Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein CLP1-like protein.

Parent gene

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 g11835 g11835.t6 TTS g11835.t6 18682026 18682026
chr_1 g11835 g11835.t6 isoform g11835.t6 18682091 18683159
chr_1 g11835 g11835.t6 exon g11835.t6.exon1 18682091 18682202
chr_1 g11835 g11835.t6 cds g11835.t6.CDS1 18682091 18682202
chr_1 g11835 g11835.t6 exon g11835.t6.exon2 18682266 18683159
chr_1 g11835 g11835.t6 cds g11835.t6.CDS2 18682266 18683134
chr_1 g11835 g11835.t6 TSS g11835.t6 18683648 18683648

Sequences

>g11835.t6 Gene=g11835 Length=1006
TAATACACATAGTGCAATTGAGCAAATGAGAGTAAATGCTGAAGAAAGAGAAACATGTGG
TCCTAAAGTTATGATTGTTGGTCCAACGGATGTGGGCAAATCAACTTTATGTAAAATCTT
ATTAAATTATGCTGTTCGACTAGGACACAGACCTATCTTATCAGATTTAGATGTTGGACA
AGGAAATATATCTATTCCTGGAACAATCGCTTCATTATTAATTGAAAGACCAGCATCAAT
CGAAGAAGGTTTCTTCTCTCAATTGGCACCTTTAGTAATTCACTATGGTCACAAAACTCC
TGATTTTAACAATGAACTTTACAAAATTTGCATTTCAACACTAGCAGATATAACATTAGA
ACGTTTAAATGAAGATAAAAGAACATTATCGTCTGGAATTATTATCAACACATGTGGTTG
GGTAAAAGGACAAGGGTATCAACATTTACTTCACGCTGCAAAAGAATTTAAAGTTGATGT
TATTCTCGTATTAGATCAAGAGAGACTTTATAATGAATTATTACGAGATGTTGATGCAGG
ATGTAAAGTAGTTTTTCTGCCAAAAAGTGGTGGAGTAGTTGAACGTAGTCAACAAACAAG
AGCTGAAAGCAGAGATCAAAGGATCCGGGAATATTTTTATGGTGTCCCTTTGAGATCACC
TTTGTATCCTCATTCTATTGATATTAAATTTTCTGATTTGAAACTTTATAAAATTGGCGC
GCCTGTTTTGCCTGACTCATGTATGCCTCTCGGAATGAAAGCTACTGATAATATGACAAA
ACTGTGGCCAATTCAACCTGGGCCATCTCTAATTCATCACGTACTAGCATTGAGTTTTGC
TGAAAATCCTGAACAAGATGTCTTGAAAAAAAATGTCATAGGTTTCGTTTGTGTAACAAA
TGTAGATGTCGAAAGACAAACCATAACAGTGCTTTCACCACAGCCCAGACCTTTACCAAA
TGTTGTTTTACTTTTATCCGAATTGCAGTTTATTGATAGTCATTGA

>g11835.t6 Gene=g11835 Length=326
MRVNAEERETCGPKVMIVGPTDVGKSTLCKILLNYAVRLGHRPILSDLDVGQGNISIPGT
IASLLIERPASIEEGFFSQLAPLVIHYGHKTPDFNNELYKICISTLADITLERLNEDKRT
LSSGIIINTCGWVKGQGYQHLLHAAKEFKVDVILVLDQERLYNELLRDVDAGCKVVFLPK
SGGVVERSQQTRAESRDQRIREYFYGVPLRSPLYPHSIDIKFSDLKLYKIGAPVLPDSCM
PLGMKATDNMTKLWPIQPGPSLIHHVLALSFAENPEQDVLKKNVIGFVCVTNVDVERQTI
TVLSPQPRPLPNVVLLLSELQFIDSH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11835.t6 CDD cd01983 SIMIBI 13 86 0.0042742
6 g11835.t6 Gene3D G3DSA:3.40.50.300 - 1 210 0.0000000
7 g11835.t6 Gene3D G3DSA:3.30.70.2410 - 215 326 0.0000000
3 g11835.t6 PANTHER PTHR12755 CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P 1 325 0.0000000
4 g11835.t6 PANTHER PTHR12755:SF6 POLYRIBONUCLEOTIDE 5’-HYDROXYL-KINASE CLP1 1 325 0.0000000
1 g11835.t6 Pfam PF16575 mRNA cleavage and polyadenylation factor CLP1 P-loop 19 206 0.0000000
2 g11835.t6 Pfam PF06807 Pre-mRNA cleavage complex II protein Clp1 213 324 0.0000000
5 g11835.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 13 157 0.0000000

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:0031124 mRNA 3’-end processing BP

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.

Raw TPM values