General information for g12127.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine/threonine-protein kinase SMG1.
Parent gene
- The parent gene g12127 is located on chr_1: 21190398..21195699 (- 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_1 | g12127 | g12127.t1 | isoform | g12127.t1 | 21190398 | 21195699 |
| chr_1 | g12127 | g12127.t1 | exon | g12127.t1.exon1 | 21190398 | 21190600 |
| chr_1 | g12127 | g12127.t1 | cds | g12127.t1.CDS1 | 21190398 | 21190600 |
| chr_1 | g12127 | g12127.t1 | exon | g12127.t1.exon2 | 21190794 | 21193798 |
| chr_1 | g12127 | g12127.t1 | cds | g12127.t1.CDS2 | 21190794 | 21193798 |
| chr_1 | g12127 | g12127.t1 | exon | g12127.t1.exon3 | 21195282 | 21195568 |
| chr_1 | g12127 | g12127.t1 | cds | g12127.t1.CDS3 | 21195282 | 21195568 |
| chr_1 | g12127 | g12127.t1 | exon | g12127.t1.exon4 | 21195658 | 21195699 |
| chr_1 | g12127 | g12127.t1 | cds | g12127.t1.CDS4 | 21195658 | 21195699 |
| chr_1 | g12127 | g12127.t1 | TSS | g12127.t1 | NA | NA |
| chr_1 | g12127 | g12127.t1 | TTS | g12127.t1 | NA | NA |
Sequences
>g12127.t1 Gene=g12127 Length=3537
ATGAATAAGGATGATGATGAAGAAGAAGATAGACATGACAGAGGTACTTTTCGATTATGC
TGTGAGCACGTGTTAAAGTCTCTTAAACGTGGAAGAGAAACACTTCTTACCCTATTGGAG
GCATTCGTATATGATCCACTCGTTGATTGGGCAATTGGTGAAGATAACGCAACTAGTGGT
TTGGCTAATTTAAACACTGGTGGTGGTGCTGAAAAAGGAAGCACAACAGGAGATCTCACA
ACTGCTCGAAAACTTCTTGAACGTGAAGTAACTCGTGACACGCTAGCAATTCGTTTTACA
GAAATAAAAAATGACTGGCTGCAAAATAGAGATGACGTCTACAATCAATTGTTGTTAATG
AAAACACATTTGAGTGAATTGTCAAATAGTCGATACAATTTACAGTGCTTGGAGACACGA
CGCAATGTTTTATCAAAACAAATCTCAACAGTTCGTGATGTTGAAGCACTCGGAGGAGCC
ATGCATAGTCATCAACTGAATACACTATCTCAACGTTATGCCATATATAAAAAGAAAAAG
AATGACGTCAATATGATAAAGAGTTTGTTGATAGAAAAGGCGATTGAATCGGAAAAGATG
ATAGAAGATTATGTGAATTTTATTGAGGATGAAAATAAGTTGAACAGTTGGTTGATTGAA
ATAAGAGCATCGCGTCCGCTAAGCGTTTCAGAATTTGAGATTGTAAAAGAGTTTCTTGAA
AGCTCAAATCAAGGACAGATTTATATTCAAAGCGAACATTTACAAAATGAATTGAACAAC
GCAATATTACAACGACAAAGCATCATTGAAACCGCATTTGATGCAATTTTACAATACTAC
AATGTAACATGCTTTTATCCTAAGGATCACATTCAAAACCATCGTCTATCAAAATACTCT
GCATGGTGCCGCTCACTTAGTGAGAATAAAAGCCAAGAGTTCGCACGGCAGGTTGCTATG
GCGTTTCATTCTTTGTTTAGCGACGTAATGCCAAAAGAGCCACCCGAGAATATTATTGCC
TTCAATTACTATTTACAAACATTCTTAGTTGAGGAGAATTACAAATTACAAACAAGTTAT
CAAATATGTCAACAATTTATTGGAATAGAAAACGATTCTTTCGAAATAGCAAGAGAAGAG
