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

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Transcript Info
Description: high mobility group box 1
Transcript Accession Transcript Name Contained in Gene Tax ID Strand Position Biotype
ENST00000405805 HMGB1-012 ENSG00000189403 9606 - 13:30458747-30617597 protein_coding

Homo sapiens EnsemblGRCh38

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Genes
Structures from Ensembl
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Transcripts
Structures from Ensembl
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Expression Patterns

Heat Map
Numeric Values
Transcript'; AdiposeBladderBrainBreastHeartKidneyLiverLungMuscleOvaryTestisENST00000405805
Transcript ID Adipose Bladder Brain Breast Heart Kidney Liver Lung Muscle Ovary Testis
ENST00000405805 6.188±0.00 1.619±0.00 6.254±0.00 5.494±0.00 1.808±0.92 2.920±0.00 4.426±0.00 6.024±0.94 2.368±1.37 5.851±1.32 1.491±0.00

Conserved Regions

Region IDSub-RegionRegion TypePosition
CIL_0004CF CIL_0004CF_0001 CGP 13:30456704-30660770

Gene Ontology

GO IDEvidence TypeGO Description
GO:0000122 IMP negative regulation of transcription from RNA polymerase II promoter
GO:0000793 IDA condensed chromosome
GO:0001773 ISS myeloid dendritic cell activation
GO:0002407 ISS dendritic cell chemotaxis
GO:0002437 IEP inflammatory response to antigenic stimulus
GO:0003684 ISS damaged DNA binding
GO:0003690 ISS double-stranded DNA binding
GO:0003697 ISS single-stranded DNA binding
GO:0003700 IDA sequence-specific DNA binding transcription factor activity
GO:0005125 ISS cytokine activity
GO:0005515 IPI protein binding
GO:0005576 TAS extracellular region
GO:0005615 IDA extracellular space
GO:0005634 IDA nucleus
GO:0005654 TAS nucleoplasm
GO:0006265 ISS DNA topological change
GO:0006288 IDA base-excision repair, DNA ligation
GO:0006309 TAS apoptotic DNA fragmentation
GO:0006310 ISS DNA recombination
GO:0006357 IDA regulation of transcription from RNA polymerase II promoter
GO:0006915 TAS apoptotic process
GO:0006921 TAS cellular component disassembly involved in execution phase of apoptosis
GO:0008134 IPI transcription factor binding
GO:0008301 ISS DNA binding, bending
GO:0009986 IDA cell surface
GO:0017053 IDA transcriptional repressor complex
GO:0017055 IDA negative regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0031175 ISS neuron projection development
GO:0033151 IDA V(D)J recombination
GO:0042056 ISS chemoattractant activity
GO:0043065 IDA positive regulation of apoptotic process
GO:0043280 IDA positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043388 IDA positive regulation of DNA binding
GO:0044822 IDA poly(A) RNA binding
GO:0045087 TAS innate immune response
GO:0045944 IDA positive regulation of transcription from RNA polymerase II promoter
GO:0050786 ISS RAGE receptor binding
GO:0050918 ISS positive chemotaxis
GO:0051103 ISS DNA ligation involved in DNA repair
GO:0070491 IPI repressing transcription factor binding

