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.t2 isoform g10214.t2 8262647 8265878
chr_1 g10214 g10214.t2 exon g10214.t2.exon1 8262647 8262839
chr_1 g10214 g10214.t2 exon g10214.t2.exon2 8263240 8263532
chr_1 g10214 g10214.t2 exon g10214.t2.exon3 8263935 8264020
chr_1 g10214 g10214.t2 cds g10214.t2.CDS1 8263980 8264020
chr_1 g10214 g10214.t2 exon g10214.t2.exon4 8264092 8264200
chr_1 g10214 g10214.t2 cds g10214.t2.CDS2 8264092 8264200
chr_1 g10214 g10214.t2 exon g10214.t2.exon5 8264259 8264700
chr_1 g10214 g10214.t2 cds g10214.t2.CDS3 8264259 8264700
chr_1 g10214 g10214.t2 exon g10214.t2.exon6 8264757 8265878
chr_1 g10214 g10214.t2 cds g10214.t2.CDS4 8264757 8265106
chr_1 g10214 g10214.t2 TTS g10214.t2 8265855 8265855
chr_1 g10214 g10214.t2 TSS g10214.t2 NA NA

Sequences

>g10214.t2 Gene=g10214 Length=2245
TTTTATATTATCCAATACAGCTTTTTATCCTTAATACAATATAAGTATTTCTGTATGTAT
ATATATAGATATATAAAGTTCAATTATTGAATTAATCTTTTGTAAATTAATAATTTTAAT
TTTTTAATGAGTTGTAACGTTAATCTATTGGGTAAAAAGAGAAGTATAAAAAATCACATT
TATAGCAAATACGTTTTGTGTTTCTTTTATTATTTTCTTGTTAACATTACTTTCGGTTGC
CTTAATTCTCATTTTTTGACACGAAGGAAGAAAAGATTATCGTAGTGAAGTGTAAATTTT
TTTCAAGTATAAAAAGTTGATTGAATTGTATTTGGAGCCATGTCATCAGCGTTAAGAACG
AAACCATTTGGAGGCAAAAAAGATAAGAAGAATCCACCGATTCTAAGTCATGAATTTGTT
ATTCAGAATCATGCAGATATCGTCTCATGTGTTGCAATGGTGTTTGTCGTCGGTCTAATG
ATGCAATTTTATACTTAGGCAACAAGTACATTAGCTAGCATTTTTATTGTAATGGGTCAC
AATGTGACTGATCCAACGGATGCTGCTACAAGAAACGAGCCTTTCTTATATGAATCTGGT
TGGAGAGATGGACCTGCTGTTTTCTTTTATACTCTTATCTGTATAATCATGCATGCAATT
TTGCAAGAATATGTTTTAGATAAAGTTTCCAAGAAACTTCATCTCTCAAAGTTCAAACTT
TCACGATTCAATGAGTCTGGTCAACTTGTTGTCTTTTACTTAATGTCGTTCCTTTGGGGT
GCTGAAATCATCATTCGTGAGCAATATGCTGAAAATATGTCAAAACTTTGGGTAGATTTC
CCAAATCATCCAATGACATTCTTGCACAAGCTCTACTTCATCATTCAGCTTGCTTACTAC
TTACATATGTTGCCAGAACTTTATTTCCAAAAGATTAAGAAAGATGAACAGCTACCAAAG
ATTCAACATTCTATTGCAGGGACACTTATTATTGGCTTCTTCTATTTCTTCGCTTATCGT
CGTATTGCCATTGTTTTGTTGACTCTTCATTATTTCAGCGAATTTGTTGCACATACATTT
GGACTTCTTGAAGTCTTTGACAAGGAAGAGAAATATGCTAAATTCCGCGTTTTCAACAAC
ATCATTTTCCTCCTTACCGCCTTCTCGACCTTGGTTCTTTCATTCCTCACTTTCTTCACT
GGAATAGGAAAATCAAATCCAACAAGTGGCATGACTGGTTTACTCATTGCCTTTTCTATT
CAAGGCTTTCTCATTTTCCGATTTATTACAAGTTTCCTCAAATCAAAACGTGAATCAAAG
GAGCAGCAAGCCCTTAAACAGCCATTGACAAAGAAATCAAAGGCTAGTGGTGAAACAAAG
AATGCTGCTTCAAGTAAAAAAGACCGCAAGAAGGAATCAGATTTGCCAGAAGCAGATCAA
AATGTAAGCCAAAAGAAAGTCAAGACCAAGTAAATTAAAATTGATTTCCTTTTTTGTTAA
CACCTGATGATTCTGATTATTCTCTTTTATACTTCCTTTCTATACTTGCTTCAGTTGATT
TTTTTTAAAAATTCTATCTAAGTACATTCATTAAAAAAAAGTTCTAATATTTTTGTAACA
GTTCATTCTTCATGTAAGAGCATTTATTGTAATTTTCTATATATAAAAAGAAGAAAATCT
ATATTTTTACATTGATCAAAAACGAATTTTTTTGGTTGAAATTTTTCTCGTTGCACATTA
AATTTTTTTGTAGAAAAAGTTTTATTAATAAAAAGTAACTAAATGTCCATAGACGTTAGA
AATGACATATTAAAAAAGAGAATATAATTTTAAATGATCCTATTTTTTTTTAGAAACAAT
GAGTAAAAGAAATTGTTTTTGATAATGCATAAGCAGCAAGAAAACTTATGACGAAAACAT
TTTAACTATTTTTTAAGTTCTATTATTCAGTTAATCATTTATAACATTTAAAAAATCTTA
AAATCTTAATCATAGACGGAATATTTACTTTTTTACCTCCCACATCCAATTTTCATTCTA
CAATAGGTTTTGTATATTAAATGGTAAAAATTCCGTCTGTGATTTTATAATCTTTTTATT
TTTTTACATTGTAAAAATGAAGAAAATTTCCGATATTTTTTTGAGAGTAAAAAGGCGATG
AAAAAAATATATAAAAGAAGATAAGAAATAAATAATTTTTGTATGTTTCAATGCAAAAAG
AGAATATTTTGCTGTGTTTTTTAAT

