C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Gene Info

Description: ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)
Gene AccessionGene NameTax IDStrandPositionGene Biotype
ENSMUSG00000030720 Cln3 10090 - 7:126571207-126585817 protein_coding
  Transcript Accession Transcript Name Position Transcript Biotype
  ENSMUST00000032962 Cln3-001 126571400-126583247 protein_coding
  ENSMUST00000084589 Cln3-002 126571207-126585817 protein_coding
  ENSMUST00000098036 Cln3-003 126572086-126583190 protein_coding
  ENSMUST00000116269 Cln3-201 126571400-126584280 protein_coding
  ENSMUST00000124177 Cln3-005 126572122-126577863 retained_intron
  ENSMUST00000125508 Cln3-011 126579409-126583523 protein_coding
  ENSMUST00000128049 Cln3-006 126583322-126584786 processed_transcript
  ENSMUST00000128225 Cln3-014 126579211-126583226 processed_transcript
  ENSMUST00000128970 Cln3-008 126579263-126584220 protein_coding
  ENSMUST00000134246 Cln3-015 126580270-126583114 retained_intron
  ENSMUST00000134406 Cln3-016 126580831-126583316 retained_intron
  ENSMUST00000134498 Cln3-013 126581513-126583342 processed_transcript
  ENSMUST00000138285 Cln3-018 126572090-126575087 processed_transcript
  ENSMUST00000139766 Cln3-017 126572108-126572728 processed_transcript
  ENSMUST00000147086 Cln3-009 126581715-126583554 protein_coding
  ENSMUST00000150311 Cln3-007 126581661-126584578 protein_coding
  ENSMUST00000150587 Cln3-010 126581658-126583566 protein_coding
  ENSMUST00000150917 Cln3-012 126579247-126583362 nonsense_mediated_decay
  ENSMUST00000153790 Cln3-004 126578359-126584307 retained_intron

Mus musculus EnsemblGRCm38

Genome
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Genes
Gene structures from Ensembl
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Transcripts
Structures from Ensembl
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Expression Patterns

Heat Map
Numeric Values
Transcript'; AdiposeAdrenalBladderBrainBreastColonHeartKidneyLiverLungMuscleOvaryPlacentaTestisENSMUST00000032962ENSMUST00000098036ENSMUST00000124177ENSMUST00000128225ENSMUST00000128970ENSMUST00000134246
Transcript ID Adipose Adrenal Bladder Brain Breast Colon Heart Kidney Liver Lung Muscle Ovary Placenta Testis
ENSMUST00000032962 7.160±0.53 11.942±4.04 3.073±0.05 3.164±2.06 9.231±4.96 9.736±5.19 N/A 5.801±0.95 2.424±0.84 7.546±1.40 0.615±0.25 15.028±3.41 N/A 3.630±1.46
ENSMUST00000098036 8.927±0.93 N/A 5.623±1.10 2.693±1.79 9.791±0.00 7.981±1.85 2.342±0.90 8.220±1.60 3.630±1.59 N/A 2.459±0.34 10.601±2.82 32.639±6.56 2.939±1.43
ENSMUST00000124177 9.714±0.00 N/A N/A 6.163±1.51 16.148±3.05 20.172±4.07 3.815±1.15 11.454±0.68 5.746±0.99 13.117±0.43 N/A 17.104±2.29 N/A N/A
ENSMUST00000128225 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 4.503±1.75
ENSMUST00000128970 N/A N/A N/A N/A N/A 13.161±0.00 3.510±0.60 9.793±0.00 N/A N/A 1.916±0.00 N/A N/A N/A
ENSMUST00000134246 N/A N/A N/A 5.609±0.00 N/A N/A N/A N/A N/A N/A N/A 21.871±0.00 N/A N/A

Conserved Regions

Region IDSub-RegionRegion TypePosition
CIL_0005TS CIL_0005TS_0002 CGP 7:126571207-126589112

Gene Ontology
GO IDEvidence TypeGO Description
GO:0000046 IMP autophagic vacuole fusion
GO:0000139 ISS Golgi membrane
GO:0001508 IMP action potential
GO:0001575 ISS globoside metabolic process
GO:0005515 IPI protein binding
GO:0005634 ISS nucleus
GO:0005737 ISS cytoplasm
GO:0005764 IDA lysosome
GO:0005765 IEA:ISS lysosomal membrane
GO:0005769 IDA:ISS early endosome
GO:0005770 IDA late endosome
GO:0005776 IDA autophagic vacuole
GO:0005783 ISS endoplasmic reticulum
GO:0005794 ISS Golgi apparatus
GO:0005795 ISS Golgi stack
GO:0005802 ISS trans-Golgi network
GO:0005886 ISS plasma membrane
GO:0005901 ISS caveola
GO:0006520 IMP cellular amino acid metabolic process
GO:0006672 ISS ceramide metabolic process
GO:0006678 ISS glucosylceramide metabolic process
GO:0006681 ISS galactosylceramide metabolic process
GO:0006684 ISS sphingomyelin metabolic process
GO:0006865 IMP amino acid transport
GO:0006898 ISS receptor-mediated endocytosis
GO:0007034 IBA vacuolar transport
GO:0007040 IMP lysosome organization
GO:0007042 IBA:ISS lysosomal lumen acidification
GO:0008021 ISS synaptic vesicle
GO:0008306 IMP associative learning
GO:0010468 ISO regulation of gene expression
GO:0015809 IBA:ISS arginine transport
GO:0016021 ISS integral component of membrane
GO:0016236 IMP macroautophagy
GO:0016242 IMP negative regulation of macroautophagy
GO:0016485 IMP protein processing
GO:0030176 ISS integral component of endoplasmic reticulum membrane
GO:0031301 IBA integral component of organelle membrane
GO:0031410 IDA cytoplasmic vesicle
GO:0035235 IMP ionotropic glutamate receptor signaling pathway
GO:0035752 ISS lysosomal lumen pH elevation
GO:0042133 IMP neurotransmitter metabolic process
GO:0042987 ISS amyloid precursor protein catabolic process
GO:0043005 ISS neuron projection
GO:0043066 ISS negative regulation of apoptotic process
GO:0043086 IMP negative regulation of catalytic activity
GO:0043524 IDA negative regulation of neuron apoptotic process
GO:0045121 ISS membrane raft
GO:0045861 IMP negative regulation of proteolysis
GO:0047496 ISS vesicle transport along microtubule
GO:0048306 IPI calcium-dependent protein binding
GO:0050885 IMP neuromuscular process controlling balance
GO:0051480 IDA cytosolic calcium ion homeostasis
GO:0061024 IMP membrane organization

Homologs

ENSEMBL Accession Gene Name Description Biotype Species
ENSDARG00000037865 cln3 ceroid-lipofuscinosis, neuronal 3 protein_coding Danio_rerio
ENSG00000188603 CLN3 ceroid-lipofuscinosis, neuronal 3 protein_coding Homo_sapiens
ENSG00000261832 CLN3 battenin isoform d protein_coding Homo_sapiens

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