Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein crooked neck.

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 g9568 g9568.t2 TTS g9568.t2 4071566 4071566
chr_1 g9568 g9568.t2 isoform g9568.t2 4071635 4072541
chr_1 g9568 g9568.t2 exon g9568.t2.exon1 4071635 4072541
chr_1 g9568 g9568.t2 cds g9568.t2.CDS1 4071635 4072477
chr_1 g9568 g9568.t2 TSS g9568.t2 NA NA

Sequences

>g9568.t2 Gene=g9568 Length=907
GTTGTATTATGCAAATTTCGAAATACGTCAAAAGAATCTTCAAGTAGCAAGAAAAACTCT
TGGTATGGCAATTGGAATGTGTCCGCGTGATAAAATATATCGTGGTTATATAGAACTTGA
AATTCAATTGCGTGAATTCGATCGTTGTCGCATTTTATATGAAAAATTCTTAGAATTTAA
TCCAGAAAATTGCATAACATGGATAAAGTTCAGTGAACTCGAAACACTTCTTGGTGATAT
CGATAGAGCAAGAGCAATTTATGAACTGGCTATAAATCAACCACGTTTAGATATGCCAGA
ATTATTATGGAAAAGCTATATTGATTTTGAAGTGTCACAAGGTGAAATTGAATTAGCAAG
ACAACTTTATGAAAGATTACTAGAAAGAACAGGTCACGTCAAAGTGTGGATAAGTTACGC
TAAATTTGAACTTACTTCTGAGACAACAGAAGACAATATGAATGTGTCACTAGCAAGGAG
AGTTTTTGAGAGAGGAAATGAATGTCAAAAAAATCTTAATGATCGAGAGTCACGTGTTCT
TTTACTAGAATCATGGAGAGATTTTGAAAAGGACAATGGCGATGAGGAATCACTTGAAAA
AGTTCTTAAAAAAATGCCAAGAAGAGTTAAAAAGAGACAAAAGATTGTCTCAGAAACTGG
TGAAACTGAAGGATGGGAAGAAGTTTTCGATTATATCTTTCCAGAAGATGAAATGGCTAA
ATCTAATCTCAAACTTTTGGCAGCCGCTAAAAATTGGAAGAAAAATATTCAACCTGCTGT
AACATCTTTATCCACTACTGAAAATCAAGAAACAAATGATAATGATGGCAGTAAAAGCAA
TGATGAAAGTGATGAAGATCAAGAAGAAAATAATTCCGGTAATAACGACAATGAAGATGA
AAATTAA

>g9568.t2 Gene=g9568 Length=280
MAIGMCPRDKIYRGYIELEIQLREFDRCRILYEKFLEFNPENCITWIKFSELETLLGDID
RARAIYELAINQPRLDMPELLWKSYIDFEVSQGEIELARQLYERLLERTGHVKVWISYAK
FELTSETTEDNMNVSLARRVFERGNECQKNLNDRESRVLLLESWRDFEKDNGDEESLEKV
LKKMPRRVKKRQKIVSETGETEGWEEVFDYIFPEDEMAKSNLKLLAAAKNWKKNIQPAVT
SLSTTENQETNDNDGSKSNDESDEDQEENNSGNNDNEDEN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9568.t2 Coils Coil Coil 274 280 -
10 g9568.t2 Gene3D G3DSA:1.25.40.10 - 2 204 2.7E-31
8 g9568.t2 MobiDBLite mobidb-lite consensus disorder prediction 239 280 -
9 g9568.t2 MobiDBLite mobidb-lite consensus disorder prediction 258 280 -
2 g9568.t2 PANTHER PTHR11246 PRE-MRNA SPLICING FACTOR 2 236 2.0E-86
3 g9568.t2 PANTHER PTHR11246:SF3 CROOKED NECK-LIKE PROTEIN 1 2 236 2.0E-86
1 g9568.t2 Pfam PF02184 HAT (Half-A-TPR) repeat 94 122 3.0E-5
7 g9568.t2 SMART SM00386 hat_new_1 23 55 0.36
6 g9568.t2 SMART SM00386 hat_new_1 57 91 4.7E-7
5 g9568.t2 SMART SM00386 hat_new_1 93 124 7.6E-7
4 g9568.t2 SUPERFAMILY SSF48452 TPR-like 9 180 9.1E-30

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 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