General information for g5973.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ubiquitin carboxyl-terminal hydrolase CYLD.
Parent gene
- The parent gene g5973 is located on chr_2: 13112492..13117401 (+ 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 | g5973 | g5973.t5 | TSS | g5973.t5 | 13111511 | 13111511 |
| chr_2 | g5973 | g5973.t5 | isoform | g5973.t5 | 13111657 | 13116518 |
| chr_2 | g5973 | g5973.t5 | exon | g5973.t5.exon1 | 13111657 | 13111659 |
| chr_2 | g5973 | g5973.t5 | exon | g5973.t5.exon2 | 13112372 | 13113031 |
| chr_2 | g5973 | g5973.t5 | cds | g5973.t5.CDS1 | 13112492 | 13113031 |
| chr_2 | g5973 | g5973.t5 | exon | g5973.t5.exon3 | 13113652 | 13114636 |
| chr_2 | g5973 | g5973.t5 | cds | g5973.t5.CDS2 | 13113652 | 13114636 |
| chr_2 | g5973 | g5973.t5 | exon | g5973.t5.exon4 | 13115565 | 13116083 |
| chr_2 | g5973 | g5973.t5 | cds | g5973.t5.CDS3 | 13115565 | 13116083 |
| chr_2 | g5973 | g5973.t5 | exon | g5973.t5.exon5 | 13116145 | 13116518 |
| chr_2 | g5973 | g5973.t5 | cds | g5973.t5.CDS4 | 13116145 | 13116518 |
| chr_2 | g5973 | g5973.t5 | TTS | g5973.t5 | NA | NA |
Sequences
>g5973.t5 Gene=g5973 Length=2541
CAACAAAGCAGAAATAAACAAACATACCTAGTGATATACATAGTATTAAAATGAAACAAT
AGAAGTAAAGTAAGGAACAAAAGCTAATTAGAAGATTGAAGCTGTGAATTTTTGAAGCAA
AGAATGAATAAATATAAAGACACTACAATGGAGTTATCATCGCCTTATGCAATTGTAATC
GAAGATCGAGCTCATGCAATATTAAATATTCCTGATGCAGGACCAGAGCATAATATTGAA
TTATGTAGAGGCACAATGATTGAAATCATAAAACCAAGCAGTCAAAACTATTACACAATC
ATGATACATGATTATCATCAAAAGAATTTGGCGTTTGAAAACAATTTATATAAAATAAAA
GCAAGTGTTTTTTGCATTGTACCAAAAGAAATTTGGCCATTTCTTATTGCCATCACCGAT
TCAATTGATAGAGCAAATATTTCTATGGACGAAGCCTTCATCGATTATATACTAAATTTG
AGAATCAAGGGTTTTGTTTCTGTCAATTCACAATACTTTGGTATGTGCCCTATTCGACAA
TCACTACAATTTTTACCAGATCGAGAGCCACGAGATAAATCAAATGAATATAATTGCATA
ATTCGTTACATCGGACCTGTGAAAGAGATTGGTCCAGGCTACTTCTTTGGTTTAGAGCTA
TTGAACCTTAATAAAGGACATTCACCACAAGAGTTGGAAATAAAAAGTTTTTCAAAAAAT
TACATCGACTGTGATTCAAATCTTGCATTTATTTTACCAGTGAACTTCATTCGAAAACCA
AAAGGATTGAAAAAGAATTCAACTCGTTCGGCAATTGGGAACATCCTTTGTGGTCTAAAA
GAAAAAGTAAAACCACAAAAAAATACATTGACGAGACATTCCTATATAGATTCGTCCGTT
ACTGATTCTGCCAGTGAACGTTCATCTTCTTCAACAAGCAAGCGTCCCTTGACACCAGAA
TTGGTGAATGATAATAAGAATGGTATGATGAATGTTAATAAATTTCCATCGTCAATCTCT
AGTCCAAATTTGGCGAAACAAGACAGCGCTTCATCGTCAACTACAAGCGGTTCTGCAAGA
GTCATTAGCAATAGTGGTTTCGATTTGATTAATTTGTCAGAGGATTACAGTCAAATTGTT
GCAGAACGTGAATCCAAAATGGAAGAAAGAAGAATGTTGGGCTCAAGAGGAACTCAAACA
TTGAGTGGTGGAAGCAACAACATTGAATCACGTACGACTCCGAAAAGCAATAGAAAGAAG
GCAATGCTACTTCCCGCACCAAATCGTGAAATTAAGCCATCTACAATTTTACGTTTGGAA
GATCGTGACTTGATTGTAATTGATAAACAGGACATTAAAGAAGCAGTTCGAAATGAAAGT
GATGTGATAATTGTTGATCCACCAACACTTCCACAGACACCGTCAGATAATCACACGGAA
TTGAGTGACATTTTGGGCAGCGAGTGGCCAGAATCTGCCGGCGCGACTGCATCTATCTTA
AATAGTGACAAAAAATCAAATAATATATCTCCATCAGCTATAAGCAGCAATGGTTATCGA
TCAATAGAAAGAAATAAGAGTGCTAACATTGCATCTCACTTCAACAGTTCAAAGACGCGT
TATGAATCACAAAATGGCTATAAACGAAATATAAACGGAAGGCAATACGAGAATTTAGAT
CAAGACTCTGTTTCGTCTTCAGATCAAATTTCAGAGTGTCTCGTTCCTTCACCTTTAATT
