Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein Malvolio.

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 g9997 g9997.t11 TSS g9997.t11 6485973 6485973
chr_1 g9997 g9997.t11 isoform g9997.t11 6486145 6489203
chr_1 g9997 g9997.t11 exon g9997.t11.exon1 6486145 6486309
chr_1 g9997 g9997.t11 exon g9997.t11.exon2 6486766 6486792
chr_1 g9997 g9997.t11 cds g9997.t11.CDS1 6486789 6486792
chr_1 g9997 g9997.t11 exon g9997.t11.exon3 6487198 6487453
chr_1 g9997 g9997.t11 cds g9997.t11.CDS2 6487198 6487453
chr_1 g9997 g9997.t11 exon g9997.t11.exon4 6487506 6487789
chr_1 g9997 g9997.t11 cds g9997.t11.CDS3 6487506 6487789
chr_1 g9997 g9997.t11 exon g9997.t11.exon5 6487870 6488243
chr_1 g9997 g9997.t11 cds g9997.t11.CDS4 6487870 6488243
chr_1 g9997 g9997.t11 exon g9997.t11.exon6 6488425 6488542
chr_1 g9997 g9997.t11 cds g9997.t11.CDS5 6488425 6488542
chr_1 g9997 g9997.t11 exon g9997.t11.exon7 6488604 6488861
chr_1 g9997 g9997.t11 cds g9997.t11.CDS6 6488604 6488861
chr_1 g9997 g9997.t11 exon g9997.t11.exon8 6488925 6489090
chr_1 g9997 g9997.t11 cds g9997.t11.CDS7 6488925 6489090
chr_1 g9997 g9997.t11 exon g9997.t11.exon9 6489188 6489203
chr_1 g9997 g9997.t11 cds g9997.t11.CDS8 6489188 6489203
chr_1 g9997 g9997.t11 TTS g9997.t11 6489490 6489490

Sequences

>g9997.t11 Gene=g9997 Length=1664
ATGGCTGAAAGTGATGAACGACATCACGATGAAAGTGATAGAACAGTTCCTTATATAAAT
TACGAGGACCATTTTGAAGATGAGGAGGATGATCTCGGTCCTGAATTCTCAACATATTTT
TCAGACCAAAAAGTTGAAATTCCAACATTTCCTGATGACGATAAAGTCGGATTCAGTTTT
AGAAAATTATGGCTTATCTCGATCCTGGAAATATTGAAAGCGATTTACAATCTGGCTTTG
TTGCAAAATATAAATTGCTATGGGTTTTGATGTGGGCAACAATATTAGGCTTAGTAATGC
AACGTTTGGCTATGAGAATTGGTGTCGTTACTGGCCTTCATTTGGCTGAAATGTGCAATC
GACAGTACAAGAAATTTCCTCGACTTATTTTATGGATTATGATAGAAATTGCTATAATTG
GTAGTGATATGCAGGAAGTTATAGGAACAGCAATTGCTATATATTTGCTATCAATGAAAG
CTGTTCCAATTTATATCGGAGTCATAATCACAATTTTTGACACATTTACTTTCCTTTTAA
TTGACAAATATGGACTTAGAAAATTAGAATTTTTCTTTGGATTTCTTATCACTGTTATGG
CAGTCACATTTGGATATGAATTTTTTGTTGTGAAGCCAGAAATCACCGAAATAATCAAAG
GAGCTGCAATTCCATGGTGTGCCGATTGTGATAGTAGAGCATTATTGCAAGCTGTGGGAA
TTGTTGGAGCTGTTATTATGCCACACAATCTTTATCTTCATTCAGCTTTAGTAAAATCAA
GAAAAGTTGATCGACATCAGCCATCGAAAGTTAGAGAAGCCAATTATTATTTCTTCATTG
AAGCATCTATTGCACTTTTTGTTTCGTTCTTGATCAACGTCTTTGTTGTTGCTGTTTTTG
CTCACGGTCTTAATGGAAAGACCAATGAGGATGTAGTTAATGAATGTTTTAACAAGACAA
TTTATGATGAAGCCAAAGCAATTTTTACTGGTGATGAATTAGATGTCGATATTTATAAAG
GTGGAATATTTTTGGGATGTACATTTGGTATTGTTGCACTCTATGTGTGGGCAATTGGGA
TTCTTGCTGCTGGACAGAGTTCTACTATGACAGGAACATATAGTGGACAATTTGCAATGG
AAGGTTTTCTCAATCTGAAATGGTCTAGATGGCATCGTGTTCTTGTTACCCGAATGATTG
CAGTTGTTCCAACATTTGTAGTGGCATTTTATAGTGAAATTGAGCAAGTAACTAAAATGA
ATGACTACTTAAATGCAATTATGGCATTGCAACTTCCATTTGCAACAATTCCAACTATTG
CATTTTCATCATCGGTTGCAATTATGGGTGAATTCGTAAATGGCTTTTGGAATAAACTCA
TATCAATTTTACTTAGCATCACAGTGATAGGAATCAATTTGACGTTTATAATTAGTCGTT
TAGAGCTATCACATGTGTCAGGATGGTTGACAATCTTTATTGTAATATTCTCTATTCTCT
ATGTAATTTTCTGTATATATTTGGTGATTCATATGATTTGCATGCTTAAACCCGATTCAC
GAATAGCGAGATCGGTATTTGCAAGAAGGTTTGTACTAAAAACGGCGAGCTCATCAGCTG
ATGCTCATGGTGATAGTTCGGTTACAAGACCACTCGTTTATTAG

