NONHSAT119717

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Annotated Information

Name

HOTTIP: HOXA transcript at the distal tip

Characteristics

Gene located at 5°Ø end of HoxA cluster, bidirectional transcript with HOXA13 (Sasaki (2007)). ~3.8kb, transcript in human, spliced and polyadenylated (Wang (2011)). ~2.3kb transcript in mouse, different splice isoforms, currently known transcripts initiate downstream from the syntenic site in human.

Function

Summary:. Controls activation of 5°Ø HOXA genes. Chromosomal lopping bring it into close association with 5°Ø gene loci. HOTTIP binds WDR5 and recruits a MLL chromatin modifiying complex to maintain a domain of active chromatin over the 5°Ø of HOXA cluster (Wang (2011)). - HOTTIP controls activation of 5°Ø HOXA genes in mammals and chicken. - Impact on HOXA genes decreases with increased genomic distance from HOTTIP. - Phenotypic impact in chicken forelimb of HOTTIP knockdown was shorter than normal distal bones. - HOTTIP doesn°Øt affect chromosomal structure and looping but it was necessary for maintenance of H3 K4me3 chromatin marks over the distally expressed 5°Ø half of the HOXA locus. HOTTIP RNA binds WDR5 a component of MLL/Trithorax complexes recruiting a MLL complex to lay down H3 K4me3 marks. - WDR5 binding mediated by sequence(s) in 5°Ø 1kb of HOTTIP. HOTTIP appears to act in cis, its function is facilitated by the chromosomal looping that brings it into close proximity with 5°Ø HOXA genes. Conservation Present in human and mouse. Portions of HOXA13as sequence are well conserved throughout mammals (Wang (2011)). Appears to be present in chicken although there is little homology (Wang (2011)). RNA contains some highly conserved sequences which are predicted to form a conserved structure (Sasaki (2007)).

Expression

Shows collinear regulation of expression like HOX protein coding genes (Sasaki (2007)). Has bivalent chromatin marks (both H3 K4me3 and H3 K27me3) whether expression off or on, but only expressed in more distal cells (Wang (2011)). Has a similar expression profile to HOXA13, expressed in colon, prostate, placenta and uterus, as well as hand, foreskin and foot fibroblasts (Sasaki (2007), Sasaki (2007), Wang (2011)). Mouse E13.5 in-situs gave similar results (Wang (2011)). Nuclear localised, generally to a single small nuclear spot (Wang (2011)). Lowly expressed, estimated at ~0.3 copies/cell in expressing tissues (Wang (2011)).

Conservation

Present in human and mouse. Portions of HOXA13as sequence are well conserved throughout mammals (Wang (2011)). Appears to be present in chicken although there is little homology (Wang (2011)). RNA contains some highly conserved sequences which are predicted to form a conserved structure (Sasaki (2007)).

Misc

Background: Hox genes are found in 4 clusters. Genes in each cluster are expressed in certain tissues along body axes dependent on their position in the cluster. In the HoxA cluster genes near the 5°Ø are expressed in more distal tissues while genes near the 3°Ø are expressed in more proximal tissues. Expressed genes have active chromatin marks and show close physical association (likely due to chromosomal looping). Inactive genes do not associate and have repressive chromatin marks (Wang (2011)). Human clone accession: GU724873. Mouse clone accession: BC046496

Transcriptomic Nomeclature

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Regulation

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Allelic Information and Variation