GACATTCCAGGAACAGCTCTTGAGCTGGGTTCACTTGTGGAAGTAGCTTTGGAAAACGGG
AAAATAAATCTTCATGGTGTAATTCGTTGGATTGGACAGAAACATCAAGATCACGACTAT
AAAATGCCAAATGGATATAACAATACTAGTAGTAATAATTGTAATGAGTTAGTAGTTGGC
GTTGAATTAGATGAACCATGTAATGATCGTGGTTTAAGATTAACTGATGGTGTTTATAAT
GGCCAGAGATGCTTTCGATGTCCTGATAGACGTGCAATTTTTGTTTCACCTAAGCAATGT
ACAAAGGATCGTCGTTTTATTGATGAAGTCGGATCTAAAGCATCAACAATTCGATCAACA
ACACCAAGTGATGGTAAAGCTTTTGGAGCCGATTGTCCAATTATTGAAGGCTCTATTTCT
GCTTTAAAATTTGTAAATTATGATGATCTCGAGGCACATTGTGGAAAATTTAAAGGAATT
CAGGGACATCATAATTCTTGTTATCTAGACGCTACACTTTTTGCAATGTTTACTTTTACG
AGCGTCTTTGATTCTGTTTTATTTCGCCCACGAGAACCTGAAGACAATGATCAATATGAA
GAGGTTCAGCGTGTTTTGCGAGAAGAAATTGTTAATCCATTAAGGAAAAATTTATTCGTT
CGAGCTGATCGTGTAATGAAATTGAGAAAACTGCTTGATAAATTGACATCTGTTAAAGGA
CTTATTAATGAAGAAAAAGATCCAGAAGAATTTTTAAACAGCTTATTGGCTCAGATTTTA
AGAGCAGAACCGTTTCTAAAA
>g5973.t5 Gene=g5973 Length=806
MNKYKDTTMELSSPYAIVIEDRAHAILNIPDAGPEHNIELCRGTMIEIIKPSSQNYYTIM
IHDYHQKNLAFENNLYKIKASVFCIVPKEIWPFLIAITDSIDRANISMDEAFIDYILNLR
IKGFVSVNSQYFGMCPIRQSLQFLPDREPRDKSNEYNCIIRYIGPVKEIGPGYFFGLELL
NLNKGHSPQELEIKSFSKNYIDCDSNLAFILPVNFIRKPKGLKKNSTRSAIGNILCGLKE
KVKPQKNTLTRHSYIDSSVTDSASERSSSSTSKRPLTPELVNDNKNGMMNVNKFPSSISS
PNLAKQDSASSSTTSGSARVISNSGFDLINLSEDYSQIVAERESKMEERRMLGSRGTQTL
SGGSNNIESRTTPKSNRKKAMLLPAPNREIKPSTILRLEDRDLIVIDKQDIKEAVRNESD
VIIVDPPTLPQTPSDNHTELSDILGSEWPESAGATASILNSDKKSNNISPSAISSNGYRS
IERNKSANIASHFNSSKTRYESQNGYKRNINGRQYENLDQDSVSSSDQISECLVPSPLID
IPGTALELGSLVEVALENGKINLHGVIRWIGQKHQDHDYKMPNGYNNTSSNNCNELVVGV
ELDEPCNDRGLRLTDGVYNGQRCFRCPDRRAIFVSPKQCTKDRRFIDEVGSKASTIRSTT
PSDGKAFGADCPIIEGSISALKFVNYDDLEAHCGKFKGIQGHHNSCYLDATLFAMFTFTS
VFDSVLFRPREPEDNDQYEEVQRVLREEIVNPLRKNLFVRADRVMKLRKLLDKLTSVKGL
INEEKDPEEFLNSLLAQILRAEPFLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5973.t5 | Gene3D | G3DSA:2.30.30.190 | - | 538 | 655 | 1.6E-23 |
| 11 | g5973.t5 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 688 | 806 | 1.7E-52 |
| 10 | g5973.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 247 | 317 | - |
| 8 | g5973.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 248 | 317 | - |
| 9 | g5973.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 353 | 375 | - |
| 7 | g5973.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 354 | 371 | - |
| 2 | g5973.t5 | PANTHER | PTHR11830:SF3 | CYLINDROMATOSIS, ISOFORM D | 91 | 806 | 5.7E-87 |
| 3 | g5973.t5 | PANTHER | PTHR11830 | 40S RIBOSOMAL PROTEIN S3A | 91 | 806 | 5.7E-87 |
| 1 | g5973.t5 | Pfam | PF01302 | CAP-Gly domain | 560 | 639 | 1.4E-12 |
| 6 | g5973.t5 | SMART | SM01052 | CAP_GLY_2 | 548 | 640 | 2.2E-7 |
| 4 | g5973.t5 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 540 | 716 | 9.82E-21 |
| 5 | g5973.t5 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 693 | 798 | 1.28E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5973/g5973.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5973.t5.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
