General information for g4469.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein shuttle craft.
Parent gene
- The parent gene g4469 is located on chr_2: 2732709..2733738 (+ 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_2 | g4469 | g4469.t4 | isoform | g4469.t4 | 2730360 | 2733610 |
| chr_2 | g4469 | g4469.t4 | exon | g4469.t4.exon1 | 2730360 | 2730400 |
| chr_2 | g4469 | g4469.t4 | TSS | g4469.t4 | 2730368 | 2730368 |
| chr_2 | g4469 | g4469.t4 | exon | g4469.t4.exon2 | 2730637 | 2732639 |
| chr_2 | g4469 | g4469.t4 | cds | g4469.t4.CDS1 | 2730650 | 2732639 |
| chr_2 | g4469 | g4469.t4 | exon | g4469.t4.exon3 | 2732694 | 2733610 |
| chr_2 | g4469 | g4469.t4 | cds | g4469.t4.CDS2 | 2732694 | 2733610 |
| chr_2 | g4469 | g4469.t4 | TTS | g4469.t4 | 2733717 | 2733717 |
Sequences
>g4469.t4 Gene=g4469 Length=2961
AGAATTCATTTGAGTGTAGAATTTTTCTGTAAATCTTTTGGAAAGTGTAAAAGAATGTCG
CCTGTATCAGGAGAAGAAAGTAGTGCAACTCAGTCAAATTTAAATGCCAACGCATCAGAA
TTTATTCCGATTATGATTAATGAAGAATCGACTCAATTAGCAACAACAAATTCAATTCAT
TCAACTACTGGTGCTATTCCCAAAAAATTTTATAAAAGTAACAATAATTATCGTCGTGAT
AAGTTTGATAGAAATCAAAGATGGAGATCTAATAATGGTAGTAGTAGTCAACGAAGAGAG
ACTTTTGCAGAACGTAATAATAGAAATGAAAATGCTAATTTCGAACCATTAGAAAGTAAT
AACCAAAATAAAAAGTTCTTTGCTAATAATAAACCACCGAAACAAAATGATAGAATGAAT
GATCAAAATCAGTATGAAGGATCATCTCAAACAATTCAAAGACAAAATATTTCACGACAG
ATTAAAAATGCACAAATGTCAAATAATAATAGATTGAAAAATAATAATCGATATGGAGAA
AATGAAGTGCTTAGTGAAAGACAATATTACAATCGTCGTAACAATAATTATGGTCGAAAT
TATAATGGAATTCGATCTAATAATGAAAATCAGAAGAAAGAAGTTGAACAAAATCAACAA
GAAGAAGTTAATGAAAAGCCAACTACAAAAAATCGTCCAAAAAAACGTGAACCGTTTAAT
CGTAAAAAGGATGAATCAAAAGCTTCAAGTGCTTCACAACGTGATCGATTGATAAAAGAA
ATTGAATCAAATACATTAGAGTGCATGATATGTTGTGAAAAGATTAAGTCTTATCAACCA
ATTTGGAGTTGCTCAAACTGTTATCACATTCTTCACTTATATTGTATCAAAACTTGGATG
AAAAATTCAAAAAATGATGAAGGTGAATGGAGATGCCCAGCATGTAATCAAATGACAAAT
CAAAAGCCTGGTGATTATTTATGTTTTTGTGGTAAACTTAAAAATCCAGCTGTAAATCGC
AATGATCTAGCTCATTCATGTGGTGAAATGTGTATGAATCAAACACTTTGTCCACATCCT
TGTCAATTAAAATGTCATCCAGGTCCGCATGAAATTTGTTATGCATCTGTTCTTAAAACA
TGTGGCTGTGGAAAAACTTCAAAAACTTATCAATGCTCAATGAAAGCAGCTTTCGAGTGT
GAATTAATTTGCGATAAGAAATTAAATTGTTCACTTCACAAATGCACTAAAATTTGTCAT
CAAGGACCTTGCAATGAATGCACTGAACAAATTGAATGTTCATGCTTTTGTGGTGCTGAA
AAAAAAATTCTTCCATGCATAGTTGATAATTTAGACAGAGTTAAATATTCATGTGAAAAA
GAGTGTGGAAAATTGTTAAGTTGCGGAAATCATACGTGCAAACAAAAATGTCATGAAGAT
GATTGTGGAAAATGCAAATTACTGCCAGAATTTGTACTTTGTTGTCCATGCACTAGAACA
CCAGTTAAAGAAGGATCGCGTACAAGCTGCATTGATCCGATACCAATCTGTGAGAATATT
TGTAAGAAAGCACTTCGATGTGGGAAACTTTCATCGCCTCATCTTTGTCAAGCAAAATGC
CATTTAAATGAGTGCCCTCCATGCAATCAGACATCAAATGTGAAATGTCGTTGTGGTCGA
AAAGAGGAAAAGATTCCTTGTAAAGAATTAACTAATAGTGATTTACGATGTAAGAAGAAA
TGCAACAAATTTAAATCTTGTGGACGGCATAAGTGTCGCTTTGATTGCTGTATTGATCCT
ATTCACAAATGTACTCTAACTTGTAATAGACTATTAAATTGTAAGCTTCACAAGTGTCAA
CGAATTTGCCATATTGATAATTGTGCACCATGTTATCGAGTCAGTTTTGATGAACTTCGA
