Gene loci information

Transcript annotation

  • This transcript has been annotated as Vanin-like protein 1.

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_3 g2572 g2572.t1 TTS g2572.t1 18809486 18809486
chr_3 g2572 g2572.t1 isoform g2572.t1 18809766 18811540
chr_3 g2572 g2572.t1 exon g2572.t1.exon1 18809766 18810550
chr_3 g2572 g2572.t1 cds g2572.t1.CDS1 18809766 18810550
chr_3 g2572 g2572.t1 exon g2572.t1.exon2 18810681 18811431
chr_3 g2572 g2572.t1 cds g2572.t1.CDS2 18810681 18811431
chr_3 g2572 g2572.t1 exon g2572.t1.exon3 18811490 18811540
chr_3 g2572 g2572.t1 cds g2572.t1.CDS3 18811490 18811540
chr_3 g2572 g2572.t1 TSS g2572.t1 18811588 18811588

Sequences

>g2572.t1 Gene=g2572 Length=1587
ATGTATTTGTTAAAATTTTTGCTACTCATTTTAATCAAAGCTTCATTACAGGCATCAACA
CCATTGTCTGCAACTTATGAAGCTGGTGTTGTAGAAATTCATTTTGGAAACCGAGCAAAT
AAAAGTTCAAATGAAATTTTGAATGAACAATTAGATTTGTACTTGAATATTATGGAAAAT
GCACCATCAAATTTGGACATTATTGTTTTTCCTGAAAGCACACTCAATAGCATGGCAACA
GCATCAGAAATTCCTGAACCGGAAGATAATATTTCACCATGTGATGATGACAAATATAAA
GTTGAAGATTTAATTAAACAAATTTCGTGTTCAGCAAATAAGCATAAAAGATATGTCGTT
ATTAATATTACAACTAAAACAAAATGTCCAGATGCAGATATGATTGCGAATAAAGATCCA
CGTAAATGTGAAGCACGTGAAGATGGTTTAAGTTATTACAACACAAATGTCGTTTTTGAT
CGAAATGGAACTGTAATTTCACGTTATCGAAAATTTAATTTGTTTGGCGAGAAAGTTGAT
AAGCCATACAAGCCTTCAATGGTTACATTTGATACAGATTTTGGTGTGAAGTTTGGACAC
TTTATCTGCTTTGATTTGATGTTCCGATATCCAGCTGTTGATTTAGTGCGTAATCATAAC
GTGACTGATATCATTTTTCCAACAATGTGGTTTAGTGAATTGCCTTATCTGTCTGCAGTT
CAAGTTCAACAAAACTGGGCTTTTTCGAATAATGTAAATTTCTTAGCAGCAGGAGCAAAT
AATGTCGCCATCGGATCAACAGGTTCAGGAATTTATGGTGGTAAAAAAGGAGCTTATGTA
GCTGATATGGCAGCAACTTCAAAAAGTCATCTTTATACAGCAACTGTTTATAAGATTAAA
AATTTTCAACAAAATGATAACATTATAATTCAGCATGATGTTAAAAAATATACAAAAGAT
GAAATGAAAAATTTGTATTTGAAACGTGATCAATTGGATGTTTATCAATTCAAATTCTTG
AATGATAGCAATGGTGATCATTCATATGATGAAAAATTGTGTGAAAGTGAAACATGCTGC
AATATAAAAGTCAATTATACAGTAACATATTCTGATAGAATTCCACATTATCAATATACT
CTTGCATTTTATCATGGAAAAAGAACTTTCGATGGATTTGCAAATGGTGGTTCTGTTGTT
TGCACAATTTTAGCATGTCAATCTACAAATATTTCTACTTGTGGAGTGCGGAATGAAGAA
TTAGATAGCATTCATATTTGGAGTTCAATTGAAATTGATGCAGAATTGCCAACGAAAGAC
GATCAATTTTTATATTTACCAACTTCACTAGATACTTCAATTTTGCCTTTACAACCTGAA
TTTTTTGAATATGAAACAAAAGAAACTGCAGCAAGTGATACAATCAAAATAACAATGAAA
TTAAACTCACATGCTGATAGTTTAATTACATTTGGAATTTATGGAAGAGATTTCAATTTA
GATGAAAATAGTGGATCAATTCACAAGATTTCTATAATTCTCATGTTAATTTTATTATTG
TTTGCTTTCTTAACAGTCTCTATATAA

>g2572.t1 Gene=g2572 Length=528
MYLLKFLLLILIKASLQASTPLSATYEAGVVEIHFGNRANKSSNEILNEQLDLYLNIMEN
APSNLDIIVFPESTLNSMATASEIPEPEDNISPCDDDKYKVEDLIKQISCSANKHKRYVV
INITTKTKCPDADMIANKDPRKCEAREDGLSYYNTNVVFDRNGTVISRYRKFNLFGEKVD
KPYKPSMVTFDTDFGVKFGHFICFDLMFRYPAVDLVRNHNVTDIIFPTMWFSELPYLSAV
QVQQNWAFSNNVNFLAAGANNVAIGSTGSGIYGGKKGAYVADMAATSKSHLYTATVYKIK
NFQQNDNIIIQHDVKKYTKDEMKNLYLKRDQLDVYQFKFLNDSNGDHSYDEKLCESETCC
NIKVNYTVTYSDRIPHYQYTLAFYHGKRTFDGFANGGSVVCTILACQSTNISTCGVRNEE
LDSIHIWSSIEIDAELPTKDDQFLYLPTSLDTSILPLQPEFFEYETKETAASDTIKITMK
LNSHADSLITFGIYGRDFNLDENSGSIHKISIILMLILLLFAFLTVSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2572.t1 Gene3D G3DSA:3.60.110.10 - 12 303 5.5E-69
3 g2572.t1 PANTHER PTHR10609:SF14 BIOTINIDASE 5 519 7.8E-122
4 g2572.t1 PANTHER PTHR10609 BIOTINIDASE-RELATED 5 519 7.8E-122
2 g2572.t1 Pfam PF00795 Carbon-nitrogen hydrolase 57 239 8.5E-12
1 g2572.t1 Pfam PF19018 Vanin C-terminal domain 326 501 5.2E-33
11 g2572.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 24 -
12 g2572.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
13 g2572.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 16 -
15 g2572.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 24 -
10 g2572.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 25 505 -
14 g2572.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 506 526 -
9 g2572.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 527 528 -
18 g2572.t1 ProSiteProfiles PS50263 Carbon-nitrogen hydrolase domain profile. 26 298 34.476
5 g2572.t1 SUPERFAMILY SSF56317 Carbon-nitrogen hydrolase 49 274 9.68E-32
7 g2572.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -
16 g2572.t1 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 18 -
6 g2572.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 23 -
17 g2572.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 505 527 -

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:0006807 nitrogen compound metabolic process 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