TGCAAGGAGCTCATTCGTTGTGATATTGATAACACAACTAGCATCGCATATGAATTAGCC
AAGATGGTTAAACGATTTCTTGCTATTGAAGCATCAACTTATGGAGCTAATAATCTTTCT
GATCTAATAATCAATGACCGCTGGTTTATGGATGAACTCACTATTCAAACAACATTTTTA
TCTAACGTCAGTGACATTGTGTTCGATTCATCATTACCATTACTTAAGAAACATCCACTT
TTTACCAACAGTTTAGAGTGTTTTAAGGCAATTAATGAGCTGTTAGAGAATTTCGATCGA
GTCAAGTATGATTTCCAATTAAATATTATACCACAAACATTAAATGGAATTATTTCGCAA
AATAAAAGTGTGCTTGATATGATATCGGAGCTATCAAACATCACAAAATCACCAATATCA
GAGATGTTAACTAAATTAGAAGAAGATTTCATGAATTGCATACAAAATCCCAATCAAAAA
GGATTATTGCGTGCAGCTGAGTTAAGTGAAGCTTACAACAGCATGTACAGTCAATATCAA
CAGAATGAAGAGAGCATGGGTAAAAGTATATTCATGGCATGCCACAGTGCTTTCGAAGAA
ATGTGCAGATTATCGAAAAAAATCATGAGTTTCGATAAAGCGCTTGCAACATTACCTGAA
GAATGGTCATCAATTGAGGAAATTGAGCAAGCACGAATGCTTTTCATTTCACCCATGAAA
ACGAGCATTTTCATTACACTCGATCAGCTATTTATGGTGAAAAGAATACAGACAATGATT
GAATTCTTTAGCTATTGTCTTCAAATTGCATGGACTTTTAAAGGATCATCGGCTGTGGCA
GTCAATTTAGATATTGAATATTTAAGTCACCCACTGAAATCTTTTATCACAGATTTGCTT
ACAAAATGTATCCTAGGTCGTGGTTCATATTGCTTGTCAATTTTAATTTGTTGTTTGCTT
CAACAAAGAAGCAATGAAGCGTATGCGTGTGGCAACAAGTGCTTCTCCTTGGATGAATTA
TGTTTCTCAATGCCATTGAACTCAAATTCAAACGCAATTAATTATGAACAGATTTTCATT
GTACTTGAAGAGAAATTTAGGAAATGCGAATCAAAGGATTTTTATCAAAAGCTAATCCAT
CAACAAACAGAATACGTAAAGCATTTGACTTACGTCATCAGCTGTCATCAATGGATACAC
GAAGATTGCTTCATTCTTCATCCTAACATTATGCCACCTCCAATTCCCCGTGGTACACTT
CTCTTGCAATTTCAGAGCTTTGTACAATCACTGTCCAGTTGGAATGCATCAATCCAAAAG
ATTGATGAAGAATTAAGACAGAATACTCTCGTGATTTTTCAGCGATTAAAGTGGGCAGCA
GGTGCTAATCCGATGATTAATGAAATGTTGAACAATTTCGAGGCAATTTCTCGAGAAAAG
CAGCTGGAGCTTGAACACAGTAATAAATACGCTGGGTATGCTCTTAACTATTCAATTGCG
ATAATCAACTATGAAATGCTGCGAAATAAGACACCCAAGGCAATTATTAGTGATGAAGAG
TTTTTAACTCTGTTGCAACAATGGGAAAATGTCTGCATCTCTGAACGTGCAGTCGCGCAT
ACTGTTAATCCAATTGAAGAAGGCTTAGTTGAATTGCTAGATCCGGAAGGGCCGATAAAT
CTAAACTGGATTGAAAACGTTACATCTCTCATTGATGACATGATAAATCAAGTGCACAAT
GAGATTGACAGTAATGAAAAGAGATTGGTGTCAGCTCAAGACAATTTACACCTGTCCGCC
CACAAGCTGCGCACACTGATGACGACACATCATCGTATCTCGACAGACATAAGGAACATG
CTAAAATCAATTCTGAAATATGATGAAGGCGGCAGCAGTAGTGAAATGCTAAGGGAATAC
TTTGCCAAGTACAAGACATATATCGACAACGTAAACGAGCTACACGGAAATGTATTGAGC
AAGGATTTTACTGACACGCTTGTAAAACAAATTAGTGAGCAGGTAGAACGTTCACTTGCC
ATCTCAAATGAAATCTATGATGAGCTCTTTGACATTGAGAAAACACTCAGCAATACTTTG
GCTGATGATGGTCAACAGAAGAAAACACGACAATTGCGAAATCAATCGGAAAATTATTCT
GGCTTCGAATATCCCGCTAGTCCGATGAAAAAAGTTGCTGGATCTAATCAAAAAGAACAA
