General information for g12335.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Dynein intermediate chain 2, ciliary.
Parent gene
- The parent gene g12335 is located on chr_1: 22631833..22636763 (+ 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 | g12335 | g12335.t1 | isoform | g12335.t1 | 22630077 | 22632839 |
| chr_1 | g12335 | g12335.t1 | exon | g12335.t1.exon1 | 22630077 | 22630265 |
| chr_1 | g12335 | g12335.t1 | cds | g12335.t1.CDS1 | 22630077 | 22630265 |
| chr_1 | g12335 | g12335.t1 | exon | g12335.t1.exon2 | 22630361 | 22630673 |
| chr_1 | g12335 | g12335.t1 | cds | g12335.t1.CDS2 | 22630361 | 22630673 |
| chr_1 | g12335 | g12335.t1 | exon | g12335.t1.exon3 | 22630877 | 22631440 |
| chr_1 | g12335 | g12335.t1 | cds | g12335.t1.CDS3 | 22630877 | 22631440 |
| chr_1 | g12335 | g12335.t1 | exon | g12335.t1.exon4 | 22631528 | 22631767 |
| chr_1 | g12335 | g12335.t1 | cds | g12335.t1.CDS4 | 22631528 | 22631767 |
| chr_1 | g12335 | g12335.t1 | exon | g12335.t1.exon5 | 22631833 | 22632839 |
| chr_1 | g12335 | g12335.t1 | cds | g12335.t1.CDS5 | 22631833 | 22632839 |
| chr_1 | g12335 | g12335.t1 | TSS | g12335.t1 | NA | NA |
| chr_1 | g12335 | g12335.t1 | TTS | g12335.t1 | NA | NA |
Sequences
>g12335.t1 Gene=g12335 Length=2313
ATGGCAGAGCAAAATAATATAAAAAGAGTTTCCATTGTGTCAAAGGAAACTTCTTCTTTT
GATGATCACATTGGAGATAGTGATGATGCTACATTAGATGATTTTTTTAGTGATGAATGC
CTCGATGATGATGATAATGATGAGCATGAGCTTGATGAAGAAGCCAAAAAAGCTAGGCGA
AGATTAAAACAAATTCGTGCCTCAACCTTTGTCCGTGGTGGCATTGGTGAAGGTGACGAA
GATTCTTGGCTTCGATCACGTCAACTTATAAGACCCGACGATCAAATGGACCTCACTGAT
TCTGAGCTTTGCGAGGAAATTCCAAAAGTTCTCTCATGTGAAAATAAAAATATTCCGCAA
AATTTGGTGATTTTTAGTTTTCGTGAGGGTGCTTACATTCCTTTACCAAGAACATCAAAT
GTCATTACACTTTTTGAACATGAGGGAACTGCAATTCATGTTGAAAGTGCTGAAGCAAAA
GCACAAATTGCTAGGGATGGAGAACCACTGGCAATTCCTGGTTTCGCAGATTTAAAATCC
GGTTCACAAACGGGAACAACGACTCCGGATATCGATCGTACAGCAGATGCAGAAAATGCA
GAAGGTGAAAATGAAGAGAATGAAGATGACGCTGGATCTGAAGCAGGTGGCGAGGCAGAT
GCAGAAGGAGAAGAAGAACAAAAAGAAGTCGCTGTTGGGACACCAACTGGTCCAAAGAAA
AAGCTCACAAATCAGTTCAACTTTTGCGAACGAGCTGCTCTGACTTATAACAGTCCTTCA
CGTTCAGTCGAGACTCAAACAGTTCCGCCACCACGTTCAAGTTTCGGTGCGAATGTCGTG
CAATGGCACATCTATGACTCTTACAATGAGGACTTTGAACGATTGAAGCGTGAGAAGGAA
AAGGAAATGTTAAAGGAGAAAAAACCAGGCCTACAGAAACATGTTGAAATGAAGCGTGGC
GATGCAAAGACGAAAGCAGCAGAAGAGTTTAATAGAAAATATTTTCAGAAATGTCAGATT
CTTGAACGCATGGTTAATCAAAATATTTTCGATGAAATTTCTCATGATTATCGCTATTAT
GAGGATCCATCAGACGAATATCGTGAAGACGATGGCACATTATTGCCATTATGGAAGTTT
ACGTACGATAAATGCAAGAAAATGAGCGTTACGGATATTTGTCTGAATACTTATTATTAT
GACCTATTTGCTGTTTGTTTCGGATCATTTGATTTCATTAAACAAGTCAGTGAAGGCCAT
GTTTGTTTATTTTCTATTAAAAATCCATCTTTTCCGGAATATCGAATTACAACTGAATCT
GGTGCAATGTGCTGTGATATTCATAAGAAATATCCTTATTTGATTGTTATTGGTCAATAT
GATGGAAATGTTTGTGTTTATAATCTTCAAGTTGGCACAAAAGAAGCAGTTTATGTTTCT
CAAGGTGTTAATGGTAAACATTCGGAAGCAGTCAATGAAATAAAATGGGGAGAAGATATG
