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.t7 TSS g9997.t7 6485973 6485973
chr_1 g9997 g9997.t7 isoform g9997.t7 6486145 6489203
chr_1 g9997 g9997.t7 exon g9997.t7.exon1 6486145 6486309
chr_1 g9997 g9997.t7 exon g9997.t7.exon2 6486766 6486830
chr_1 g9997 g9997.t7 cds g9997.t7.CDS1 6486815 6486830
chr_1 g9997 g9997.t7 exon g9997.t7.exon3 6487198 6487453
chr_1 g9997 g9997.t7 cds g9997.t7.CDS2 6487198 6487453
chr_1 g9997 g9997.t7 exon g9997.t7.exon4 6487506 6487789
chr_1 g9997 g9997.t7 cds g9997.t7.CDS3 6487506 6487789
chr_1 g9997 g9997.t7 exon g9997.t7.exon5 6487870 6488243
chr_1 g9997 g9997.t7 cds g9997.t7.CDS4 6487870 6488243
chr_1 g9997 g9997.t7 exon g9997.t7.exon6 6488425 6488542
chr_1 g9997 g9997.t7 cds g9997.t7.CDS5 6488425 6488542
chr_1 g9997 g9997.t7 exon g9997.t7.exon7 6488604 6488861
chr_1 g9997 g9997.t7 cds g9997.t7.CDS6 6488604 6488861
chr_1 g9997 g9997.t7 exon g9997.t7.exon8 6488925 6489090
chr_1 g9997 g9997.t7 cds g9997.t7.CDS7 6488925 6489090
chr_1 g9997 g9997.t7 exon g9997.t7.exon9 6489188 6489203
chr_1 g9997 g9997.t7 cds g9997.t7.CDS8 6489188 6489203
chr_1 g9997 g9997.t7 TTS g9997.t7 6489490 6489490

Sequences

>g9997.t7 Gene=g9997 Length=1702
ATGGCTGAAAGTGATGAACGACATCACGATGAAAGTGATAGAACAGTTCCTTATATAAAT
TACGAGGACCATTTTGAAGATGAGGAGGATGATCTCGGTCCTGAATTCTCAACATATTTT
TCAGACCAAAAAGTTGAAATTCCAACATTTCCTGATGACGATAAAGTCGGATTCAGTTTT
AGAAAATTATGGGTAAATAAAATTTATTTCTATCATGAAAATTTTAATATCTTATCTCGA
TCCTGGAAATATTGAAAGCGATTTACAATCTGGCTTTGTTGCAAAATATAAATTGCTATG
GGTTTTGATGTGGGCAACAATATTAGGCTTAGTAATGCAACGTTTGGCTATGAGAATTGG
TGTCGTTACTGGCCTTCATTTGGCTGAAATGTGCAATCGACAGTACAAGAAATTTCCTCG
ACTTATTTTATGGATTATGATAGAAATTGCTATAATTGGTAGTGATATGCAGGAAGTTAT
AGGAACAGCAATTGCTATATATTTGCTATCAATGAAAGCTGTTCCAATTTATATCGGAGT
CATAATCACAATTTTTGACACATTTACTTTCCTTTTAATTGACAAATATGGACTTAGAAA
ATTAGAATTTTTCTTTGGATTTCTTATCACTGTTATGGCAGTCACATTTGGATATGAATT
TTTTGTTGTGAAGCCAGAAATCACCGAAATAATCAAAGGAGCTGCAATTCCATGGTGTGC
CGATTGTGATAGTAGAGCATTATTGCAAGCTGTGGGAATTGTTGGAGCTGTTATTATGCC
ACACAATCTTTATCTTCATTCAGCTTTAGTAAAATCAAGAAAAGTTGATCGACATCAGCC
ATCGAAAGTTAGAGAAGCCAATTATTATTTCTTCATTGAAGCATCTATTGCACTTTTTGT
TTCGTTCTTGATCAACGTCTTTGTTGTTGCTGTTTTTGCTCACGGTCTTAATGGAAAGAC
CAATGAGGATGTAGTTAATGAATGTTTTAACAAGACAATTTATGATGAAGCCAAAGCAAT
TTTTACTGGTGATGAATTAGATGTCGATATTTATAAAGGTGGAATATTTTTGGGATGTAC
ATTTGGTATTGTTGCACTCTATGTGTGGGCAATTGGGATTCTTGCTGCTGGACAGAGTTC
TACTATGACAGGAACATATAGTGGACAATTTGCAATGGAAGGTTTTCTCAATCTGAAATG
GTCTAGATGGCATCGTGTTCTTGTTACCCGAATGATTGCAGTTGTTCCAACATTTGTAGT
GGCATTTTATAGTGAAATTGAGCAAGTAACTAAAATGAATGACTACTTAAATGCAATTAT
GGCATTGCAACTTCCATTTGCAACAATTCCAACTATTGCATTTTCATCATCGGTTGCAAT
TATGGGTGAATTCGTAAATGGCTTTTGGAATAAACTCATATCAATTTTACTTAGCATCAC
AGTGATAGGAATCAATTTGACGTTTATAATTAGTCGTTTAGAGCTATCACATGTGTCAGG
ATGGTTGACAATCTTTATTGTAATATTCTCTATTCTCTATGTAATTTTCTGTATATATTT
GGTGATTCATATGATTTGCATGCTTAAACCCGATTCACGAATAGCGAGATCGGTATTTGC
AAGAAGGTTTGTACTAAAAACGGCGAGCTCATCAGCTGATGCTCATGGTGATAGTTCGGT
TACAAGACCACTCGTTTATTAG

