Gene loci information

Transcript annotation

  • This transcript has been annotated as Translocating chain-associated membrane protein 1-like 1.

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 g10214 g10214.t4 TSS g10214.t4 8263065 8263065
chr_1 g10214 g10214.t4 isoform g10214.t4 8263386 8264700
chr_1 g10214 g10214.t4 exon g10214.t4.exon1 8263386 8263532
chr_1 g10214 g10214.t4 cds g10214.t4.CDS1 8263386 8263532
chr_1 g10214 g10214.t4 exon g10214.t4.exon2 8263947 8264020
chr_1 g10214 g10214.t4 cds g10214.t4.CDS2 8263947 8264020
chr_1 g10214 g10214.t4 exon g10214.t4.exon3 8264092 8264200
chr_1 g10214 g10214.t4 cds g10214.t4.CDS3 8264092 8264200
chr_1 g10214 g10214.t4 exon g10214.t4.exon4 8264259 8264700
chr_1 g10214 g10214.t4 cds g10214.t4.CDS4 8264259 8264699
chr_1 g10214 g10214.t4 TTS g10214.t4 8265443 8265443

Sequences

>g10214.t4 Gene=g10214 Length=772
ATGTCATCAGCGTTAAGAACGAAACCATTTGGAGGCAAAAAAGATAAGAAGAATCCACCG
ATTCTAAGTCATGAATTTGTTATTCAGAATCATGCAGATATCGTCTCATGTGTTGCAATG
GTGTTTGTCGTCGGTCTAATGATGCAAGCAACAAGTACATTAGCTAGCATTTTTATTGTA
ATGGGTCACAATGTGACTGATCCAACGGATGCTGCTACAAGAAACGAGCCTTTCTTATAT
GAATCTGGTTGGAGAGATGGACCTGCTGTTTTCTTTTATACTCTTATCTGTATAATCATG
CATGCAATTTTGCAAGAATATGTTTTAGATAAAGTTTCCAAGAAACTTCATCTCTCAAAG
TTCAAACTTTCACGATTCAATGAGTCTGGTCAACTTGTTGTCTTTTACTTAATGTCGTTC
CTTTGGGGTGCTGAAATCATCATTCGTGAGCAATATGCTGAAAATATGTCAAAACTTTGG
GTAGATTTCCCAAATCATCCAATGACATTCTTGCACAAGCTCTACTTCATCATTCAGCTT
GCTTACTACTTACATATGTTGCCAGAACTTTATTTCCAAAAGATTAAGAAAGATGAACAG
CTACCAAAGATTCAACATTCTATTGCAGGGACACTTATTATTGGCTTCTTCTATTTCTTC
GCTTATCGTCGTATTGCCATTGTTTTGTTGACTCTTCATTATTTCAGCGAATTTGTTGCA
CATACATTTGGACTTCTTGAAGTCTTTGACAAGGAAGAGAAATATGCTAAAT

>g10214.t4 Gene=g10214 Length=257
MSSALRTKPFGGKKDKKNPPILSHEFVIQNHADIVSCVAMVFVVGLMMQATSTLASIFIV
MGHNVTDPTDAATRNEPFLYESGWRDGPAVFFYTLICIIMHAILQEYVLDKVSKKLHLSK
FKLSRFNESGQLVVFYLMSFLWGAEIIIREQYAENMSKLWVDFPNHPMTFLHKLYFIIQL
AYYLHMLPELYFQKIKKDEQLPKIQHSIAGTLIIGFFYFFAYRRIAIVLLTLHYFSEFVA
HTFGLLEVFDKEEKYAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g10214.t4 PANTHER PTHR12371:SF11 TRANSLOCATING CHAIN-ASSOCIATED MEMBRANE PROTEIN 14 255 2.7E-110
4 g10214.t4 PANTHER PTHR12371 TRANSLOCATION ASSOCIATED MEMBRANE PROTEIN 14 255 2.7E-110
1 g10214.t4 Pfam PF08390 TRAM1-like protein 56 121 8.7E-18
2 g10214.t4 Pfam PF03798 TLC domain 125 251 2.1E-15
13 g10214.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 33 -
19 g10214.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 34 60 -
17 g10214.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 89 -
18 g10214.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 109 -
11 g10214.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 110 129 -
23 g10214.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 148 -
16 g10214.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 173 -
20 g10214.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 174 192 -
14 g10214.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 203 -
22 g10214.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 221 -
15 g10214.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 222 226 -
21 g10214.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 249 -
12 g10214.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 250 257 -
10 g10214.t4 ProSiteProfiles PS50922 TLC domain profile. 124 257 10.219
8 g10214.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 38 60 -
5 g10214.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 87 109 -
9 g10214.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 148 -
7 g10214.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 187 -
6 g10214.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 208 230 -

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:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation BP
GO:0016021 integral component of membrane CC

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