Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t9 TSS g10214.t9 8263065 8263065
chr_1 g10214 g10214.t9 isoform g10214.t9 8263386 8265878
chr_1 g10214 g10214.t9 exon g10214.t9.exon1 8263386 8263532
chr_1 g10214 g10214.t9 cds g10214.t9.CDS1 8263386 8263532
chr_1 g10214 g10214.t9 exon g10214.t9.exon2 8263947 8264020
chr_1 g10214 g10214.t9 cds g10214.t9.CDS2 8263947 8264020
chr_1 g10214 g10214.t9 exon g10214.t9.exon3 8264092 8264159
chr_1 g10214 g10214.t9 cds g10214.t9.CDS3 8264092 8264159
chr_1 g10214 g10214.t9 exon g10214.t9.exon4 8264308 8264700
chr_1 g10214 g10214.t9 cds g10214.t9.CDS4 8264308 8264700
chr_1 g10214 g10214.t9 exon g10214.t9.exon5 8264757 8265878
chr_1 g10214 g10214.t9 cds g10214.t9.CDS5 8264757 8265106
chr_1 g10214 g10214.t9 TTS g10214.t9 8265855 8265855

Sequences

>g10214.t9 Gene=g10214 Length=1804
ATGTCATCAGCGTTAAGAACGAAACCATTTGGAGGCAAAAAAGATAAGAAGAATCCACCG
ATTCTAAGTCATGAATTTGTTATTCAGAATCATGCAGATATCGTCTCATGTGTTGCAATG
GTGTTTGTCGTCGGTCTAATGATGCAAGCAACAAGTACATTAGCTAGCATTTTTATTGTA
ATGGGTCACAATGTGACTGATCCAACGGATGCTGCTACAAGAAACGAGCCTTTCTTATAT
GAATCTGGTTGGAGAGATGGACCTGCTGTTTTCTTTTATACTCTTATCTATGAGTCTGGT
CAACTTGTTGTCTTTTACTTAATGTCGTTCCTTTGGGGTGCTGAAATCATCATTCGTGAG
CAATATGCTGAAAATATGTCAAAACTTTGGGTAGATTTCCCAAATCATCCAATGACATTC
TTGCACAAGCTCTACTTCATCATTCAGCTTGCTTACTACTTACATATGTTGCCAGAACTT
TATTTCCAAAAGATTAAGAAAGATGAACAGCTACCAAAGATTCAACATTCTATTGCAGGG
ACACTTATTATTGGCTTCTTCTATTTCTTCGCTTATCGTCGTATTGCCATTGTTTTGTTG
ACTCTTCATTATTTCAGCGAATTTGTTGCACATACATTTGGACTTCTTGAAGTCTTTGAC
AAGGAAGAGAAATATGCTAAATTCCGCGTTTTCAACAACATCATTTTCCTCCTTACCGCC
TTCTCGACCTTGGTTCTTTCATTCCTCACTTTCTTCACTGGAATAGGAAAATCAAATCCA
ACAAGTGGCATGACTGGTTTACTCATTGCCTTTTCTATTCAAGGCTTTCTCATTTTCCGA
TTTATTACAAGTTTCCTCAAATCAAAACGTGAATCAAAGGAGCAGCAAGCCCTTAAACAG
CCATTGACAAAGAAATCAAAGGCTAGTGGTGAAACAAAGAATGCTGCTTCAAGTAAAAAA
GACCGCAAGAAGGAATCAGATTTGCCAGAAGCAGATCAAAATGTAAGCCAAAAGAAAGTC
AAGACCAAGTAAATTAAAATTGATTTCCTTTTTTGTTAACACCTGATGATTCTGATTATT
CTCTTTTATACTTCCTTTCTATACTTGCTTCAGTTGATTTTTTTTAAAAATTCTATCTAA
GTACATTCATTAAAAAAAAGTTCTAATATTTTTGTAACAGTTCATTCTTCATGTAAGAGC
ATTTATTGTAATTTTCTATATATAAAAAGAAGAAAATCTATATTTTTACATTGATCAAAA
ACGAATTTTTTTGGTTGAAATTTTTCTCGTTGCACATTAAATTTTTTTGTAGAAAAAGTT
TTATTAATAAAAAGTAACTAAATGTCCATAGACGTTAGAAATGACATATTAAAAAAGAGA
ATATAATTTTAAATGATCCTATTTTTTTTTAGAAACAATGAGTAAAAGAAATTGTTTTTG
ATAATGCATAAGCAGCAAGAAAACTTATGACGAAAACATTTTAACTATTTTTTAAGTTCT
ATTATTCAGTTAATCATTTATAACATTTAAAAAATCTTAAAATCTTAATCATAGACGGAA
TATTTACTTTTTTACCTCCCACATCCAATTTTCATTCTACAATAGGTTTTGTATATTAAA
TGGTAAAAATTCCGTCTGTGATTTTATAATCTTTTTATTTTTTTACATTGTAAAAATGAA
GAAAATTTCCGATATTTTTTTGAGAGTAAAAAGGCGATGAAAAAAATATATAAAAGAAGA
TAAGAAATAAATAATTTTTGTATGTTTCAATGCAAAAAGAGAATATTTTGCTGTGTTTTT
TAAT