CAAGATGGTGAAGTAAATTTTTATTCTCTATCAGCTGATGGTCGTGTTTTCAATTGGGTG
CTGATGCAGAACAAATTGACATTGACCACTATCATAACTTTATTTGTTGACGTCAATCCT
GTTAGTGGACCAGATGGCACAGTTATGAAAATGAAAGCAAGCGGAACATGCATGGTCTTT
CATCCAACTAATAAGGAAATTTTTCAAGTTGGTACTGAAGATGGATTGATATTTAAATGC
AGCACTGCTTACAGTTCAAAATATTTGATGATTTATCAAGCTCATTATTTGTCAGTTCAT
CGAATGGATTTTAACAAATTTAATTCAAATATTTTCATATCTTGTTCGGGTGATTGGCGT
GTAAAAATTTGGGAAGATATGCGAAGTGATCCTTTATTTATTTTTGATTTGGGTGCAAGT
GTTGGTGATGTCAAATGGGCGCCTTATTCAAGTACTGTTTTTGCTGCTGTTACAACTGAA
GGAAGAGTTTACGTTTTTGATTTAAATGTCAATAAGTACAAAGCAATATGCTCACAACAA
GTTGTGCCACGAAAGAAAAATAAGCTGACAAGAATTGTCTTTAATCACAAGCTTCCATTT
ATAATTGTTGGTGATGATAAAGGAACAAGCATAACAATGAAATTATCACCAAATTTGAGA
CTTCCATGCAAGCCACCAAAGAAACAACAATGGCTTGATCAATTGACATTGCAGATTCAA
AAATTGGAACGACTTTTGTCATTGGTTCGAGAATTACCTGATGGAATTGAAGAAGCACAA
GATGATGTTGCAACTGAAGTTGGATCAAATTAA
>g12335.t1 Gene=g12335 Length=770
MAEQNNIKRVSIVSKETSSFDDHIGDSDDATLDDFFSDECLDDDDNDEHELDEEAKKARR
RLKQIRASTFVRGGIGEGDEDSWLRSRQLIRPDDQMDLTDSELCEEIPKVLSCENKNIPQ
NLVIFSFREGAYIPLPRTSNVITLFEHEGTAIHVESAEAKAQIARDGEPLAIPGFADLKS
GSQTGTTTPDIDRTADAENAEGENEENEDDAGSEAGGEADAEGEEEQKEVAVGTPTGPKK
KLTNQFNFCERAALTYNSPSRSVETQTVPPPRSSFGANVVQWHIYDSYNEDFERLKREKE
KEMLKEKKPGLQKHVEMKRGDAKTKAAEEFNRKYFQKCQILERMVNQNIFDEISHDYRYY
EDPSDEYREDDGTLLPLWKFTYDKCKKMSVTDICLNTYYYDLFAVCFGSFDFIKQVSEGH
VCLFSIKNPSFPEYRITTESGAMCCDIHKKYPYLIVIGQYDGNVCVYNLQVGTKEAVYVS
QGVNGKHSEAVNEIKWGEDMQDGEVNFYSLSADGRVFNWVLMQNKLTLTTIITLFVDVNP
VSGPDGTVMKMKASGTCMVFHPTNKEIFQVGTEDGLIFKCSTAYSSKYLMIYQAHYLSVH
RMDFNKFNSNIFISCSGDWRVKIWEDMRSDPLFIFDLGASVGDVKWAPYSSTVFAAVTTE
GRVYVFDLNVNKYKAICSQQVVPRKKNKLTRIVFNHKLPFIIVGDDKGTSITMKLSPNLR
LPCKPPKKQQWLDQLTLQIQKLERLLSLVRELPDGIEEAQDDVATEVGSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g12335.t1 | Coils | Coil | Coil | 41 | 68 | - |
| 11 | g12335.t1 | Coils | Coil | Coil | 285 | 305 | - |
| 13 | g12335.t1 | Coils | Coil | Coil | 732 | 752 | - |
| 10 | g12335.t1 | Gene3D | G3DSA:2.130.10.10 | - | 363 | 534 | 2.0E-11 |
| 9 | g12335.t1 | Gene3D | G3DSA:2.130.10.10 | - | 545 | 714 | 5.0E-17 |
| 8 | g12335.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 243 | - |
| 7 | g12335.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 225 | - |
| 1 | g12335.t1 | PANTHER | PTHR12442:SF11 | DYNEIN INTERMEDIATE CHAIN 1, AXONEMAL | 83 | 750 | 3.3E-190 |
| 2 | g12335.t1 | PANTHER | PTHR12442 | DYNEIN INTERMEDIATE CHAIN | 83 | 750 | 3.3E-190 |
| 6 | g12335.t1 | SMART | SM00320 | WD40_4 | 429 | 468 | 7.6 |
| 4 | g12335.t1 | SMART | SM00320 | WD40_4 | 585 | 625 | 4.6E-5 |
| 5 | g12335.t1 | SMART | SM00320 | WD40_4 | 628 | 667 | 5.9 |
| 3 | g12335.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 389 | 712 | 2.38E-35 |
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 transcript has been annotated with K10409 (dynein axonemal intermediate chain 1)
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.
