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
Gene AccessionGene NameTax IDStrandPositionGene Biotype
ENSG00000188603 CLN3 9606 - 16:28477279-28495575 protein_coding
  Transcript Accession Transcript Name Position Transcript Biotype
  ENST00000333496 CLN3-006 28477280-28492042 protein_coding
  ENST00000355477 CLN3-201 28477279-28492082 protein_coding
  ENST00000357806 CLN3-008 28477291-28491983 protein_coding
  ENST00000357857 CLN3-012 28477329-28491853 protein_coding
  ENST00000359984 CLN3-202 28477279-28492082 protein_coding
  ENST00000360019 CLN3-203 28477279-28492302 protein_coding
  ENST00000395653 CLN3-007 28477361-28492023 protein_coding
  ENST00000561505 CLN3-031 28486362-28492049 protein_coding
  ENST00000561689 CLN3-023 28477516-28491759 retained_intron
  ENST00000563874 CLN3-002 28477280-28494576 retained_intron
  ENST00000564091 CLN3-034 28477279-28482377 nonsense_mediated_decay
  ENST00000564574 CLN3-004 28482178-28492070 retained_intron
  ENST00000565047 CLN3-016 28482516-28491826 processed_transcript
  ENST00000565140 CLN3-035 28477516-28491759 nonsense_mediated_decay
  ENST00000565236 CLN3-029 28489314-28492042 processed_transcript
  ENST00000565316 CLN3-020 28477516-28491759 protein_coding
  ENST00000565354 CLN3-033 28477387-28484014 retained_intron
  ENST00000565688 CLN3-030 28484017-28492063 protein_coding
  ENST00000565778 CLN3-014 28482513-28491827 protein_coding
  ENST00000566040 CLN3-025 28492105-28495575 processed_transcript
  ENST00000566057 CLN3-018 28477516-28491759 nonsense_mediated_decay
  ENST00000566083 CLN3-013 28482512-28491837 retained_intron
  ENST00000566472 CLN3-028 28492137-28493986 processed_transcript
  ENST00000566816 CLN3-024 28493554-28495556 processed_transcript
  ENST00000566824 CLN3-003 28482503-28492072 retained_intron
  ENST00000567160 CLN3-026 28492190-28495545 processed_transcript
  ENST00000567495 CLN3-015 28482477-28491832 nonsense_mediated_decay
  ENST00000567804 CLN3-027 28489290-28492773 protein_coding
  ENST00000567963 CLN3-005 28477329-28492055 protein_coding
  ENST00000568076 CLN3-022 28477516-28491759 retained_intron
  ENST00000568422 CLN3-011 28477483-28491856 nonsense_mediated_decay
  ENST00000568443 CLN3-017 28487662-28492302 protein_coding
  ENST00000568452 CLN3-021 28477516-28491759 retained_intron
  ENST00000568472 CLN3-032 28482164-28491773 processed_transcript
  ENST00000568497 CLN3-010 28482356-28491858 nonsense_mediated_decay
  ENST00000568558 CLN3-009 28482150-28491859 protein_coding
  ENST00000569030 CLN3-019 28477516-28491759 nonsense_mediated_decay
  ENST00000569430 CLN3-001 28477279-28495534 protein_coding

Homo sapiens EnsemblGRCh38

Genome
Exciting message
Genes
Gene structures from Ensembl
Connecting
Transcripts
Structures from Ensembl
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Expression Patterns

