t1 | ProSiteProfiles | PS51714 | Bms1-type guanine nucleotide-binding (G) domain profile. | 82 | 247 | 10.543 |
| 13 | g7345.t1 | SMART | SM00785 | aarp2cn2 | 232 | 318 | 9.3E-45 |
| 12 | g7345.t1 | SMART | SM01362 | DUF663_2 | 659 | 976 | 1.4E-127 |
| 5 | g7345.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 78 | 215 | 8.62E-17 |
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:0042254 | ribosome biogenesis | BP |
| GO:0005634 | nucleus | CC |
| GO:0005525 | GTP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14569 (ribosome biogenesis protein BMS1)
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.