TGTGAATGTGGATTTACTGTAATTTATCCACCTGTTCCATGTAACACAAAGATTAGTGAC
TGTCCAAAGAAATGTACACGCACACATAAATGCAATCATCAAGTAATACATAATTGTCAT
TCAGAATCTGAATGCCCACCATGTGTATTTTTGACAAGTAAATTCTGTTATGGAAAACAT
GAAGAACGAAAGACAATTCCTTGCAACCAAGAGTCTTTCTGTTGTGGAATGCCATGCGGC
AAATTATTGAAATGTGGTCGGCATACTTGTATTAAAACATGTCATCAAGGAGAATGTGAG
AAAAAGGATGATTTTTGCAAGCAAAAATGTACAATGAAACGATTTGAGTGTGATCACAAT
TGTAATGCACAATGTCATGAAGGAAAATGTCCGGACAATATATCTTGTCGTGAAAAAGTT
CAAGTTTCATGTGTATGTGGAAATCTCAAAGAATTCAAGACATGCGAACAAGTTGAATAT
GAGAATAAAAAACTTCAAAGAATTCACATTACTATGCAAATGCAAGAAATGCAACAAAGT
GATGGAATAACTGATCTTAAAACAATGCTTGGTGATTTCAAAAAGACTACGAAAATTCTT
GAATGTAATGATGAATGCAAGACTTTAGAGCGAAATCGTCGTCTTGATATTGCATTCAAA
GTTCAAAATCCAACACTTGCTTCTACACCTCGATTCGTTCCTACCTATAGTGATCACGTT
CGAAATTATTATAAAAAAGATCCAACTTTCGTTAATATGGTGCATGATAAATTGACTGAG
TTAGTAAAATTAGCAAAAGAAAGTAAAGCTCCATATCGTTGTCATTCATTTCCTTCAATG
AATCGTGATAAGCGTCATGTTATACATGACATGGCAGAATTATTTGGTATTGAAACGCAA
GCTTATGATGCTGAACCTAATCGAAATATTGTTGCAACAGCTACACGAGAATATTGTTGG
CTTCCATCAATGAGTATGGCTGAAATTGCTAGTCGCGAAAATGGAGCTCGTCGACCGCCA
TCAAATCAAACTTTTAAATGA
>g4469.t4 Gene=g4469 Length=968
MSPVSGEESSATQSNLNANASEFIPIMINEESTQLATTNSIHSTTGAIPKKFYKSNNNYR
RDKFDRNQRWRSNNGSSSQRRETFAERNNRNENANFEPLESNNQNKKFFANNKPPKQNDR
MNDQNQYEGSSQTIQRQNISRQIKNAQMSNNNRLKNNNRYGENEVLSERQYYNRRNNNYG
RNYNGIRSNNENQKKEVEQNQQEEVNEKPTTKNRPKKREPFNRKKDESKASSASQRDRLI
KEIESNTLECMICCEKIKSYQPIWSCSNCYHILHLYCIKTWMKNSKNDEGEWRCPACNQM
TNQKPGDYLCFCGKLKNPAVNRNDLAHSCGEMCMNQTLCPHPCQLKCHPGPHEICYASVL
KTCGCGKTSKTYQCSMKAAFECELICDKKLNCSLHKCTKICHQGPCNECTEQIECSCFCG
AEKKILPCIVDNLDRVKYSCEKECGKLLSCGNHTCKQKCHEDDCGKCKLLPEFVLCCPCT
RTPVKEGSRTSCIDPIPICENICKKALRCGKLSSPHLCQAKCHLNECPPCNQTSNVKCRC
GRKEEKIPCKELTNSDLRCKKKCNKFKSCGRHKCRFDCCIDPIHKCTLTCNRLLNCKLHK
CQRICHIDNCAPCYRVSFDELRCECGFTVIYPPVPCNTKISDCPKKCTRTHKCNHQVIHN
CHSESECPPCVFLTSKFCYGKHEERKTIPCNQESFCCGMPCGKLLKCGRHTCIKTCHQGE
CEKKDDFCKQKCTMKRFECDHNCNAQCHEGKCPDNISCREKVQVSCVCGNLKEFKTCEQV
EYENKKLQRIHITMQMQEMQQSDGITDLKTMLGDFKKTTKILECNDECKTLERNRRLDIA
FKVQNPTLASTPRFVPTYSDHVRNYYKKDPTFVNMVHDKLTELVKLAKESKAPYRCHSFP
SMNRDKRHVIHDMAELFGIETQAYDAEPNRNIVATATREYCWLPSMSMAEIASRENGARR
PPSNQTFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4469.t4 | CDD | cd16696 | RING-CH-C4HC3_NFX1 | 249 | 298 | 3.50266E-16 |
| 21 | g4469.t4 | CDD | cd06008 | NF-X1-zinc-finger | 382 | 428 | 6.39665E-11 |
| 20 | g4469.t4 | CDD | cd06008 | NF-X1-zinc-finger | 440 | 482 | 7.23683E-8 |
| 19 | g4469.t4 | CDD | cd06008 | NF-X1-zinc-finger | 499 | 551 | 4.18607E-10 |
| 17 | g4469.t4 | CDD | cd06008 | NF-X1-zinc-finger | 586 | 636 | 9.36772E-7 |
| 18 | g4469.t4 | CDD | cd06008 | NF-X1-zinc-finger | 697 | 743 | 1.5918E-6 |
| 15 | g4469.t4 | CDD | cd02643 | R3H_NF-X1 | 863 | 936 | 2.33184E-32 |
| 14 | g4469.t4 | Coils | Coil | Coil | 183 | 208 | - |