>g10214.t9 Gene=g10214 Length=343
MSSALRTKPFGGKKDKKNPPILSHEFVIQNHADIVSCVAMVFVVGLMMQATSTLASIFIV
MGHNVTDPTDAATRNEPFLYESGWRDGPAVFFYTLIYESGQLVVFYLMSFLWGAEIIIRE
QYAENMSKLWVDFPNHPMTFLHKLYFIIQLAYYLHMLPELYFQKIKKDEQLPKIQHSIAG
TLIIGFFYFFAYRRIAIVLLTLHYFSEFVAHTFGLLEVFDKEEKYAKFRVFNNIIFLLTA
FSTLVLSFLTFFTGIGKSNPTSGMTGLLIAFSIQGFLIFRFITSFLKSKRESKEQQALKQ
PLTKKSKASGETKNAASSKKDRKKESDLPEADQNVSQKKVKTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10214.t9 MobiDBLite mobidb-lite consensus disorder prediction 294 343 -
13 g10214.t9 MobiDBLite mobidb-lite consensus disorder prediction 314 343 -
2 g10214.t9 PANTHER PTHR12371:SF11 TRANSLOCATING CHAIN-ASSOCIATED MEMBRANE PROTEIN 14 96 2.1E-98
4 g10214.t9 PANTHER PTHR12371 TRANSLOCATION ASSOCIATED MEMBRANE PROTEIN 14 96 2.1E-98
3 g10214.t9 PANTHER PTHR12371:SF11 TRANSLOCATING CHAIN-ASSOCIATED MEMBRANE PROTEIN 98 339 2.1E-98
5 g10214.t9 PANTHER PTHR12371 TRANSLOCATION ASSOCIATED MEMBRANE PROTEIN 98 339 2.1E-98
1 g10214.t9 Pfam PF03798 TLC domain 98 239 3.4E-15
17 g10214.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 33 -
23 g10214.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 34 60 -
20 g10214.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 143 -
24 g10214.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 144 162 -
16 g10214.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 163 173 -
28 g10214.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 174 191 -
22 g10214.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 192 196 -
25 g10214.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 197 218 -
18 g10214.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 219 229 -
27 g10214.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 230 252 -
21 g10214.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 253 263 -
26 g10214.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 264 283 -
19 g10214.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 284 343 -
15 g10214.t9 ProSiteProfiles PS50922 TLC domain profile. 94 293 8.984
12 g10214.t9 SMART SM00724 lag1_27 94 290 4.7E-20
7 g10214.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 38 60 -
6 g10214.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
10 g10214.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 155 -
11 g10214.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 175 192 -
9 g10214.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 234 256 -
8 g10214.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 261 283 -

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