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.t20 isoform g9997.t20 6487514 6488630
chr_1 g9997 g9997.t20 exon g9997.t20.exon1 6487514 6487789
chr_1 g9997 g9997.t20 cds g9997.t20.CDS1 6487531 6487789
chr_1 g9997 g9997.t20 exon g9997.t20.exon2 6487870 6488243
chr_1 g9997 g9997.t20 cds g9997.t20.CDS2 6487870 6488243
chr_1 g9997 g9997.t20 exon g9997.t20.exon3 6488425 6488542
chr_1 g9997 g9997.t20 cds g9997.t20.CDS3 6488425 6488542
chr_1 g9997 g9997.t20 exon g9997.t20.exon4 6488604 6488630
chr_1 g9997 g9997.t20 cds g9997.t20.CDS4 6488604 6488629
chr_1 g9997 g9997.t20 TTS g9997.t20 6489490 6489490
chr_1 g9997 g9997.t20 TSS g9997.t20 NA NA

Sequences

>g9997.t20 Gene=g9997 Length=795
CTATATATTTGCTATCAATGAAAGCTGTTCCAATTTATATCGGAGTCATAATCACAATTT
TTGACACATTTACTTTCCTTTTAATTGACAAATATGGACTTAGAAAATTAGAATTTTTCT
TTGGATTTCTTATCACTGTTATGGCAGTCACATTTGGATATGAATTTTTTGTTGTGAAGC
CAGAAATCACCGAAATAATCAAAGGAGCTGCAATTCCATGGTGTGCCGATTGTGATAGTA
GAGCATTATTGCAAGCTGTGGGAATTGTTGGAGCTGTTATTATGCCACACAATCTTTATC
TTCATTCAGCTTTAGTAAAATCAAGAAAAGTTGATCGACATCAGCCATCGAAAGTTAGAG
AAGCCAATTATTATTTCTTCATTGAAGCATCTATTGCACTTTTTGTTTCGTTCTTGATCA
ACGTCTTTGTTGTTGCTGTTTTTGCTCACGGTCTTAATGGAAAGACCAATGAGGATGTAG
TTAATGAATGTTTTAACAAGACAATTTATGATGAAGCCAAAGCAATTTTTACTGGTGATG
AATTAGATGTCGATATTTATAAAGGTGGAATATTTTTGGGATGTACATTTGGTATTGTTG
CACTCTATGTGTGGGCAATTGGGATTCTTGCTGCTGGACAGAGTTCTACTATGACAGGAA
CATATAGTGGACAATTTGCAATGGAAGGTTTTCTCAATCTGAAATGGTCTAGATGGCATC
GTGTTCTTGTTACCCGAATGATTGCAGTTGTTCCAACATTTGTAGTGGCATTTTATAGTG
AAATTGAGCAAGTAA

>g9997.t20 Gene=g9997 Length=259
MKAVPIYIGVIITIFDTFTFLLIDKYGLRKLEFFFGFLITVMAVTFGYEFFVVKPEITEI
IKGAAIPWCADCDSRALLQAVGIVGAVIMPHNLYLHSALVKSRKVDRHQPSKVREANYYF
FIEASIALFVSFLINVFVVAVFAHGLNGKTNEDVVNECFNKTIYDEAKAIFTGDELDVDI
YKGGIFLGCTFGIVALYVWAIGILAAGQSSTMTGTYSGQFAMEGFLNLKWSRWHRVLVTR
MIAVVPTFVVAFYSEIEQV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g9997.t20 PANTHER PTHR11706:SF40 NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 2 3 258 6.8E-120
3 g9997.t20 PANTHER PTHR11706 SOLUTE CARRIER PROTEIN FAMILY 11 MEMBER 3 258 6.8E-120
7 g9997.t20 PRINTS PR00447 Natural resistance-associated macrophage protein signature 3 22 5.3E-60
4 g9997.t20 PRINTS PR00447 Natural resistance-associated macrophage protein signature 28 49 5.3E-60
8 g9997.t20 PRINTS PR00447 Natural resistance-associated macrophage protein signature 80 103 5.3E-60
6 g9997.t20 PRINTS PR00447 Natural resistance-associated macrophage protein signature 207 226 5.3E-60
5 g9997.t20 PRINTS PR00447 Natural resistance-associated macrophage protein signature 235 252 5.3E-60
1 g9997.t20 Pfam PF01566 Natural resistance-associated macrophage protein 4 255 5.6E-71
20 g9997.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
26 g9997.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 23 -
16 g9997.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 24 34 -
25 g9997.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 53 -
22 g9997.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 54 75 -
24 g9997.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 95 -
17 g9997.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 96 115 -
27 g9997.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 143 -
21 g9997.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 144 184 -
23 g9997.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 185 206 -
18 g9997.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 207 236 -
28 g9997.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 237 254 -
19 g9997.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 255 259 -
15 g9997.t20 TIGRFAM TIGR01197 nramp: metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family 3 257 5.4E-93
12 g9997.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 23 -
14 g9997.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 30 52 -
11 g9997.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 76 98 -
10 g9997.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 119 141 -
9 g9997.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 184 206 -
13 g9997.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 236 253 -

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

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