General information for g9568.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein crooked neck.
Parent gene
- The parent gene g9568 is located on chr_1: 4071635..4073943 (- 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 | g9568 | g9568.t1 | TTS | g9568.t1 | 4071566 | 4071566 |
| chr_1 | g9568 | g9568.t1 | isoform | g9568.t1 | 4071635 | 4073943 |
| chr_1 | g9568 | g9568.t1 | exon | g9568.t1.exon1 | 4071635 | 4072541 |
| chr_1 | g9568 | g9568.t1 | cds | g9568.t1.CDS1 | 4071635 | 4072541 |
| chr_1 | g9568 | g9568.t1 | exon | g9568.t1.exon2 | 4072597 | 4073486 |
| chr_1 | g9568 | g9568.t1 | cds | g9568.t1.CDS2 | 4072597 | 4073486 |
| chr_1 | g9568 | g9568.t1 | exon | g9568.t1.exon3 | 4073547 | 4073663 |
| chr_1 | g9568 | g9568.t1 | cds | g9568.t1.CDS3 | 4073547 | 4073663 |
| chr_1 | g9568 | g9568.t1 | exon | g9568.t1.exon4 | 4073722 | 4073943 |
| chr_1 | g9568 | g9568.t1 | cds | g9568.t1.CDS4 | 4073722 | 4073943 |
| chr_1 | g9568 | g9568.t1 | TSS | g9568.t1 | 4074012 | 4074012 |
Sequences
>g9568.t1 Gene=g9568 Length=2136
ATGGAGAAACCACAAAAAATGCCGAAAGTTGCAAAAGTAAAGAACAAAGCGCCAGCAGAA
ATTCAAATTACTGCTGAGCAGCTTTTGCGTGAAGCAAAAGAGAGAGATTTAGAAATTTTA
CCGCCACCACCAAAACAAAAGATTTCTGATGAAGCCGAATTAGCAGATTATCAGCAAAGA
AAAAGGAAAACTTTTGAAGACAATTTAAGAAAGAATCGCAGTGTTGTATCAAACTGGATA
AAATATGCATCTTGGGAAGAATCACAGAAGGAAATCAAACGAGCGAGATCAATTTGGGAG
CGTGCTCTTGATAATGATCATCGAAATATTACAATATGGCTGAAATATGCAGAAATGGAA
ATGAAGAACAAACAGATAAATCATGCAAGAAATTTATGGGATCGCGCAATAACAATTATG
CCTCGAGTAAATCAGTTTTGGTATAAATACACATATATGGAAGAAATGCTTGAGAATGTT
GCTGGTGCAAGACAAGTTTTTGAACGTTGGATGGATTGGCAACCTGAAGAACAAGCATGG
CAGACCTACATAAATTTTGAATTACGCTATAAAGAACTCGATAGAGCTAGAAAAATATAT
GAGCGTTTTGTAATGGTTCATCCTGAAGTTAAAAATTGGATAAAATATGCAAGATTTGAA
GAAACTCATGGATTTACCAACAGTGCGAGAAATGTCTATGAAAGAGCTATAGAATTTTTT
GGTGATGATCATATGGATGAAAGATTGTATATTGCATTTGCCAAATTTGAAGAAAATCAA
CGTGAACATGAAAGAGCCCGTGTAATTTATAAATATGCTCTTGAACATTTAAGCAAAGAC
AAGTCGCTAGAGCTCTATAAAGCATATAGCATTCATGAAAAAAAATTTGGCGATAAGGCT
GGTATTGAAGATGTCATAACGTCAAAAAGAAAATTTCAGTATGAGCAAGAAATTGCCGAA
AATCCCACAAATTATGATGCATGGTTTGACTTTATTCGTATTATTGAAAATGAAGGTGAT
GTTGAAGTTACAAGAGATACCTATGAGAGAGCGATCGCTAATGTTCCACCAGCTAATGAT
AAAAACTTTTGGCGTAGATACATTTATTTATGGATCAATTATGCACTTTTTGAAGAACTT
CAAACTGAAGATATGGAAAGAACGAGACAAATTTATAAAACATGTCTAGAACTCATACCA
CATAAAATTTTCACATTTAGTAAAATATGGTTGTATTATGCAAATTTCGAAATACGTCAA
AAGAATCTTCAAGTAGCAAGAAAAACTCTTGGTATGGCAATTGGAATGTGTCCGCGTGAT
AAAATATATCGTGGTTATATAGAACTTGAAATTCAATTGCGTGAATTCGATCGTTGTCGC
ATTTTATATGAAAAATTCTTAGAATTTAATCCAGAAAATTGCATAACATGGATAAAGTTC
AGTGAACTCGAAACACTTCTTGGTGATATCGATAGAGCAAGAGCAATTTATGAACTGGCT
ATAAATCAACCACGTTTAGATATGCCAGAATTATTATGGAAAAGCTATATTGATTTTGAA
GTGTCACAAGGTGAAATTGAATTAGCAAGACAACTTTATGAAAGATTACTAGAAAGAACA
GGTCACGTCAAAGTGTGGATAAGTTACGCTAAATTTGAACTTACTTCTGAGACAACAGAA
GACAATATGAATGTGTCACTAGCAAGGAGAGTTTTTGAGAGAGGAAATGAATGTCAAAAA
AATCTTAATGATCGAGAGTCACGTGTTCTTTTACTAGAATCATGGAGAGATTTTGAAAAG
GACAATGGCGATGAGGAATCACTTGAAAAAGTTCTTAAAAAAATGCCAAGAAGAGTTAAA
AAGAGACAAAAGATTGTCTCAGAAACTGGTGAAACTGAAGGATGGGAAGAAGTTTTCGAT
TATATCTTTCCAGAAGATGAAATGGCTAAATCTAATCTCAAACTTTTGGCAGCCGCTAAA
AATTGGAAGAAAAATATTCAACCTGCTGTAACATCTTTATCCACTACTGAAAATCAAGAA
