Gene loci information

Transcript annotation

  • This transcript has been annotated as Tetratricopeptide repeat protein 37.

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 g7169 g7169.t4 isoform g7169.t4 21770675 21773407
chr_2 g7169 g7169.t4 exon g7169.t4.exon1 21770675 21772074
chr_2 g7169 g7169.t4 cds g7169.t4.CDS1 21770892 21772074
chr_2 g7169 g7169.t4 exon g7169.t4.exon2 21772152 21772634
chr_2 g7169 g7169.t4 cds g7169.t4.CDS2 21772152 21772634
chr_2 g7169 g7169.t4 exon g7169.t4.exon3 21772690 21773018
chr_2 g7169 g7169.t4 cds g7169.t4.CDS3 21772690 21773018
chr_2 g7169 g7169.t4 exon g7169.t4.exon4 21773081 21773407
chr_2 g7169 g7169.t4 cds g7169.t4.CDS4 21773081 21773407
chr_2 g7169 g7169.t4 TTS g7169.t4 21774368 21774368
chr_2 g7169 g7169.t4 TSS g7169.t4 NA NA

Sequences

>g7169.t4 Gene=g7169 Length=2539
CAATAAACTTTTAAAAGCAACAGCTCATCGTATTAAGGGAGAGTATGAGCTTGCTATAGA
AACATTAAAGGATATTGAAAATCATGATGCATTCCTTGAAATTGGTAGAAACCTTTTTGA
ATTACAAAAGTACGAAGAATCATTAGTAAATATTCTCAAAGCTACTAAATTGGATCCGAA
TAATTCAGAATGTTTTTATTGGCTTGGTAAAATTTATATGATTTCTAACGATGAGCATCG
AAGTCAAAAATGCCTTGAAAAATGCTTACATCTCAATGCACAGAATGAGAAAGCTATTAC
AATTCTTTCATCTATCTATCGTAAAAACAAGGAATGGGATAATAATTTACAGATTTTAGA
AAACTCTGTGCAGTCTGTGAGTGGTGTTTATCAGAAAACTGCATTCTTTCAATTAGGCCT
TCATCATCTTGCTCAACAAAGTTACGATAATGCAATTACTGCATTCAGAAATGTCCTCAA
ATATGACAAAAATAGTGTGGAATGCTGGGAGGCTTTAGCTGACAGTTATTTGGCACGTGG
TTCATTTAATTCTGCCTTAAATGTATTTCAAAAAAGTGTAGAATTAAATCCTAATAATCA
TTATGCAAAACTTCAAATTGCAAAAATCAAATATACATTGCAACAATATCAAGAATCAAT
TGCGGATTATGAAGAACTTCTTAAAATTATTCCAGACTATTTGCCTGCTTTATATGGAAT
TGCAGAAAGCCATTTTGGAAGGGCTTGTTATTTACACGAAAACCATCGAAGTGGACGAGC
TCGCGACCATTGTCAAAGTACACTTTCCTATCTTGAACAAGCTATTAAACTTGAGCCATC
ATTTCTCTGTTTATGGAGAACATTGGGAAACATTTTGGAATTTGTTGCAACATTGCCAGA
AATTTATAATTATTTAATATTACCAGCAGCAATAGTTTGTGAAAATTCTTCGCAACGACT
AAATGGAGATGCATTGATGGATTTGGCTCAAAAATGCTACTGTCGATGTTTGAAAATTAA
TAAACAAGATGAATTTGTGTGGTTTGATTATGTGGCTAACTATTACAAACGTTCACTTAG
AATGAAGAGTGACAATGATAATAAAATGAAATTTCTTAAATTCGCATACAATGGGGCAAA
GCATTTGGTCAAACTGGCACCATCCAAATGGCAAAACTGGAACCTATTAGGAATAATTTG
TACAACAAACGAAATAAACGATTCTGCTTTAGGCCAACATTGCTTTATTAAAGCAATAAA
TTTGGATAAAAAAACATTTACAAGTTGGTCAAATCTAGGGGTGTTTTATTTGAAGCATGG
TGAAATAAAGCTAGCAAATAAAGCATTTAGTCGTGCACAACAATCAGACACATCATTTTT
AAATGCTTGGATTGGCCAAGCTTTGATTGCAGAACTAATTGGAGATAAAGATGAAGCTAT
GGATTTGTTTCGACATTGCACTCAACTAGGTTTTCATCATGAATCATCAATCGGATATCC
CAATTATGTATGTTCGATTCTCAATGAACCAAATTATGCAAGCATACCAAAATATAAATA
TGCGATTGATGCGATGAACGCAATTCCATTAGCACTAGATAACATACAATGGCACTGTAT
GTATGAACAAGATTTGACATTTGAAGCTCTTTCGTACGTAGGTTATCTGAGTAATTGTCA
GAAGCTATTCAAACAAGCTTGTATAGCTTATGAAAAAGCATTGAAATTGGCGAGAAGTGA
TGTTCAGAGAGATAAATGTTTAACTGATTTAGGATTTTGCTATTTGAGAGCAAATGAAAA
CGAAAAAGCTTCAAAAGCTTTTAGTGACATTAAAGAAGCATCATTTTTATCAACGGTTGG
ACTTGCTTTGGCTTATTATAAAGATGCAAATTATCAAGATTGTTATGAGACATATCAAAA
AGCAATAGAATGGCTTGCAACGAATGATGAAGAAAAATCAACTGTTCTAGTAGCGATGGC
TTCTATGATTTATGCTTTTCAAGGAGTGGATGATGCTAAAATGGTTCTTTTTCAATGTAT
TCAATTGAAACCCATATCTGTTGAGGGACTTTTGTCTCTATGTGCAATCAGTTTATTAAA
AAAAGACAAACAATTGAGCGAATTAGTCATAAAAGAATTGAAAAATTATGAGTACGATGA
GAATTATGGACATCATGTATCATTTATGGTTTCACAATATTACATCAAATACAGCACAAA
AGCTGAAGCTATAGTCTATATTTCATCGCGAATTCATGAATTTCCTGATCGAGCACCATT
ACGAAAACTTCTTGCAGTTGTACTATTAGAAACATACAAAGACAATAAGGTTTTGATGAG
AGTAGCAAGTAAAATGGCCCAAAGTGCTCTGTCGATTCGTATTAAAAATCGTAATGTTTT
ATTATCGGAAGAAGCTGCTGAATTGTTAGCACTTTCAAGCATGACTATTGAGTGTTTTGA
TGCACAGTCGGCAAAAATATTTGCACAAAAAGCTGTTCACACTTGTCCACATTATTGGAA
AATTTTGAAAATACTTTGA