>g9997.t7 Gene=g9997 Length=495
MKILISYLDPGNIESDLQSGFVAKYKLLWVLMWATILGLVMQRLAMRIGVVTGLHLAEMC
NRQYKKFPRLILWIMIEIAIIGSDMQEVIGTAIAIYLLSMKAVPIYIGVIITIFDTFTFL
LIDKYGLRKLEFFFGFLITVMAVTFGYEFFVVKPEITEIIKGAAIPWCADCDSRALLQAV
GIVGAVIMPHNLYLHSALVKSRKVDRHQPSKVREANYYFFIEASIALFVSFLINVFVVAV
FAHGLNGKTNEDVVNECFNKTIYDEAKAIFTGDELDVDIYKGGIFLGCTFGIVALYVWAI
GILAAGQSSTMTGTYSGQFAMEGFLNLKWSRWHRVLVTRMIAVVPTFVVAFYSEIEQVTK
MNDYLNAIMALQLPFATIPTIAFSSSVAIMGEFVNGFWNKLISILLSITVIGINLTFIIS
RLELSHVSGWLTIFIVIFSILYVIFCIYLVIHMICMLKPDSRIARSVFARRFVLKTASSS
ADAHGDSSVTRPLVY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g9997.t7 Hamap MF_00221 Divalent metal cation transporter MntH [mntH]. 1 422 34.729141
2 g9997.t7 PANTHER PTHR11706:SF40 NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 2 4 462 3.0E-199
3 g9997.t7 PANTHER PTHR11706 SOLUTE CARRIER PROTEIN FAMILY 11 MEMBER 4 462 3.0E-199
9 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 72 98 3.4E-84
8 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 102 121 3.4E-84
7 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 127 148 3.4E-84
10 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 179 202 3.4E-84
5 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 306 325 3.4E-84
11 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 334 351 3.4E-84
6 g9997.t7 PRINTS PR00447 Natural resistance-associated macrophage protein signature 366 385 3.4E-84
1 g9997.t7 Pfam PF01566 Natural resistance-associated macrophage protein 13 396 2.8E-115
33 g9997.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
45 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 50 -
25 g9997.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 51 69 -
39 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 70 97 -
30 g9997.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 98 102 -
38 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 122 -
26 g9997.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 123 133 -
44 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 152 -
35 g9997.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 153 174 -
41 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 175 194 -
27 g9997.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 195 214 -
42 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 215 242 -
34 g9997.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 243 283 -
36 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 284 305 -
24 g9997.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 306 335 -
46 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 336 355 -
32 g9997.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 356 366 -
37 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 367 389 -
28 g9997.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 390 400 -
40 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 401 419 -
31 g9997.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 420 430 -
43 g9997.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 431 455 -
29 g9997.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 456 495 -
23 g9997.t7 TIGRFAM TIGR01197 nramp: metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family 4 390 6.6E-154
20 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 29 51 -
18 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 71 93 -
16 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 103 122 -
19 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
21 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 175 197 -
15 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -
12 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 283 305 -
17 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 335 353 -
22 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 368 390 -
14 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 397 419 -
13 g9997.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 429 451 -

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