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.t18 TSS g9997.t18 6485973 6485973
chr_1 g9997 g9997.t18 isoform g9997.t18 6486145 6489203
chr_1 g9997 g9997.t18 exon g9997.t18.exon1 6486145 6486351
chr_1 g9997 g9997.t18 cds g9997.t18.CDS1 6486345 6486351
chr_1 g9997 g9997.t18 exon g9997.t18.exon2 6487198 6487453
chr_1 g9997 g9997.t18 cds g9997.t18.CDS2 6487198 6487453
chr_1 g9997 g9997.t18 exon g9997.t18.exon3 6487506 6487789
chr_1 g9997 g9997.t18 cds g9997.t18.CDS3 6487506 6487789
chr_1 g9997 g9997.t18 exon g9997.t18.exon4 6487870 6488243
chr_1 g9997 g9997.t18 cds g9997.t18.CDS4 6487870 6488243
chr_1 g9997 g9997.t18 exon g9997.t18.exon5 6488425 6488542
chr_1 g9997 g9997.t18 cds g9997.t18.CDS5 6488425 6488542
chr_1 g9997 g9997.t18 exon g9997.t18.exon6 6488604 6488861
chr_1 g9997 g9997.t18 cds g9997.t18.CDS6 6488604 6488861
chr_1 g9997 g9997.t18 exon g9997.t18.exon7 6488925 6489090
chr_1 g9997 g9997.t18 cds g9997.t18.CDS7 6488925 6489090
chr_1 g9997 g9997.t18 exon g9997.t18.exon8 6489188 6489203
chr_1 g9997 g9997.t18 cds g9997.t18.CDS8 6489188 6489203
chr_1 g9997 g9997.t18 TTS g9997.t18 6489490 6489490

Sequences

>g9997.t18 Gene=g9997 Length=1679
ATGGCTGAAAGTGATGAACGACATCACGATGAAAGTGATAGAACAGTTCCTTATATAAAT
TACGAGGACCATTTTGAAGATGAGGAGGATGATCTCGGTCCTGAATTCTCAACATATTTT
TCAGACCAAAAAGTTGAAATTCCAACATTTCCTGATGACGATAAAGTAATTTTGAATATT
TTAACTCATAGTGAAACTTAATGTCATCTTATCTCGATCCTGGAAATATTGAAAGCGATT
TACAATCTGGCTTTGTTGCAAAATATAAATTGCTATGGGTTTTGATGTGGGCAACAATAT
TAGGCTTAGTAATGCAACGTTTGGCTATGAGAATTGGTGTCGTTACTGGCCTTCATTTGG
CTGAAATGTGCAATCGACAGTACAAGAAATTTCCTCGACTTATTTTATGGATTATGATAG
AAATTGCTATAATTGGTAGTGATATGCAGGAAGTTATAGGAACAGCAATTGCTATATATT
TGCTATCAATGAAAGCTGTTCCAATTTATATCGGAGTCATAATCACAATTTTTGACACAT
TTACTTTCCTTTTAATTGACAAATATGGACTTAGAAAATTAGAATTTTTCTTTGGATTTC
TTATCACTGTTATGGCAGTCACATTTGGATATGAATTTTTTGTTGTGAAGCCAGAAATCA
CCGAAATAATCAAAGGAGCTGCAATTCCATGGTGTGCCGATTGTGATAGTAGAGCATTAT
TGCAAGCTGTGGGAATTGTTGGAGCTGTTATTATGCCACACAATCTTTATCTTCATTCAG
CTTTAGTAAAATCAAGAAAAGTTGATCGACATCAGCCATCGAAAGTTAGAGAAGCCAATT
ATTATTTCTTCATTGAAGCATCTATTGCACTTTTTGTTTCGTTCTTGATCAACGTCTTTG
TTGTTGCTGTTTTTGCTCACGGTCTTAATGGAAAGACCAATGAGGATGTAGTTAATGAAT
GTTTTAACAAGACAATTTATGATGAAGCCAAAGCAATTTTTACTGGTGATGAATTAGATG
TCGATATTTATAAAGGTGGAATATTTTTGGGATGTACATTTGGTATTGTTGCACTCTATG
TGTGGGCAATTGGGATTCTTGCTGCTGGACAGAGTTCTACTATGACAGGAACATATAGTG
GACAATTTGCAATGGAAGGTTTTCTCAATCTGAAATGGTCTAGATGGCATCGTGTTCTTG
TTACCCGAATGATTGCAGTTGTTCCAACATTTGTAGTGGCATTTTATAGTGAAATTGAGC
AAGTAACTAAAATGAATGACTACTTAAATGCAATTATGGCATTGCAACTTCCATTTGCAA
CAATTCCAACTATTGCATTTTCATCATCGGTTGCAATTATGGGTGAATTCGTAAATGGCT
TTTGGAATAAACTCATATCAATTTTACTTAGCATCACAGTGATAGGAATCAATTTGACGT
TTATAATTAGTCGTTTAGAGCTATCACATGTGTCAGGATGGTTGACAATCTTTATTGTAA
TATTCTCTATTCTCTATGTAATTTTCTGTATATATTTGGTGATTCATATGATTTGCATGC
TTAAACCCGATTCACGAATAGCGAGATCGGTATTTGCAAGAAGGTTTGTACTAAAAACGG
CGAGCTCATCAGCTGATGCTCATGGTGATAGTTCGGTTACAAGACCACTCGTTTATTAG

