Gene loci information

Transcript annotation

  • This transcript has been annotated as Lambda-crystallin-like protein.

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_2 g8532 g8532.t7 isoform g8532.t7 31139101 31139967
chr_2 g8532 g8532.t7 exon g8532.t7.exon1 31139101 31139426
chr_2 g8532 g8532.t7 cds g8532.t7.CDS1 31139173 31139426
chr_2 g8532 g8532.t7 exon g8532.t7.exon2 31139487 31139701
chr_2 g8532 g8532.t7 cds g8532.t7.CDS2 31139487 31139701
chr_2 g8532 g8532.t7 exon g8532.t7.exon3 31139756 31139967
chr_2 g8532 g8532.t7 cds g8532.t7.CDS3 31139756 31139967
chr_2 g8532 g8532.t7 TTS g8532.t7 31140081 31140081
chr_2 g8532 g8532.t7 TSS g8532.t7 NA NA

Sequences

>g8532.t7 Gene=g8532 Length=753
ACTGCAAAACAGCAATATAGCTGTATTTCAGGATGCACTGATATCAAAGAAGCTGTAACA
GGAGCTTTTTTTATGCAAGAGTGTGTCCCAGAAAATATTGAATTGAAGAAAAAATTGTAC
AAACAATTGGATGAAATTGTTGATGATAAAATCATTATTTCTTCATCAACTTCGACATTT
ATGCCTTCTATTTTCTCTGATGATATGAAACATCGTGCACAAGTTTTAGTTTCTCATCCA
GTTAATCCACCTTACTATGTACCACTTGTTGAAATTGTTCCTTCTAAACATACACGAAAA
GATATTCCAACAATTACAAGAGCTTTAATGACTGAAGTTGGTCAAAAACCTGTTGTTCTT
TCTCGTGAAATTGAGGGATTTGCATTGAATCGAATTCAATATGCAATTTTAAATGAATGC
TGGCGTTTAATTGCTGATGGTATTTTGGATGTTAAAGATATTGATTCAGTAATGTCTGAT
GGATTGGGAATGAGATATGCTTTCCTAGGGCCAATGGAGACAGCTCATTTAAATGCAGAA
GGTTTCCTTTCATATTGCGATCGATATTCAAAGACAATTTATGCTGTCAGTGAAACGATG
GGACCAGTTCCGAAAATGGAAGGTCCCGTTATGGAGCAAGTTGCTAAGGAATTGGAACAA
ATGTGTCCTCTTGAAGATTTAGAAAAACGCCGAAAGTGGCGCGACACATGTTTAACAGAG
TTGAGTAAGATGAAAAAAGAATTAAATGATTGA

>g8532.t7 Gene=g8532 Length=226
MQECVPENIELKKKLYKQLDEIVDDKIIISSSTSTFMPSIFSDDMKHRAQVLVSHPVNPP
YYVPLVEIVPSKHTRKDIPTITRALMTEVGQKPVVLSREIEGFALNRIQYAILNECWRLI
ADGILDVKDIDSVMSDGLGMRYAFLGPMETAHLNAEGFLSYCDRYSKTIYAVSETMGPVP
KMEGPVMEQVAKELEQMCPLEDLEKRRKWRDTCLTELSKMKKELND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8532.t7 Gene3D G3DSA:3.40.50.720 - 1 102 4.5E-31
9 g8532.t7 Gene3D G3DSA:1.10.1040.10 - 103 226 4.3E-47
3 g8532.t7 PANTHER PTHR48075 3-HYDROXYACYL-COA DEHYDROGENASE FAMILY PROTEIN 1 225 3.9E-93
4 g8532.t7 PANTHER PTHR48075:SF1 LAMBDA-CRYSTALLIN HOMOLOG 1 225 3.9E-93
2 g8532.t7 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 2 96 4.8E-27
1 g8532.t7 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 102 174 3.8E-14
7 g8532.t7 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature. 99 123 -
5 g8532.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 99 2.1E-22
6 g8532.t7 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 102 171 4.25E-12

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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0070403 NAD+ binding MF
GO:0006631 fatty acid metabolic process BP
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

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