Gene loci information

Transcript annotation

  • This transcript has been annotated as Mitochondrial basic amino acids transporter.

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 g4576 g4576.t1 TTS g4576.t1 3279097 3279097
chr_2 g4576 g4576.t1 isoform g4576.t1 3279206 3280605
chr_2 g4576 g4576.t1 exon g4576.t1.exon1 3279206 3279834
chr_2 g4576 g4576.t1 cds g4576.t1.CDS1 3279206 3279834
chr_2 g4576 g4576.t1 exon g4576.t1.exon2 3279897 3280358
chr_2 g4576 g4576.t1 cds g4576.t1.CDS2 3279897 3280358
chr_2 g4576 g4576.t1 exon g4576.t1.exon3 3280572 3280605
chr_2 g4576 g4576.t1 cds g4576.t1.CDS3 3280572 3280605
chr_2 g4576 g4576.t1 TSS g4576.t1 3281296 3281296

Sequences

>g4576.t1 Gene=g4576 Length=1125
ATGGCATTAGACTTTGTTGCTGGATGTCTTGGAGGATGTTGCGGACTGCTAGTTGGCCAC
CCGTTTGATACAGTGAAAGTGCATTTACAAACACAAGATTATAAAAATCCGCTTTATCGC
GGCACATATGACTGCCTCAAAAAAATTGTACAAAAAGAATCACTACATGGACTTTATCGA
GGCCTCTCATCACCTTTAGCCTCAATTTCAGTACTGAATGCAATTGTATTTGGCGTATAT
GGAAACGTACAACGACAAACGAAGGATCCAGAATCATTATTTGCACACTTTTGTGCTGGC
ACAGCAGCTGGACTTAGTCAAACATTGATTTGCAGTCCTATGGAATTGGTTAAATCTCGA
TTACAAATTCAAAATAATATTCCAAATGCAGTAAAACACAAAAATCCTTTTCAAGCATTA
AAATATTTGTGGAATACCGAAGGACGTCGTGGTGTTTTCAAAGGTTTGGGAATCACAATT
GCTAGAGATGTTCCAGGCTTTTCAAGTTATTTCGTTTCTTTTGAAATGATGATGCGACAA
ACAAAAGATCCAAGTGCTTTTTACACACTCATTGCTGGTGGTTTAGCTGGAACATTCTCA
TGGATTATATCTTTCCCTGTTGATGTTGTAAAATCTCGTCTACAAGTTGATGGCATTGAT
GGAAGACCAAGATATAATGGAGCCATTGACTGCATAAAGAAAAGCTATCAAGCTGAAGGA
TTAGCATTTTTCACAAGAGGATTGAATTCAACACTTATTAGAGCCTTTCCAATGAATGCC
GTTTGTTTCCTCGTGGTTTCACAAGTCATGAAATTCTTCCAAAATAAAAGTCTTGATGTG
TCGATTTCACAAAGTGAACCACTGCCAATTGTCGATTACAATCAAGGTTTCATCACACGT
GTCTTTAATCGTATTCATCATGGCTCACCATATCAACATAAATCAATAAGGTACCTGATT
TTCTTGGATGGCTTCCACGAAGCAACATGCCATGCAGACATGATAGATTTATCGGATCAA
CTCAGGGAACAGAGGAAAACCTTTGAATACTATTACAAAATGAACGATGGTGTTATGACT
AAAAATTTATCAGAAGATGAATTAAAAACGCCAATTATTTGTTAA

>g4576.t1 Gene=g4576 Length=374
MALDFVAGCLGGCCGLLVGHPFDTVKVHLQTQDYKNPLYRGTYDCLKKIVQKESLHGLYR
GLSSPLASISVLNAIVFGVYGNVQRQTKDPESLFAHFCAGTAAGLSQTLICSPMELVKSR
LQIQNNIPNAVKHKNPFQALKYLWNTEGRRGVFKGLGITIARDVPGFSSYFVSFEMMMRQ
TKDPSAFYTLIAGGLAGTFSWIISFPVDVVKSRLQVDGIDGRPRYNGAIDCIKKSYQAEG
LAFFTRGLNSTLIRAFPMNAVCFLVVSQVMKFFQNKSLDVSISQSEPLPIVDYNQGFITR
VFNRIHHGSPYQHKSIRYLIFLDGFHEATCHADMIDLSDQLREQRKTFEYYYKMNDGVMT
KNLSEDELKTPIIC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4576.t1 Gene3D G3DSA:1.50.40.10 Mitochondrial carrier domain 1 283 2.2E-74
4 g4576.t1 PANTHER PTHR45624:SF10 MITOCHONDRIAL BASIC AMINO ACIDS TRANSPORTER 2 273 2.6E-93
5 g4576.t1 PANTHER PTHR45624 MITOCHONDRIAL BASIC AMINO ACIDS TRANSPORTER-RELATED 2 273 2.6E-93
10 g4576.t1 PRINTS PR00926 Mitochondrial carrier protein signature 4 17 2.2E-7
8 g4576.t1 PRINTS PR00926 Mitochondrial carrier protein signature 17 31 2.2E-7
9 g4576.t1 PRINTS PR00926 Mitochondrial carrier protein signature 106 124 2.2E-7
7 g4576.t1 PRINTS PR00926 Mitochondrial carrier protein signature 153 171 2.2E-7
6 g4576.t1 PRINTS PR00926 Mitochondrial carrier protein signature 193 215 2.2E-7
1 g4576.t1 Pfam PF00153 Mitochondrial carrier protein 4 86 5.5E-18
2 g4576.t1 Pfam PF00153 Mitochondrial carrier protein 91 180 2.4E-20
3 g4576.t1 Pfam PF00153 Mitochondrial carrier protein 184 276 6.7E-21
15 g4576.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 56 -
20 g4576.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 81 -
16 g4576.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 82 92 -
19 g4576.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 111 -
14 g4576.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 185 -
21 g4576.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 186 207 -
17 g4576.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 208 251 -
18 g4576.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 252 273 -
13 g4576.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 274 374 -
25 g4576.t1 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 1 86 21.762
26 g4576.t1 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 91 180 19.724
24 g4576.t1 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 184 272 25.409
11 g4576.t1 SUPERFAMILY SSF103506 Mitochondrial carrier 3 266 5.62E-75
23 g4576.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
22 g4576.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 205 -

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:0055085 transmembrane transport BP

KEGG

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