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.t7 TSS g10214.t7 8263065 8263065
chr_1 g10214 g10214.t7 isoform g10214.t7 8263386 8265709
chr_1 g10214 g10214.t7 exon g10214.t7.exon1 8263386 8263532
chr_1 g10214 g10214.t7 cds g10214.t7.CDS1 8263386 8263532
chr_1 g10214 g10214.t7 exon g10214.t7.exon2 8263947 8264020
chr_1 g10214 g10214.t7 cds g10214.t7.CDS2 8263947 8264020
chr_1 g10214 g10214.t7 exon g10214.t7.exon3 8264092 8264204
chr_1 g10214 g10214.t7 cds g10214.t7.CDS3 8264092 8264204
chr_1 g10214 g10214.t7 exon g10214.t7.exon4 8264263 8264700
chr_1 g10214 g10214.t7 cds g10214.t7.CDS4 8264263 8264700
chr_1 g10214 g10214.t7 exon g10214.t7.exon5 8264757 8265709
chr_1 g10214 g10214.t7 cds g10214.t7.CDS5 8264757 8265106
chr_1 g10214 g10214.t7 TTS g10214.t7 8265855 8265855

Sequences

>g10214.t7 Gene=g10214 Length=1725
ATGTCATCAGCGTTAAGAACGAAACCATTTGGAGGCAAAAAAGATAAGAAGAATCCACCG
ATTCTAAGTCATGAATTTGTTATTCAGAATCATGCAGATATCGTCTCATGTGTTGCAATG
GTGTTTGTCGTCGGTCTAATGATGCAAGCAACAAGTACATTAGCTAGCATTTTTATTGTA
ATGGGTCACAATGTGACTGATCCAACGGATGCTGCTACAAGAAACGAGCCTTTCTTATAT
GAATCTGGTTGGAGAGATGGACCTGCTGTTTTCTTTTATACTCTTATCTGTATAATCATG
CATGCAATTTTGCAAGAATATGTTTTAGATGTGATTTCCAAGAAACTTCATCTCTCAAAG
TTCAAACTTTCACGATTCAATGAGTCTGGTCAACTTGTTGTCTTTTACTTAATGTCGTTC
CTTTGGGGTGCTGAAATCATCATTCGTGAGCAATATGCTGAAAATATGTCAAAACTTTGG
GTAGATTTCCCAAATCATCCAATGACATTCTTGCACAAGCTCTACTTCATCATTCAGCTT
GCTTACTACTTACATATGTTGCCAGAACTTTATTTCCAAAAGATTAAGAAAGATGAACAG
CTACCAAAGATTCAACATTCTATTGCAGGGACACTTATTATTGGCTTCTTCTATTTCTTC
GCTTATCGTCGTATTGCCATTGTTTTGTTGACTCTTCATTATTTCAGCGAATTTGTTGCA
CATACATTTGGACTTCTTGAAGTCTTTGACAAGGAAGAGAAATATGCTAAATTCCGCGTT
TTCAACAACATCATTTTCCTCCTTACCGCCTTCTCGACCTTGGTTCTTTCATTCCTCACT
TTCTTCACTGGAATAGGAAAATCAAATCCAACAAGTGGCATGACTGGTTTACTCATTGCC
TTTTCTATTCAAGGCTTTCTCATTTTCCGATTTATTACAAGTTTCCTCAAATCAAAACGT
GAATCAAAGGAGCAGCAAGCCCTTAAACAGCCATTGACAAAGAAATCAAAGGCTAGTGGT
GAAACAAAGAATGCTGCTTCAAGTAAAAAAGACCGCAAGAAGGAATCAGATTTGCCAGAA
GCAGATCAAAATGTAAGCCAAAAGAAAGTCAAGACCAAGTAAATTAAAATTGATTTCCTT
TTTTGTTAACACCTGATGATTCTGATTATTCTCTTTTATACTTCCTTTCTATACTTGCTT
CAGTTGATTTTTTTTAAAAATTCTATCTAAGTACATTCATTAAAAAAAAGTTCTAATATT
TTTGTAACAGTTCATTCTTCATGTAAGAGCATTTATTGTAATTTTCTATATATAAAAAGA
AGAAAATCTATATTTTTACATTGATCAAAAACGAATTTTTTTGGTTGAAATTTTTCTCGT
TGCACATTAAATTTTTTTGTAGAAAAAGTTTTATTAATAAAAAGTAACTAAATGTCCATA
GACGTTAGAAATGACATATTAAAAAAGAGAATATAATTTTAAATGATCCTATTTTTTTTT
AGAAACAATGAGTAAAAGAAATTGTTTTTGATAATGCATAAGCAGCAAGAAAACTTATGA
CGAAAACATTTTAACTATTTTTTAAGTTCTATTATTCAGTTAATCATTTATAACATTTAA
AAAATCTTAAAATCTTAATCATAGACGGAATATTTACTTTTTTACCTCCCACATCCAATT
TTCATTCTACAATAGGTTTTGTATATTAAATGGTAAAAATTCCGT

>g10214.t7 Gene=g10214 Length=373
MSSALRTKPFGGKKDKKNPPILSHEFVIQNHADIVSCVAMVFVVGLMMQATSTLASIFIV
MGHNVTDPTDAATRNEPFLYESGWRDGPAVFFYTLICIIMHAILQEYVLDVISKKLHLSK
FKLSRFNESGQLVVFYLMSFLWGAEIIIREQYAENMSKLWVDFPNHPMTFLHKLYFIIQL
AYYLHMLPELYFQKIKKDEQLPKIQHSIAGTLIIGFFYFFAYRRIAIVLLTLHYFSEFVA
HTFGLLEVFDKEEKYAKFRVFNNIIFLLTAFSTLVLSFLTFFTGIGKSNPTSGMTGLLIA
FSIQGFLIFRFITSFLKSKRESKEQQALKQPLTKKSKASGETKNAASSKKDRKKESDLPE
ADQNVSQKKVKTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10214.t7 MobiDBLite mobidb-lite consensus disorder prediction 324 373 -
15 g10214.t7 MobiDBLite mobidb-lite consensus disorder prediction 344 373 -
3 g10214.t7 PANTHER PTHR12371:SF11 TRANSLOCATING CHAIN-ASSOCIATED MEMBRANE PROTEIN 14 369 2.9E-125
4 g10214.t7 PANTHER PTHR12371 TRANSLOCATION ASSOCIATED MEMBRANE PROTEIN 14 369 2.9E-125
1 g10214.t7 Pfam PF08390 TRAM1-like protein 56 121 2.3E-16
2 g10214.t7 Pfam PF03798 TLC domain 125 271 2.7E-15
19 g10214.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 33 -
26 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 34 60 -
25 g10214.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 89 -
30 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 109 -
17 g10214.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 110 129 -
28 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 148 -
24 g10214.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 173 -
32 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 174 192 -
21 g10214.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 203 -
27 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 221 -
23 g10214.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 222 226 -
31 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 248 -
18 g10214.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 249 259 -
33 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 260 282 -
22 g10214.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 283 293 -
29 g10214.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 294 313 -
20 g10214.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 314 373 -
16 g10214.t7 ProSiteProfiles PS50922 TLC domain profile. 124 323 9.761
13 g10214.t7 SMART SM00724 lag1_27 124 320 2.1E-22
10 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 38 60 -
7 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
11 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 132 149 -
9 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 169 191 -
5 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 204 221 -
8 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 225 247 -
12 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 260 282 -
6 g10214.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 292 314 -

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

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. There were no conditions that were differentially expressed