| 13 | g4469.t4 | Gene3D | G3DSA:3.30.1370.50 | - | 865 | 958 | 2.5E-10 |
| 34 | g4469.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 54 | 105 | - |
| 38 | g4469.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 55 | 69 | - |
| 33 | g4469.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 105 | - |
| 36 | g4469.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 238 | - |
| 37 | g4469.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 190 | - |
| 35 | g4469.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 238 | - |
| 9 | g4469.t4 | PANTHER | PTHR12360:SF12 | TRANSCRIPTIONAL REPRESSOR NF-X1 | 110 | 940 | 3.3E-224 |
| 10 | g4469.t4 | PANTHER | PTHR12360 | NUCLEAR TRANSCRIPTION FACTOR, X-BOX BINDING 1 NFX1 | 110 | 940 | 3.3E-224 |
| 4 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 392 | 410 | 0.0045 |
| 5 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 450 | 468 | 0.0024 |
| 2 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 509 | 530 | 1.0 |
| 8 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 569 | 579 | 190.0 |
| 3 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 598 | 613 | 0.17 |
| 6 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 707 | 722 | 2.3E-4 |
| 7 | g4469.t4 | Pfam | PF01422 | NF-X1 type zinc finger | 740 | 758 | 0.41 |
| 1 | g4469.t4 | Pfam | PF01424 | R3H domain | 871 | 935 | 3.5E-15 |
| 32 | g4469.t4 | ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 250 | 297 | - |
| 41 | g4469.t4 | ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 247 | 300 | 9.179 |
| 39 | g4469.t4 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 250 | 298 | 11.014 |
| 40 | g4469.t4 | ProSiteProfiles | PS51061 | R3H domain profile. | 870 | 938 | 13.478 |
| 29 | g4469.t4 | SMART | SM00438 | znfxneu3 | 339 | 357 | 0.48 |
| 25 | g4469.t4 | SMART | SM00438 | znfxneu3 | 392 | 411 | 0.0047 |
| 27 | g4469.t4 | SMART | SM00438 | znfxneu3 | 450 | 469 | 0.0014 |
| 23 | g4469.t4 | SMART | SM00438 | znfxneu3 | 509 | 532 | 0.27 |
| 28 | g4469.t4 | SMART | SM00438 | znfxneu3 | 569 | 588 | 29.0 |
| 26 | g4469.t4 | SMART | SM00438 | znfxneu3 | 596 | 615 | 9.4E-4 |
| 30 | g4469.t4 | SMART | SM00438 | znfxneu3 | 653 | 672 | 4.6 |
| 31 | g4469.t4 | SMART | SM00438 | znfxneu3 | 707 | 730 | 0.0051 |
| 24 | g4469.t4 | SMART | SM00438 | znfxneu3 | 739 | 760 | 0.023 |
| 22 | g4469.t4 | SMART | SM00393 | R3H_4 | 861 | 937 | 3.4E-6 |
| 11 | g4469.t4 | SUPERFAMILY | SSF57850 | RING/U-box | 240 | 304 | 1.41E-11 |
| 12 | g4469.t4 | SUPERFAMILY | SSF82708 | R3H domain | 846 | 959 | 2.55E-16 |
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 |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12236 (transcriptional repressor NF-X1)
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.