>g7169.t4 Gene=g7169 Length=773
MISNDEHRSQKCLEKCLHLNAQNEKAITILSSIYRKNKEWDNNLQILENSVQSVSGVYQK
TAFFQLGLHHLAQQSYDNAITAFRNVLKYDKNSVECWEALADSYLARGSFNSALNVFQKS
VELNPNNHYAKLQIAKIKYTLQQYQESIADYEELLKIIPDYLPALYGIAESHFGRACYLH
ENHRSGRARDHCQSTLSYLEQAIKLEPSFLCLWRTLGNILEFVATLPEIYNYLILPAAIV
CENSSQRLNGDALMDLAQKCYCRCLKINKQDEFVWFDYVANYYKRSLRMKSDNDNKMKFL
KFAYNGAKHLVKLAPSKWQNWNLLGIICTTNEINDSALGQHCFIKAINLDKKTFTSWSNL
GVFYLKHGEIKLANKAFSRAQQSDTSFLNAWIGQALIAELIGDKDEAMDLFRHCTQLGFH
HESSIGYPNYVCSILNEPNYASIPKYKYAIDAMNAIPLALDNIQWHCMYEQDLTFEALSY
VGYLSNCQKLFKQACIAYEKALKLARSDVQRDKCLTDLGFCYLRANENEKASKAFSDIKE
ASFLSTVGLALAYYKDANYQDCYETYQKAIEWLATNDEEKSTVLVAMASMIYAFQGVDDA
KMVLFQCIQLKPISVEGLLSLCAISLLKKDKQLSELVIKELKNYEYDENYGHHVSFMVSQ
YYIKYSTKAEAIVYISSRIHEFPDRAPLRKLLAVVLLETYKDNKVLMRVASKMAQSALSI
RIKNRNVLLSEEAAELLALSSMTIECFDAQSAKIFAQKAVHTCPHYWKILKIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g7169.t4 Coils Coil Coil 134 154 -
18 g7169.t4 Gene3D G3DSA:1.25.40.10 - 2 104 2.3E-12
15 g7169.t4 Gene3D G3DSA:1.25.40.10 - 105 233 4.5E-17
16 g7169.t4 Gene3D G3DSA:1.25.40.10 - 238 418 5.1E-15
17 g7169.t4 Gene3D G3DSA:1.25.40.10 - 474 678 2.7E-10
2 g7169.t4 PANTHER PTHR15704 SUPERKILLER 3 PROTEIN-RELATED 2 770 5.1E-148
3 g7169.t4 PANTHER PTHR15704:SF7 TETRATRICOPEPTIDE REPEAT PROTEIN 37 2 770 5.1E-148
1 g7169.t4 Pfam PF14559 Tetratricopeptide repeat 71 133 1.1E-7
28 g7169.t4 ProSiteProfiles PS50293 TPR repeat region circular profile. 1 161 27.35
22 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 60 93 9.558
26 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 94 127 12.184
21 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 128 161 7.316
20 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 354 387 8.26
27 g7169.t4 ProSiteProfiles PS50293 TPR repeat region circular profile. 354 421 11.315
23 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 388 421 5.428
25 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 475 508 5.9
24 g7169.t4 ProSiteProfiles PS50005 TPR repeat profile. 543 576 6.431
29 g7169.t4 ProSiteProfiles PS50293 TPR repeat region circular profile. 543 576 6.633
8 g7169.t4 SMART SM00028 tpr_5 60 93 10.0
11 g7169.t4 SMART SM00028 tpr_5 94 127 0.0023
12 g7169.t4 SMART SM00028 tpr_5 128 161 0.7
14 g7169.t4 SMART SM00028 tpr_5 169 202 130.0
7 g7169.t4 SMART SM00028 tpr_5 354 387 13.0
13 g7169.t4 SMART SM00028 tpr_5 388 421 81.0
10 g7169.t4 SMART SM00028 tpr_5 475 508 2.6
9 g7169.t4 SMART SM00028 tpr_5 543 576 35.0
4 g7169.t4 SUPERFAMILY SSF48452 TPR-like 62 172 9.73E-23
6 g7169.t4 SUPERFAMILY SSF48452 TPR-like 170 284 9.01E-5
5 g7169.t4 SUPERFAMILY SSF48452 TPR-like 298 630 1.33E-20

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:0006401 RNA catabolic process BP
GO:0005515 protein binding MF
GO:0055087 Ski complex CC

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