>g9997.t18 Gene=g9997 Length=492
MSSYLDPGNIESDLQSGFVAKYKLLWVLMWATILGLVMQRLAMRIGVVTGLHLAEMCNRQ
YKKFPRLILWIMIEIAIIGSDMQEVIGTAIAIYLLSMKAVPIYIGVIITIFDTFTFLLID
KYGLRKLEFFFGFLITVMAVTFGYEFFVVKPEITEIIKGAAIPWCADCDSRALLQAVGIV
GAVIMPHNLYLHSALVKSRKVDRHQPSKVREANYYFFIEASIALFVSFLINVFVVAVFAH
GLNGKTNEDVVNECFNKTIYDEAKAIFTGDELDVDIYKGGIFLGCTFGIVALYVWAIGIL
AAGQSSTMTGTYSGQFAMEGFLNLKWSRWHRVLVTRMIAVVPTFVVAFYSEIEQVTKMND
YLNAIMALQLPFATIPTIAFSSSVAIMGEFVNGFWNKLISILLSITVIGINLTFIISRLE
LSHVSGWLTIFIVIFSILYVIFCIYLVIHMICMLKPDSRIARSVFARRFVLKTASSSADA
HGDSSVTRPLVY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g9997.t18 Hamap MF_00221 Divalent metal cation transporter MntH [mntH]. 1 419 34.557926
2 g9997.t18 PANTHER PTHR11706:SF40 NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 2 3 459 6.3E-199
3 g9997.t18 PANTHER PTHR11706 SOLUTE CARRIER PROTEIN FAMILY 11 MEMBER 3 459 6.3E-199
11 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 69 95 3.3E-84
7 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 99 118 3.3E-84
6 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 124 145 3.3E-84
5 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 176 199 3.3E-84
9 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 303 322 3.3E-84
8 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 331 348 3.3E-84
10 g9997.t18 PRINTS PR00447 Natural resistance-associated macrophage protein signature 363 382 3.3E-84
1 g9997.t18 Pfam PF01566 Natural resistance-associated macrophage protein 10 393 2.8E-115
35 g9997.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 23 -
41 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 47 -
27 g9997.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 66 -
40 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 94 -
34 g9997.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 95 99 -
36 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 119 -
26 g9997.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 130 -
37 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 149 -
32 g9997.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 150 171 -
46 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 191 -
28 g9997.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 192 211 -
38 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 212 239 -
30 g9997.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 240 280 -
43 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 281 302 -
25 g9997.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 303 332 -
44 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 333 352 -
33 g9997.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 353 363 -
45 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 364 386 -
24 g9997.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 387 397 -
42 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 398 416 -
31 g9997.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 417 427 -
39 g9997.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 428 452 -
29 g9997.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 453 492 -
23 g9997.t18 TIGRFAM TIGR01197 nramp: metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family 3 387 2.3E-153
15 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
20 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 89 -
21 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 118 -
17 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 127 149 -
16 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 172 194 -
19 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 215 237 -
22 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 280 302 -
13 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 332 350 -
12 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 365 387 -
18 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 394 416 -
14 g9997.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 426 448 -

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