Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein shuttle craft.

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_2 g4469 g4469.t7 TSS g4469.t7 2730368 2730368
chr_2 g4469 g4469.t7 isoform g4469.t7 2730650 2731963
chr_2 g4469 g4469.t7 exon g4469.t7.exon1 2730650 2731723
chr_2 g4469 g4469.t7 cds g4469.t7.CDS1 2730650 2731723
chr_2 g4469 g4469.t7 exon g4469.t7.exon2 2731793 2731963
chr_2 g4469 g4469.t7 cds g4469.t7.CDS2 2731793 2731963
chr_2 g4469 g4469.t7 TTS g4469.t7 NA NA

Sequences

>g4469.t7 Gene=g4469 Length=1245
ATGTCGCCTGTATCAGGAGAAGAAAGTAGTGCAACTCAGTCAAATTTAAATGCCAACGCA
TCAGAATTTATTCCGATTATGATTAATGAAGAATCGACTCAATTAGCAACAACAAATTCA
ATTCATTCAACTACTGGTGCTATTCCCAAAAAATTTTATAAAAGTAACAATAATTATCGT
CGTGATAAGTTTGATAGAAATCAAAGATGGAGATCTAATAATGGTAGTAGTAGTCAACGA
AGAGAGACTTTTGCAGAACGTAATAATAGAAATGAAAATGCTAATTTCGAACCATTAGAA
AGTAATAACCAAAATAAAAAGTTCTTTGCTAATAATAAACCACCGAAACAAAATGATAGA
ATGAATGATCAAAATCAGTATGAAGGATCATCTCAAACAATTCAAAGACAAAATATTTCA
CGACAGATTAAAAATGCACAAATGTCAAATAATAATAGATTGAAAAATAATAATCGATAT
GGAGAAAATGAAGTGCTTAGTGAAAGACAATATTACAATCGTCGTAACAATAATTATGGT
CGAAATTATAATGGAATTCGATCTAATAATGAAAATCAGAAGAAAGAAGTTGAACAAAAT
CAACAAGAAGAAGTTAATGAAAAGCCAACTACAAAAAATCGTCCAAAAAAACGTGAACCG
TTTAATCGTAAAAAGGATGAATCAAAAGCTTCAAGTGCTTCACAACGTGATCGATTGATA
AAAGAAATTGAATCAAATACATTAGAGTGCATGATATGTTGTGAAAAGATTAAGTCTTAT
CAACCAATTTGGAGTTGCTCAAACTGTTATCACATTCTTCACTTATATTGTATCAAAACT
TGGATGAAAAATTCAAAAAATGATGAAGGTGAATGGAGATGCCCAGCATGTAATCAAATG
ACAAATCAAAAGCCTGGTGATTATTTATGTTTTTGTGGTAAACTTAAAAATCCAGCTGTA
AATCGCAATGATCTAGCTCATTCATGTGGTGAAATGTGTATGAATCAAACACTTTGTCCA
CATCCTTGTCAATTAAAATGTCATCCAGGTCCGCATGAAATTTGTTATGCATCTTGTGAA
TTAATTTGCGATAAGAAATTAAATTGTTCACTTCACAAATGCACTAAAATTTGTCATCAA
GGACCTTGCAATGAATGCACTGAACAAATTGAATGTTCATGCTTTTGTGGTGCTGAAAAA
AAAATTCTTCCATGCATAGTTGATAATTTAGACAGAGTTAAATAT

>g4469.t7 Gene=g4469 Length=415
MSPVSGEESSATQSNLNANASEFIPIMINEESTQLATTNSIHSTTGAIPKKFYKSNNNYR
RDKFDRNQRWRSNNGSSSQRRETFAERNNRNENANFEPLESNNQNKKFFANNKPPKQNDR
MNDQNQYEGSSQTIQRQNISRQIKNAQMSNNNRLKNNNRYGENEVLSERQYYNRRNNNYG
RNYNGIRSNNENQKKEVEQNQQEEVNEKPTTKNRPKKREPFNRKKDESKASSASQRDRLI
KEIESNTLECMICCEKIKSYQPIWSCSNCYHILHLYCIKTWMKNSKNDEGEWRCPACNQM
TNQKPGDYLCFCGKLKNPAVNRNDLAHSCGEMCMNQTLCPHPCQLKCHPGPHEICYASCE
LICDKKLNCSLHKCTKICHQGPCNECTEQIECSCFCGAEKKILPCIVDNLDRVKY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4469.t7 CDD cd16696 RING-CH-C4HC3_NFX1 249 298 1.78824E-18
9 g4469.t7 CDD cd06008 NF-X1-zinc-finger 359 405 1.0573E-13
7 g4469.t7 Coils Coil Coil 183 208 -
6 g4469.t7 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 219 306 2.1E-9
14 g4469.t7 MobiDBLite mobidb-lite consensus disorder prediction 54 105 -
18 g4469.t7 MobiDBLite mobidb-lite consensus disorder prediction 55 69 -
13 g4469.t7 MobiDBLite mobidb-lite consensus disorder prediction 89 105 -
16 g4469.t7 MobiDBLite mobidb-lite consensus disorder prediction 146 238 -
17 g4469.t7 MobiDBLite mobidb-lite consensus disorder prediction 146 190 -
15 g4469.t7 MobiDBLite mobidb-lite consensus disorder prediction 191 238 -
2 g4469.t7 PANTHER PTHR12360:SF12 TRANSCRIPTIONAL REPRESSOR NF-X1 107 357 5.5E-56
4 g4469.t7 PANTHER PTHR12360 NUCLEAR TRANSCRIPTION FACTOR, X-BOX BINDING 1 NFX1 107 357 5.5E-56
1 g4469.t7 PANTHER PTHR12360:SF12 TRANSCRIPTIONAL REPRESSOR NF-X1 358 406 5.5E-56
3 g4469.t7 PANTHER PTHR12360 NUCLEAR TRANSCRIPTION FACTOR, X-BOX BINDING 1 NFX1 358 406 5.5E-56
10 g4469.t7 ProSitePatterns PS01359 Zinc finger PHD-type signature. 250 297 -
20 g4469.t7 ProSiteProfiles PS50016 Zinc finger PHD-type profile. 247 300 9.179
19 g4469.t7 ProSiteProfiles PS50089 Zinc finger RING-type profile. 250 298 11.014
12 g4469.t7 SMART SM00438 znfxneu3 339 357 0.48
11 g4469.t7 SMART SM00438 znfxneu3 369 388 0.0047
5 g4469.t7 SUPERFAMILY SSF57850 RING/U-box 240 304 2.94E-12

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:0005634 nucleus CC
GO:0008270 zinc ion binding MF
GO:0003700 DNA-binding transcription factor activity 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. There were no conditions that were differentially expressed