>g9997.t11 Gene=g9997 Length=491
MAYLDPGNIESDLQSGFVAKYKLLWVLMWATILGLVMQRLAMRIGVVTGLHLAEMCNRQY
KKFPRLILWIMIEIAIIGSDMQEVIGTAIAIYLLSMKAVPIYIGVIITIFDTFTFLLIDK
YGLRKLEFFFGFLITVMAVTFGYEFFVVKPEITEIIKGAAIPWCADCDSRALLQAVGIVG
AVIMPHNLYLHSALVKSRKVDRHQPSKVREANYYFFIEASIALFVSFLINVFVVAVFAHG
LNGKTNEDVVNECFNKTIYDEAKAIFTGDELDVDIYKGGIFLGCTFGIVALYVWAIGILA
AGQSSTMTGTYSGQFAMEGFLNLKWSRWHRVLVTRMIAVVPTFVVAFYSEIEQVTKMNDY
LNAIMALQLPFATIPTIAFSSSVAIMGEFVNGFWNKLISILLSITVIGINLTFIISRLEL
SHVSGWLTIFIVIFSILYVIFCIYLVIHMICMLKPDSRIARSVFARRFVLKTASSSADAH
GDSSVTRPLVY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g9997.t11 Hamap MF_00221 Divalent metal cation transporter MntH [mntH]. 1 418 34.660103
2 g9997.t11 PANTHER PTHR11706:SF40 NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 2 1 458 2.8E-199
3 g9997.t11 PANTHER PTHR11706 SOLUTE CARRIER PROTEIN FAMILY 11 MEMBER 1 458 2.8E-199
5 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 68 94 3.2E-84
9 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 98 117 3.2E-84
11 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 123 144 3.2E-84
8 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 175 198 3.2E-84
7 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 302 321 3.2E-84
10 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 330 347 3.2E-84
6 g9997.t11 PRINTS PR00447 Natural resistance-associated macrophage protein signature 362 381 3.2E-84
1 g9997.t11 Pfam PF01566 Natural resistance-associated macrophage protein 9 392 2.8E-115
35 g9997.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 22 -
43 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 23 46 -
29 g9997.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 65 -
36 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 93 -
31 g9997.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 94 98 -
46 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 118 -
26 g9997.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 119 129 -
41 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 148 -
33 g9997.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 170 -
38 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 190 -
28 g9997.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 191 210 -
45 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 211 238 -
32 g9997.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 239 279 -
37 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 280 301 -
27 g9997.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 302 331 -
40 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 332 351 -
30 g9997.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 352 362 -
42 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 363 385 -
24 g9997.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 386 396 -
39 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 397 415 -
34 g9997.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 416 426 -
44 g9997.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 427 451 -
25 g9997.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 452 491 -
23 g9997.t11 TIGRFAM TIGR01197 nramp: metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family 1 386 9.4E-154
15 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
17 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
21 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 117 -
20 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -
18 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
19 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 214 236 -
16 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 279 301 -
14 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 331 349 -
22 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 364 386 -
13 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 393 415 -
12 g9997.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 425 447 -

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:0016020 membrane CC
GO:0046873 metal ion transmembrane transporter activity MF
GO:0030001 metal ion transport BP

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.

Raw TPM values