ACAAATGATAATGATGGCAGTAAAAGCAATGATGAAAGTGATGAAGATCAAGAAGAAAAT
AATTCCGGTAATAACGACAATGAAGATGAAAATTAA
>g9568.t1 Gene=g9568 Length=711
MEKPQKMPKVAKVKNKAPAEIQITAEQLLREAKERDLEILPPPPKQKISDEAELADYQQR
KRKTFEDNLRKNRSVVSNWIKYASWEESQKEIKRARSIWERALDNDHRNITIWLKYAEME
MKNKQINHARNLWDRAITIMPRVNQFWYKYTYMEEMLENVAGARQVFERWMDWQPEEQAW
QTYINFELRYKELDRARKIYERFVMVHPEVKNWIKYARFEETHGFTNSARNVYERAIEFF
GDDHMDERLYIAFAKFEENQREHERARVIYKYALEHLSKDKSLELYKAYSIHEKKFGDKA
GIEDVITSKRKFQYEQEIAENPTNYDAWFDFIRIIENEGDVEVTRDTYERAIANVPPAND
KNFWRRYIYLWINYALFEELQTEDMERTRQIYKTCLELIPHKIFTFSKIWLYYANFEIRQ
KNLQVARKTLGMAIGMCPRDKIYRGYIELEIQLREFDRCRILYEKFLEFNPENCITWIKF
SELETLLGDIDRARAIYELAINQPRLDMPELLWKSYIDFEVSQGEIELARQLYERLLERT
GHVKVWISYAKFELTSETTEDNMNVSLARRVFERGNECQKNLNDRESRVLLLESWRDFEK
DNGDEESLEKVLKKMPRRVKKRQKIVSETGETEGWEEVFDYIFPEDEMAKSNLKLLAAAK
NWKKNIQPAVTSLSTTENQETNDNDGSKSNDESDEDQEENNSGNNDNEDEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g9568.t1 | Gene3D | G3DSA:1.25.40.10 | - | 72 | 306 | 2.1E-53 |
| 22 | g9568.t1 | Gene3D | G3DSA:1.25.40.10 | - | 307 | 520 | 3.4E-45 |
| 23 | g9568.t1 | Gene3D | G3DSA:1.25.40.10 | - | 529 | 631 | 2.5E-10 |
| 20 | g9568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 670 | 711 | - |
| 21 | g9568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 689 | 711 | - |
| 4 | g9568.t1 | PANTHER | PTHR11246 | PRE-MRNA SPLICING FACTOR | 1 | 667 | 0.0 |
| 5 | g9568.t1 | PANTHER | PTHR11246:SF3 | CROOKED NECK-LIKE PROTEIN 1 | 1 | 667 | 0.0 |
| 3 | g9568.t1 | Pfam | PF02184 | HAT (Half-A-TPR) repeat | 90 | 120 | 5.5E-5 |
| 2 | g9568.t1 | Pfam | PF02184 | HAT (Half-A-TPR) repeat | 191 | 221 | 9.7E-20 |
| 1 | g9568.t1 | Pfam | PF02184 | HAT (Half-A-TPR) repeat | 525 | 553 | 9.6E-5 |
| 26 | g9568.t1 | ProSiteProfiles | PS50293 | TPR repeat region circular profile. | 76 | 177 | 11.888 |
| 25 | g9568.t1 | ProSiteProfiles | PS50293 | TPR repeat region circular profile. | 440 | 507 | 7.677 |
| 13 | g9568.t1 | SMART | SM00386 | hat_new_1 | 56 | 88 | 0.0056 |
| 17 | g9568.t1 | SMART | SM00386 | hat_new_1 | 90 | 122 | 6.7E-8 |
| 11 | g9568.t1 | SMART | SM00386 | hat_new_1 | 124 | 156 | 2.0E-4 |
| 16 | g9568.t1 | SMART | SM00386 | hat_new_1 | 158 | 189 | 0.0016 |
| 15 | g9568.t1 | SMART | SM00386 | hat_new_1 | 191 | 222 | 3.8E-7 |
| 18 | g9568.t1 | SMART | SM00386 | hat_new_1 | 224 | 259 | 7.6E-6 |
| 7 | g9568.t1 | SMART | SM00386 | hat_new_1 | 261 | 295 | 0.14 |
| 14 | g9568.t1 | SMART | SM00386 | hat_new_1 | 339 | 373 | 5.2E-6 |
| 8 | g9568.t1 | SMART | SM00386 | hat_new_1 | 383 | 419 | 6.6E-6 |
| 9 | g9568.t1 | SMART | SM00386 | hat_new_1 | 421 | 452 | 71.0 |
| 12 | g9568.t1 | SMART | SM00386 | hat_new_1 | 454 | 486 | 0.36 |
| 10 | g9568.t1 | SMART | SM00386 | hat_new_1 | 488 | 522 | 4.7E-7 |
| 19 | g9568.t1 | SMART | SM00386 | hat_new_1 | 524 | 555 | 7.6E-7 |
| 6 | g9568.t1 | SUPERFAMILY | SSF48452 | TPR-like | 66 | 508 | 1.23E-79 |
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:0006396 | RNA processing | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12869 (crooked neck)
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.
