Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-processing factor 6.

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 g14248 g14248.t1 TTS g14248.t1 35833344 35833344
chr_1 g14248 g14248.t1 isoform g14248.t1 35833411 35836240
chr_1 g14248 g14248.t1 exon g14248.t1.exon1 35833411 35836093
chr_1 g14248 g14248.t1 cds g14248.t1.CDS1 35833411 35836093
chr_1 g14248 g14248.t1 exon g14248.t1.exon2 35836152 35836240
chr_1 g14248 g14248.t1 cds g14248.t1.CDS2 35836152 35836240
chr_1 g14248 g14248.t1 TSS g14248.t1 35836284 35836284

Sequences

>g14248.t1 Gene=g14248 Length=2772
ATGACAACAAATACTCTCGCAAATAAAAATAAAAAGCATTTTCTTGGTATTCCGGCACCA
TTAGGATATGTTGCTGGTGTTGGCAGAGGTGCAACTGGTTTCACAACTCGTTCTGATATT
GGTCCTGCAAGAGACGCTAACGATGTATCAGATGATAGACATGCTCCACCAACAAAGCGC
AAGAAGAAGGACGAAACAGAAGAAGATGATGATGAAGATTTAAACGATTCTAATTATGAT
GAATTTTCTGGATACTCTGGAGGACTATTTTCAAAAGATCCATATGATAAAGATGACGCT
GAAGCAGATGCAATTTATGAGTCGATTGATAAACGTATGGATGAGAAACGAAGAGAATAT
CGTGAGAAAAAAGAGAAAGAATTTTTAGAGCAATATCGTCAAGAGAGACCAAAAATTCAG
CAACAATTTTCTGACATCAAAAGAACGCTCGCTCTAGTTTCAGAAGCTGAATGGGCAGCA
TTGCCTGAAGTTGGTGATGCTAGAAATCGAAAACAAAGAAATCCTCGTGCTGAAAAGTTT
ACTCCTCTGCCAGATTCAGTTTTATCAAGAAATTTAGGTGGTGAAACAACAACAACAATC
GATCCAAGTTCAGGTCTTGCGTCTATGGTACCTGGTGCTTTAACACCAAGTGGAGATTTA
GATTTAGTTAAAATTGGTCAAGCAAGAAACACTTTGATGAATGTAAAATTATCACAAGTT
TCTGACTCTGTTACTGGTCAAACTGTTGTTGATCCAAAAGGATATTTAACTGATTTGCAA
AGCATGATTCCTACATATGGAGGAGATATTAATGACATAAAGAAAGCTCGATTATTACTC
AAAAGTGTTCGTGAGACAAATCCTAATCATCCTCCAGCTTGGATTGCTTCATCACGTCTT
GAAGAAGTCACTGGAAAAGTTCAAATGGCACGAAATCTTATCATGCGTGGTTGTGAAATT
AATCCAACAAGCGAAGATTTATGGCTAGAAGCAGCTCGTCTTCAACCACCTGAAACAGCA
AAAGGAGTAATTGCACAAGCAGTTCGTCATATTCCTACATCCGTTAGAATTTGGATAAAA
