Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative MICAL-like protein 2.

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 g11954 g11954.t5 TSS g11954.t5 19774608 19774608
chr_1 g11954 g11954.t5 isoform g11954.t5 19775063 19776052
chr_1 g11954 g11954.t5 exon g11954.t5.exon1 19775063 19775437
chr_1 g11954 g11954.t5 cds g11954.t5.CDS1 19775173 19775437
chr_1 g11954 g11954.t5 exon g11954.t5.exon2 19775498 19775697
chr_1 g11954 g11954.t5 cds g11954.t5.CDS2 19775498 19775697
chr_1 g11954 g11954.t5 exon g11954.t5.exon3 19775762 19775908
chr_1 g11954 g11954.t5 cds g11954.t5.CDS3 19775762 19775908
chr_1 g11954 g11954.t5 exon g11954.t5.exon4 19775981 19776052
chr_1 g11954 g11954.t5 cds g11954.t5.CDS4 19775981 19776052
chr_1 g11954 g11954.t5 TTS g11954.t5 NA NA

Sequences

>g11954.t5 Gene=g11954 Length=794
CAACTGATTCGCTGCCATATCTCAACAAGTCATCACACGGAAAATGGAAAAGAAGAAAAG
GCAAAGCACCAACTTTACCTTTTGCTCTTCCACAGCGACGTGTTTTACAAATGTTGCCAT
TGCAAGAAATTCGTCATGAACTAGAAATCATCGAAGTGCAGCAGCAGGGATTAGAAAAGC
AAGGTGTTCAGCTAGAAAAAATGATAAGAGAACGTTGTGAAGGCGATAATCGTACAACTG
AAGAACTTTTAGAGCAATTACCCAATGCAAAGAATCCAAAGGAAGTTGAAGAACTCATAT
TACAATTATTTGAGTTAGTGAATGAAAAAAATGAGCTATTTAGACGTCAAGCAGAGTTGA
TGTATTTAAGGAGAGCCCATCGTCTTGAAGAAGAACAAGCGGATGTTGAATATGAAATAA
GAAAGTTAATGGCTCAACCTGAACATAATAAGACTGACTCAGATAAAGCTAGAGAAGAAG
CATTGATAGCGAGACTTGTGGAAATTGTTCAATTAAGAAATGAAGTTGTTGATTGTCTAG
AAATGGATCGATTGCGAGAAGCAGAAGAAGATTTGAGTATTAAACAAAGAATGGAAAGTC
ACACAGCTAAACTTGACCAAGAATATCTTAATCAAACACCAACAAAATTATCGAAGAAAG
AAAAGAAGAAACTAAAAGAGGCAAAAAAGATGAAAAACAAGAAACTCAATGATGCCGATA
AAGATTTAGATACCAGTGAAATGAAAGCAGAAACGGGCGAAAAAAAGAAGAAGAAGAAAA
AATTTTTGTTCTAA

>g11954.t5 Gene=g11954 Length=227
MLPLQEIRHELEIIEVQQQGLEKQGVQLEKMIRERCEGDNRTTEELLEQLPNAKNPKEVE
ELILQLFELVNEKNELFRRQAELMYLRRAHRLEEEQADVEYEIRKLMAQPEHNKTDSDKA
REEALIARLVEIVQLRNEVVDCLEMDRLREAEEDLSIKQRMESHTAKLDQEYLNQTPTKL
SKKEKKKLKEAKKMKNKKLNDADKDLDTSEMKAETGEKKKKKKKFLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11954.t5 Coils Coil Coil 4 24 -
8 g11954.t5 Coils Coil Coil 89 109 -
9 g11954.t5 Coils Coil Coil 185 205 -
6 g11954.t5 MobiDBLite mobidb-lite consensus disorder prediction 168 227 -
5 g11954.t5 MobiDBLite mobidb-lite consensus disorder prediction 194 221 -
2 g11954.t5 PANTHER PTHR23167:SF59 MICAL-LIKE 1A-RELATED 2 203 1.2E-56
3 g11954.t5 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 2 203 1.2E-56
1 g11954.t5 Pfam PF12130 Bivalent Mical/EHBP Rab binding domain 7 157 7.6E-48
10 g11954.t5 ProSiteProfiles PS51848 bMERB domain profile. 1 159 50.035
4 g11954.t5 SMART SM01203 DUF3585_4 1 159 3.3E-64

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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