Homologs

ENSEMBL Accession Gene Name Biotype Species E-Value Bit Score
ENSMUST00000110505 Hmgb1-003 protein_coding Mus_musculus 0 1467
ENSMUST00000085546 Hmgb1-001 protein_coding Mus_musculus 0 1467
ENSMUST00000178049 Gm21596-201 processed_pseudogene Mus_musculus 0 1458
ENSMUST00000093196 Hmgb1-002 protein_coding Mus_musculus 0 1086
ENSMUST00000120421 Gm15387-001 processed_pseudogene Mus_musculus 0 904
ENSMUST00000084171 Gm5518-201 processed_pseudogene Mus_musculus 0 893
ENSMUST00000179479 Hmgb1-ps9-201 processed_pseudogene Mus_musculus 0 893
ENSMUST00000179821 RP24-388H6.4-001 processed_pseudogene Mus_musculus 0 876
ENSMUST00000173370 Hmgb1-ps7-001 processed_pseudogene Mus_musculus 0 876
ENSMUST00000119715 Gm5937-001 processed_pseudogene Mus_musculus 0 861
ENSMUST00000118415 Hmgb1-ps3-001 processed_pseudogene Mus_musculus 0 854
ENSMUST00000117548 Hmgb1-ps2-001 processed_pseudogene Mus_musculus 0 848
ENSMUST00000118281 Hmgb1-ps4-001 processed_pseudogene Mus_musculus 0 828
ENSMUST00000120637 Gm13121-001 processed_pseudogene Mus_musculus 0 791
ENSMUST00000119927 Gm12331-001 processed_pseudogene Mus_musculus 0 787
ENSMUST00000119350 Hmgb1-ps1-001 processed_pseudogene Mus_musculus 0 776
ENSMUST00000119503 Hmgb1-ps6-001 processed_pseudogene Mus_musculus 0 771
ENSMUST00000176164 Gm3307-001 processed_pseudogene Mus_musculus 0 765
ENSMUST00000181542 Hmgb1-ps8-001 processed_pseudogene Mus_musculus 0 754
ENSMUST00000179326 Gm5473-201 processed_pseudogene Mus_musculus 0 743
ENSMUST00000073196 Gm10075-201 pseudogene Mus_musculus 0 737
ENSMUST00000117362 Gm12568-001 processed_pseudogene Mus_musculus 0 730
ENSMUST00000121058 Hmgb1-ps5-001 processed_pseudogene Mus_musculus 0 728
ENSMUST00000118053 Gm13379-001 processed_pseudogene Mus_musculus 0 725
ENSMUST00000119126 Gm9078-001 processed_pseudogene Mus_musculus 0 713
ENSMUST00000180890 Gm26585-001 processed_pseudogene Mus_musculus 0 708
ENSMUST00000120842 Gm8152-001 processed_pseudogene Mus_musculus 0 704
ENSMUST00000120873 Gm13932-001 processed_pseudogene Mus_musculus 0 702
ENSMUST00000162030 AC098736.2-001 processed_pseudogene Mus_musculus 0 699
ENSMUST00000121589 Gm11645-001 processed_pseudogene Mus_musculus 0 697
ENSMUST00000117107 Gm15560-001 processed_pseudogene Mus_musculus 0 678
ENSMUST00000139443 Hmgb1-006 retained_intron Mus_musculus 0 675
ENSMUST00000117940 Hmgb1-rs18-001 processed_pseudogene Mus_musculus 0 662
ENSMUST00000122269 Gm14473-001 processed_pseudogene Mus_musculus 0 645
ENSMUST00000190177 RP24-229N7.1-001 processed_pseudogene Mus_musculus 0 640
ENSMUST00000118469 Gm15778-001 processed_pseudogene Mus_musculus 0 634
ENSMUST00000121009 Gm14049-001 processed_pseudogene Mus_musculus 0 632
ENSMUST00000120015 Gm6461-001 processed_pseudogene Mus_musculus 0 628
ENSMUST00000117499 Gm12261-001 processed_pseudogene Mus_musculus 0 625
ENSMUST00000121222 Gm5396-001 processed_pseudogene Mus_musculus 0 623
ENSMUST00000120175 Gm11830-001 processed_pseudogene Mus_musculus 0 623
ENSMUST00000184467 Gm7870-001 processed_pseudogene Mus_musculus 0 610
ENSMUST00000179328 Gm8807-201 processed_pseudogene Mus_musculus 0 604
ENSMUST00000183926 Gm27254-001 processed_pseudogene Mus_musculus 0 586
ENSMUST00000182688 Gm7909-001 processed_pseudogene Mus_musculus 0 573
ENSMUST00000120970 Gm15750-001 processed_pseudogene Mus_musculus 0 569
ENSMUST00000138553 Hmgb1-007 protein_coding Mus_musculus 0 555
ENSMUST00000119766 Gm12118-001 processed_pseudogene Mus_musculus 0 549
ENSMUST00000133667 Hmgb1-004 retained_intron Mus_musculus 0 460
ENSMUST00000186576 RP24-241N3.1-001 processed_pseudogene Mus_musculus 0 448
ENSMUST00000155086 Hmgb1-009 retained_intron Mus_musculus 0 433
ENSMUST00000125605 Hmgb1-008 protein_coding Mus_musculus 0 424
ENSMUST00000168653 Gm3851-001 processed_pseudogene Mus_musculus 0 377
ENSMUST00000120168 Gm13902-001 processed_pseudogene Mus_musculus 0 374
ENSMUST00000155154 Ppm1e-002 processed_transcript Mus_musculus 0 303
ENSMUST00000116383 Gm14448-001 processed_pseudogene Mus_musculus 0 261
ENSMUST00000123645 Hmgb1-005 retained_intron Mus_musculus 0 246
ENSMUST00000189012 RP23-338I1.1-001 processed_pseudogene Mus_musculus 1.00053e-42 180
ENSMUST00000128343 Gm3160-001 processed_pseudogene Mus_musculus 3e-18 99

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