GCTGCAGATCTTGAAGTTGAGACAAAAGCTAAACGACGTGTTTTTAGAAAAGCACTTGAG
CACATACCCAATTCTGTTCGTTTATGGAAAGCAGCTGTCGAAATTGAGAATCCAAATGAT
GCGCGAATTTTACTATCACGTGCTGTTGAATGTTGTAACACGAGTGTTGAATTGTGGCTT
GCTCTTGCACGTTTAGAAACGTATGAAAATGCAAGAAAAGTTCTTAATAAAGCGAGAGAA
AATATTCCAACAGACAAACAAATTTGGACAACAGCAGCAAAACTTGAAGAAGCTAACGGA
AACAATCATATGGTTGAGAAAATTATTGACCGTTCAATTTCATCACTAAGTGCTAATGGG
GTTGAAATTAATCGTGATCAATGGTTGCAAGAGGCCATTGAGTCTGAAAAAGCGGGAAGT
GTTTTGACATGTCAAGCGATAATTAAAGCAGTTATTGGAATTGGTGTTGAGGAAGAAGAT
TGCAAGCAAACATGGATTGATGATGCAGAAAACTGTGCAAAAGAGAATGCATTTGAATGT
GCTCGAGCTATTTATGCTCATGCTTTACAAGTCTTTCCTAATAAAAAAAGCATTTGGTTA
CGAGCAGCACATTTTGAGAAAACTCATGGTACTAGAGAAAGTCTTGAATCACTACTTCAG
AAAGCAGTTCAAAATTGTCCAAAAGCTGAAGTTCTTTGGCTAATGGGAGCTAAATCTAAA
TGGCTAGCTGGTGATGTTCCAGCAGCTCGTAGCATTTTGAATTATGCTTTCCAAGCTAAT
CCAAATTCTGAAGAAATTTGGCTTGCTGCAGTTAAATTAGAATCAGAAAATGCCGAATAT
GAACGAGCTAGAAAATTACTTGCAAAAGCCAGAAGTTCTGCACCAACACCGAGAGTTATG
ATGAAATCAGCAAAACTTGAATGGGGATTGGAAAATTTGAATGAAGCACTTAATCTTCTT
GAAGAAGCAGTGAAAGTTTTTCCTACATTTCCGAAATTGTGGATGATGAAAGGTCAAATT
GAAGATCAGCAAGGTAAAATTGAAGTCGCTATTGAAACATACAACACTGGACTAAAACAA
TGTCCAAATTCAATTCCATTGTGGATTTTGTTATCTGCATTAGAAGAAAAGCGAGGTGTT
TTGACCAAAGCACGTTCAGTTTTAGAGCGTGGTCGTTTGAAAAATCCAAAAACAGCTACT
CTCTGGTTACATGCAATTCGCATTGAAATTCGTGCTGGAATGAAAGAAATTGCACAAACA
CTTTTAGCTCGAGCTTTACAGGAATGTCCAAATTCAGGTGAATTATGGGCTGAGGCGATA
TTTTTAGAACCACGACCGCTTCGTAAGTCGAAATCTATTGATGCACTGAAGAAATGTGAG
CATGATCCTCACGTACTTCTTGCTGTATCAAAACTTATTTGGAGTGAAAGAAAAATTCAA
AAATGTCGTGAATGGTTTACTAGAACTGTAAAAAGTGATTCAGATTTTGGAGATGCATGG
GGTTACTTTTATAAATTTGAATTAATGTTTGGCACAGAAGAGCAACAACAAGAAATTTTA
AAGAGATGTATTGCAGCAGAGCCAAAACATGGAGAAGAGTGGTGTAAAGTTAGCAAAAGT
ATTGCAAATTGGCGATTCAAAACTGAGGATGTGTTGAAGGCTTTAGTAAAAATTCTTCCA
ATACCAATTTAA