Heat Map
Numeric Values
Transcript'; AdiposeBladderBrainBreastColonHeartKidneyLiverLungMuscleOvaryPlacentaTestisENST00000333496ENST00000355477ENST00000357806ENST00000357857ENST00000359984ENST00000360019ENST00000395653ENST00000564091ENST00000565236ENST00000565316ENST00000565354ENST00000565688ENST00000565778ENST00000566057ENST00000566472ENST00000566824ENST00000567495ENST00000567804ENST00000568422ENST00000569030
Transcript ID Adipose Bladder Brain Breast Colon Heart Kidney Liver Lung Muscle Ovary Placenta Testis
ENST00000333496 N/A N/A N/A N/A 4.250±1.79 2.245±0.00 4.543±3.00 3.853±0.00 7.541±0.00 N/A 10.855±0.00 24.417±2.72 N/A
ENST00000355477 N/A N/A 0.227±0.00 N/A N/A N/A N/A N/A N/A N/A 11.898±0.00 N/A N/A
ENST00000357806 N/A N/A N/A N/A N/A 2.259±0.00 N/A N/A N/A 4.960±0.00 N/A N/A N/A
ENST00000357857 N/A N/A N/A N/A N/A 4.196±0.00 N/A 7.015±0.00 N/A N/A 9.090±0.00 17.134±1.21 N/A
ENST00000359984 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 6.275±0.00 23.632±0.41 4.721±0.00
ENST00000360019 N/A N/A N/A 1.628±0.00 N/A N/A N/A N/A N/A N/A 13.336±0.00 N/A N/A
ENST00000395653 N/A N/A N/A N/A N/A N/A 8.303±0.00 N/A N/A N/A N/A N/A N/A
ENST00000564091 N/A N/A 1.804±0.00 N/A N/A N/A 25.770±0.00 7.249±6.22 N/A N/A 5.213±0.00 N/A N/A
ENST00000565236 N/A N/A N/A N/A N/A 0.497±0.00 N/A N/A N/A N/A N/A N/A N/A
ENST00000565316 14.891±0.00 0.541±0.00 N/A 18.269±0.00 10.081±0.00 N/A 9.949±0.00 7.834±0.00 N/A 5.838±0.00 N/A N/A 7.316±0.00
ENST00000565354 N/A 1.466±0.00 N/A N/A N/A N/A 1.128±0.00 N/A N/A N/A N/A N/A N/A
ENST00000565688 N/A 1.992±0.00 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A
ENST00000565778 N/A N/A N/A N/A N/A N/A N/A 1.218±0.00 N/A N/A N/A N/A N/A
ENST00000566057 N/A N/A N/A N/A N/A N/A N/A N/A N/A 4.290±0.00 N/A N/A N/A
ENST00000566472 N/A N/A N/A N/A 5.879±0.00 N/A N/A N/A N/A N/A N/A N/A N/A
ENST00000566824 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 2.265±0.00 N/A N/A
ENST00000567495 N/A N/A N/A N/A N/A N/A N/A N/A N/A 0.596±0.00 N/A N/A N/A
ENST00000567804 N/A N/A 0.911±0.00 1.960±0.00 N/A 0.347±0.00 N/A N/A N/A N/A N/A N/A N/A
ENST00000568422 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 39.412±0.00 66.340±0.00 8.740±0.00
ENST00000569030 N/A 1.059±0.00 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A

Conserved Regions

Region IDSub-RegionRegion TypePosition
CIL_0005TS CIL_0005TS_0001 CGP 16:28477279-28498970

Gene Ontology
GO IDEvidence TypeGO Description
GO:0000046 ISS autophagic vacuole fusion
GO:0000139 IDA Golgi membrane
GO:0001508 ISS action potential
GO:0001575 IMP globoside metabolic process
GO:0005515 IPI protein binding
GO:0005634 IDA nucleus
GO:0005737 IDA cytoplasm
GO:0005739 TAS mitochondrion
GO:0005764 IDA lysosome
GO:0005765 IEA lysosomal membrane
GO:0005769 IDA early endosome
GO:0005770 ISS late endosome
GO:0005776 ISS autophagic vacuole
GO:0005783 IDA endoplasmic reticulum
GO:0005794 IDA Golgi apparatus
GO:0005795 IDA Golgi stack
GO:0005802 IDA trans-Golgi network
GO:0005886 IDA plasma membrane
GO:0005901 IDA caveola
GO:0006520 ISS cellular amino acid metabolic process
GO:0006672 IDA ceramide metabolic process
GO:0006678 IMP glucosylceramide metabolic process
GO:0006681 IMP galactosylceramide metabolic process
GO:0006684 IMP sphingomyelin metabolic process
GO:0006898 IMP receptor-mediated endocytosis
GO:0007034 IBA vacuolar transport
GO:0007040 ISS lysosome organization
GO:0007042 IMP lysosomal lumen acidification
GO:0008021 IDA synaptic vesicle
GO:0008219 IEA cell death
GO:0008306 ISS associative learning
GO:0015809 IDA arginine transport
GO:0016020 IEA membrane
GO:0016021 IEA integral component of membrane
GO:0016236 NAS macroautophagy
GO:0016242 ISS negative regulation of macroautophagy
GO:0016485 ISS protein processing
GO:0030163 NAS protein catabolic process
GO:0030176 IDA integral component of endoplasmic reticulum membrane
GO:0035235 ISS ionotropic glutamate receptor signaling pathway
GO:0035752 IDA lysosomal lumen pH elevation
GO:0042133 ISS neurotransmitter metabolic process
GO:0042987 IDA amyloid precursor protein catabolic process
GO:0043005 IDA neuron projection
GO:0043066 IMP negative regulation of apoptotic process
GO:0043086 ISS negative regulation of catalytic activity
GO:0043524 ISS negative regulation of neuron apoptotic process
GO:0045121 IDA membrane raft
GO:0045861 ISS negative regulation of proteolysis
GO:0047496 IMP vesicle transport along microtubule
GO:0050885 ISS neuromuscular process controlling balance
GO:0051082 TAS unfolded protein binding
GO:0051480 ISS cytosolic calcium ion homeostasis
GO:0061024 ISS membrane organization

Homologs

ENSEMBL Accession Gene Name Description Biotype Species
ENSDARG00000037865 cln3 ceroid-lipofuscinosis, neuronal 3 protein_coding Danio_rerio
ENSMUSG00000030720 Cln3 ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) protein_coding Mus_musculus

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