CGAAAAAATGTTTATGCAGTATCTGTATGGCGTCGTATTCGTAGCAAACTCGAAGGAAGA
GATCCTGATTCAAATAAAAGTTCGCGTGTACAAGAGCAGGTCGATTGGATCATTCGTGAA
GCACAGAATCAAGAAAATTTGGCTTTGCTCTATGAAGGTTTTACATCATGGGTTTGA
>g12127.t1 Gene=g12127 Length=1178
MNKDDDEEEDRHDRGTFRLCCEHVLKSLKRGRETLLTLLEAFVYDPLVDWAIGEDNATSG
LANLNTGGGAEKGSTTGDLTTARKLLEREVTRDTLAIRFTEIKNDWLQNRDDVYNQLLLM
KTHLSELSNSRYNLQCLETRRNVLSKQISTVRDVEALGGAMHSHQLNTLSQRYAIYKKKK
NDVNMIKSLLIEKAIESEKMIEDYVNFIEDENKLNSWLIEIRASRPLSVSEFEIVKEFLE
SSNQGQIYIQSEHLQNELNNAILQRQSIIETAFDAILQYYNVTCFYPKDHIQNHRLSKYS
AWCRSLSENKSQEFARQVAMAFHSLFSDVMPKEPPENIIAFNYYLQTFLVEENYKLQTSY
QICQQFIGIENDSFEIAREECKELIRCDIDNTTSIAYELAKMVKRFLAIEASTYGANNLS
DLIINDRWFMDELTIQTTFLSNVSDIVFDSSLPLLKKHPLFTNSLECFKAINELLENFDR
VKYDFQLNIIPQTLNGIISQNKSVLDMISELSNITKSPISEMLTKLEEDFMNCIQNPNQK
GLLRAAELSEAYNSMYSQYQQNEESMGKSIFMACHSAFEEMCRLSKKIMSFDKALATLPE
EWSSIEEIEQARMLFISPMKTSIFITLDQLFMVKRIQTMIEFFSYCLQIAWTFKGSSAVA
VNLDIEYLSHPLKSFITDLLTKCILGRGSYCLSILICCLLQQRSNEAYACGNKCFSLDEL
CFSMPLNSNSNAINYEQIFIVLEEKFRKCESKDFYQKLIHQQTEYVKHLTYVISCHQWIH
EDCFILHPNIMPPPIPRGTLLLQFQSFVQSLSSWNASIQKIDEELRQNTLVIFQRLKWAA
GANPMINEMLNNFEAISREKQLELEHSNKYAGYALNYSIAIINYEMLRNKTPKAIISDEE
FLTLLQQWENVCISERAVAHTVNPIEEGLVELLDPEGPINLNWIENVTSLIDDMINQVHN
EIDSNEKRLVSAQDNLHLSAHKLRTLMTTHHRISTDIRNMLKSILKYDEGGSSSEMLREY
FAKYKTYIDNVNELHGNVLSKDFTDTLVKQISEQVERSLAISNEIYDELFDIEKTLSNTL
ADDGQQKKTRQLRNQSENYSGFEYPASPMKKVAGSNQKEQRKNVYAVSVWRRIRSKLEGR
DPDSNKSSRVQEQVDWIIREAQNQENLALLYEGFTSWV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12127.t1 | Coils | Coil | Coil | 955 | 975 | - |
| 6 | g12127.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1081 | 1100 | - |
| 2 | g12127.t1 | PANTHER | PTHR11139:SF111 | SERINE/THREONINE-PROTEIN KINASE SMG1 | 15 | 1174 | 5.5E-31 |
| 3 | g12127.t1 | PANTHER | PTHR11139 | ATAXIA TELANGIECTASIA MUTATED ATM -RELATED | 15 | 1174 | 5.5E-31 |
| 1 | g12127.t1 | Pfam | PF02260 | FATC domain | 1150 | 1177 | 2.8E-6 |
| 8 | g12127.t1 | ProSiteProfiles | PS51190 | FATC domain profile. | 1146 | 1178 | 10.527 |
| 5 | g12127.t1 | SMART | SM01343 | FATC_2 | 1146 | 1178 | 2.2E-6 |
| 4 | g12127.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 15 | 55 | 5.41E-5 |
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:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