>g14248.t1 Gene=g14248 Length=923
MTTNTLANKNKKHFLGIPAPLGYVAGVGRGATGFTTRSDIGPARDANDVSDDRHAPPTKR
KKKDETEEDDDEDLNDSNYDEFSGYSGGLFSKDPYDKDDAEADAIYESIDKRMDEKRREY
REKKEKEFLEQYRQERPKIQQQFSDIKRTLALVSEAEWAALPEVGDARNRKQRNPRAEKF
TPLPDSVLSRNLGGETTTTIDPSSGLASMVPGALTPSGDLDLVKIGQARNTLMNVKLSQV
SDSVTGQTVVDPKGYLTDLQSMIPTYGGDINDIKKARLLLKSVRETNPNHPPAWIASSRL
EEVTGKVQMARNLIMRGCEINPTSEDLWLEAARLQPPETAKGVIAQAVRHIPTSVRIWIK
AADLEVETKAKRRVFRKALEHIPNSVRLWKAAVEIENPNDARILLSRAVECCNTSVELWL
ALARLETYENARKVLNKARENIPTDKQIWTTAAKLEEANGNNHMVEKIIDRSISSLSANG
VEINRDQWLQEAIESEKAGSVLTCQAIIKAVIGIGVEEEDCKQTWIDDAENCAKENAFEC
ARAIYAHALQVFPNKKSIWLRAAHFEKTHGTRESLESLLQKAVQNCPKAEVLWLMGAKSK
WLAGDVPAARSILNYAFQANPNSEEIWLAAVKLESENAEYERARKLLAKARSSAPTPRVM
MKSAKLEWGLENLNEALNLLEEAVKVFPTFPKLWMMKGQIEDQQGKIEVAIETYNTGLKQ
CPNSIPLWILLSALEEKRGVLTKARSVLERGRLKNPKTATLWLHAIRIEIRAGMKEIAQT
LLARALQECPNSGELWAEAIFLEPRPLRKSKSIDALKKCEHDPHVLLAVSKLIWSERKIQ
KCREWFTRTVKSDSDFGDAWGYFYKFELMFGTEEQQQEILKRCIAAEPKHGEEWCKVSKS
IANWRFKTEDVLKALVKILPIPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14248.t1 Coils Coil Coil 106 126 -
17 g14248.t1 Coils Coil Coil 630 653 -
16 g14248.t1 Coils Coil Coil 663 683 -
12 g14248.t1 Gene3D G3DSA:1.25.40.10 - 268 333 1.9E-6
13 g14248.t1 Gene3D G3DSA:1.25.40.10 - 334 507 1.2E-18
14 g14248.t1 Gene3D G3DSA:1.25.40.10 - 508 692 5.4E-23
11 g14248.t1 Gene3D G3DSA:1.25.40.10 - 693 913 3.1E-34
35 g14248.t1 MobiDBLite mobidb-lite consensus disorder prediction 34 96 -
34 g14248.t1 MobiDBLite mobidb-lite consensus disorder prediction 44 67 -
4 g14248.t1 PANTHER PTHR11246:SF1 PRE-MRNA-PROCESSING FACTOR 6 11 917 0.0
5 g14248.t1 PANTHER PTHR11246 PRE-MRNA SPLICING FACTOR 11 917 0.0
2 g14248.t1 Pfam PF06424 PRP1 splicing factor, N-terminal 19 170 1.2E-54
1 g14248.t1 Pfam PF14559 Tetratricopeptide repeat 603 665 2.5E-6
3 g14248.t1 Pfam PF13181 Tetratricopeptide repeat 692 723 0.028
38 g14248.t1 ProSiteProfiles PS50293 TPR repeat region circular profile. 522 792 17.042
37 g14248.t1 ProSiteProfiles PS50005 TPR repeat profile. 657 690 6.372
36 g14248.t1 ProSiteProfiles PS50005 TPR repeat profile. 691 724 8.172
28 g14248.t1 SMART SM00386 hat_new_1 271 303 2.3
26 g14248.t1 SMART SM00386 hat_new_1 305 334 840.0
30 g14248.t1 SMART SM00386 hat_new_1 335 367 1.6
23 g14248.t1 SMART SM00386 hat_new_1 368 398 17.0
33 g14248.t1 SMART SM00386 hat_new_1 426 458 3.3E-5
24 g14248.t1 SMART SM00386 hat_new_1 536 568 1.2E-4
29 g14248.t1 SMART SM00386 hat_new_1 570 602 320.0
27 g14248.t1 SMART SM00386 hat_new_1 604 636 0.066
21 g14248.t1 SMART SM00386 hat_new_1 638 669 220.0
19 g14248.t1 SMART SM00028 tpr_5 657 690 44.0
22 g14248.t1 SMART SM00386 hat_new_1 671 703 81.0
18 g14248.t1 SMART SM00028 tpr_5 691 724 0.73
25 g14248.t1 SMART SM00386 hat_new_1 705 737 0.0099
32 g14248.t1 SMART SM00386 hat_new_1 739 771 0.009
20 g14248.t1 SMART SM00386 hat_new_1 773 805 0.66
31 g14248.t1 SMART SM00386 hat_new_1 837 869 470.0
8 g14248.t1 SUPERFAMILY SSF48452 TPR-like 271 331 9.66E-5
10 g14248.t1 SUPERFAMILY SSF48452 TPR-like 318 391 3.46E-7
7 g14248.t1 SUPERFAMILY SSF48452 TPR-like 396 478 2.77E-8
6 g14248.t1 SUPERFAMILY SSF48452 TPR-like 484 692 1.44E-24
9 g14248.t1 SUPERFAMILY SSF48452 TPR-like 692 896 1.38E-29

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
GO:0000398 mRNA splicing, via spliceosome BP

KEGG

Orthology

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.

Raw TPM values