>g10214.t2 Gene=g10214 Length=313
MGHNVTDPTDAATRNEPFLYESGWRDGPAVFFYTLICIIMHAILQEYVLDKVSKKLHLSK
FKLSRFNESGQLVVFYLMSFLWGAEIIIREQYAENMSKLWVDFPNHPMTFLHKLYFIIQL
AYYLHMLPELYFQKIKKDEQLPKIQHSIAGTLIIGFFYFFAYRRIAIVLLTLHYFSEFVA
HTFGLLEVFDKEEKYAKFRVFNNIIFLLTAFSTLVLSFLTFFTGIGKSNPTSGMTGLLIA
FSIQGFLIFRFITSFLKSKRESKEQQALKQPLTKKSKASGETKNAASSKKDRKKESDLPE
ADQNVSQKKVKTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10214.t2 MobiDBLite mobidb-lite consensus disorder prediction 264 313 -
13 g10214.t2 MobiDBLite mobidb-lite consensus disorder prediction 284 313 -
3 g10214.t2 PANTHER PTHR12371:SF11 TRANSLOCATING CHAIN-ASSOCIATED MEMBRANE PROTEIN 2 309 2.4E-94
4 g10214.t2 PANTHER PTHR12371 TRANSLOCATION ASSOCIATED MEMBRANE PROTEIN 2 309 2.4E-94
1 g10214.t2 Pfam PF08390 TRAM1-like protein 3 61 6.4E-16
2 g10214.t2 Pfam PF03798 TLC domain 65 211 1.9E-15
22 g10214.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 29 -
24 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 49 -
16 g10214.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 50 69 -
26 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 70 88 -
21 g10214.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 89 113 -
28 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 114 132 -
19 g10214.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 133 143 -
30 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 144 161 -
23 g10214.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 162 166 -
29 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 188 -
17 g10214.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 189 199 -
25 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 200 222 -
20 g10214.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 223 233 -
27 g10214.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 234 253 -
18 g10214.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 254 313 -
15 g10214.t2 ProSiteProfiles PS50922 TLC domain profile. 64 263 9.761
12 g10214.t2 SMART SM00724 lag1_27 64 260 2.1E-22
5 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
9 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 70 89 -
7 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 131 -
11 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 144 161 -
8 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 165 187 -
6 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 200 222 -
10 g10214.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 232 254 -

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.

Raw TPM values