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Evolution

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Labs working on this lncRNA

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References

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Basic Information

Transcript ID	NONHSAT119717
Source	NONCODE4.0
Same with	,
Classification	intergenic
Length	3764 nt
Genomic location	chr7+:27240040..27246878
Exon number	4
Exons	27240040..27240140,27240242..27241306,27241461..27242257,27244331..27246878
Genome context
Sequence	000001 CCCTTCCTTT ATCCCAGTGG GGCCCAGACC CGCGCAACCA GGCGGGGAGG GGAGGTGGGC GCGCGATTGG GTTGCGATCT 000080 000081 GGAGCAGTGG GGACAGGTCA GGAACCGGCG CGTATTTCTG CAGTGAGACC ACAGGACGGA CATCGGCGCC TTCGGCTTCG 000160 000161 ATGGAGTTGC GATTTTGCTC TTTCCAGGGA AACAGTGGCA GGGTGTTTGC TGCTTATCGG TTCCTGCGGA TATGCCTGGG 000240 000241 TCCCAGGACA TTCCACTGGA GGCTTGGACT GCATTTAGGA GCCCCTATCC CTTCCCTGTC CACACTGTTA GTGAGCAATT 000320 000321 TCATATGTTT GCATTTAGAC CCATAGACTC AGAACGACTC ATCACACACA CACACAGTGT ACACTGACAC ACTCACATTC 000400 000401 GCACACTTAG GTATACAGCC TGATCCTTGC TCTGACCTGG TAACAACGCT TCCTCCTCCA GAGACTTTGA GATAGAGCGA 000480 000481 GCGATCCCTG TGCACCATTC ATCCATGCTC CCACCTCGCC AGTATGGCTG GCTTAGTTCT GGAAGGGGCT TAAGAGGAAC 000560 000561 AAGCCCCAGC TGTGCTTCTG GCTGGGACTT AAACCCCCCT TCTGGGCCCT AAAGCCACGC TTCTTTGTGG ACCGGACCTG 000640 000641 ACTCTCCAGG AATCTGGGAA CCCGCTATTT CACTCTATTT TGGGACAAGA AAAAGGGGCT CTTTGGGGCC ACTTCCTGCC 000720 000721 TTCCCCTCAA GTAGGATCTC CAGCCTGCAG AGGGTGCCTA GTCCTTCTTT GCCCAAGAAC CAGTCCAAGA AGCCTTTCCT 000800 000801 CTGTGCCTGG GAAATGCAAC CTTTTCTTGG GAGCATGGTA GGGTGTTGGT GCTGAAGAAC CAAGCAGCGA CCCGTCTTGT 000880 000881 AGCTGCCATG TTTTGTCGAG GGGTTCTGGG GGTCCTGCTG CTTTAGAGCC ACATACTTCC ACTTCCTGAT TCACTACTGT 000960 000961 GAGCTGGTCA GATGCCTAAG GAACAAGCGT TCAAAGTGAA AGTGGGCACA TTACCGGAAT AGTGCTGGGG AGAGTGCTGG 001040 001041 ATTCTTTTCC ACCCCAGGCG GACTGGTGAG AAGCCAGGCT TGGACCTGTC CTCTGCTCCT AGCTTGCACA CTCAGCCCTA 001120 001121 AACTCAGAGC AGCACGCATA CCACCCCTCA CACACACCCC ACCAAGTGTG CCCTTTCCTT CTTGACTTTT TAGCAGTTCT 001200 001201 GGGTAAATAT TGATTTGCCC CCAGTTTACC TTCTCCCTGA CTGGCCATTT GCAGACTCAG GAACTAGCCT CTGTAGGGAC 001280 001281 TTGATTTTTC TGTTACTTTC TGGCCGTTTC ACCACCCCCC TTCCTCCCTC CAAGTGGCAT TGTAAAACTC ACAGTGACAA 001360 001361 AGAGACAGAG TAGGGTTCTA GGCCCCTGTT CCTGGGGACT TGAAGGCGGT TTTACATACT GGTCAGACAC GGCTGGAGGC 001440 001441 CAAGGTCAAG TTGAAAGTTG CAGTCCAGCC AGCATGAGAA CTGCCATGCG AGCGTAGAGA CACAGGCAGC AGCAAAAGGC 001520 001521 CCATTGCCCA CATCCCCTCA CTCTTAATTT TCTCTCTCTT TTTAAAATTC TCGCCTCTGA CTCTGTTCGG CTGCCCAGAA 001600 001601 TTTTTTGGTG CCTTCGTGGG GTTTTTGGGG CGGTGTTTAC CGACTCTTCT CTGCCTCCGC CCTGCTCAGC CAGGGCTTTG 001680 001681 AGCCTCTTCG GTTTTCCGGC CAGACCCGGA AAAACGAAAA CACAGCTTGG GGAGCCCCCA CTAGCCGGCG CCTGTGCCAG 001760 001761 CTCACCTCTG GCCATGGCGC AGCTGCCGGT GCACACGGCG GCCAAGGCCA GCTCCACATT CTTCCCTCCC CCTCCCACTT 001840 001841 CACCGTAGCC CCGAACCCTG CGCGCAGAGA AAGGGTCTCA GCTCCACAGA CGACTGGGTC CCTCCTCACC AAAAATGGTG 001920 001921 AGACAAGATT TCATCTGTCG GCCGAGGAGC CACAAGCAGG TACCACAAAG CCACTAGTGC ACAGGGACTC AGAAAAGACG 002000 002001 GCAGGAGCCC AAGGAAAACT CCAATTTGAG TACAGCCCTG CCTTGTTTCC CCCAGAGAGT CCCTGAGCAA GGAGACCTCC 002080 002081 ACCCCACACA CACCATTTCA GAACAACCAG GTTCCAGACT CCCATGAGGA GCATCTCCCA CTGCAGAGCC TTGGCCAGCC 002160 002161 GCGCCCGGAC TCCTCAGAGC TGGCGCAAAC TCCGTCCTCC AAAACTCGGC TCTGGGAGGC CTAAGTGACT CCGAAGCCGG 002240 002241 CGGCAGCCGC GGCAGCGGCC GTGGTGGTGG AAGAGCTCTT TTCCCCGACA GTGCCACTGA TCGCTCTTCA CTGGAGCTGG 002320 002321 AAACAGCCTT CGCGGAAAGG ACCGGAGCAT GCGTTAGAAG CAGAGGGAGC TTGGTGAAGG GCTCGGCTGG AAGGAGGAAA 002400 002401 CGCCTTCTCG CAGTGCGCGG CCAGCCCGCG GGGGACACCG GCTTGCTGGA CTGCAGGGGC CCGTGCCACC CAGGAAGTGA 002480 002481 CCTGCGGGTC ACTCAGCCGG GGCGCTGGGC GAGCGCGGGA CGGCCCGGAG AATTCCGTGC GGCTGCGACG GGAAAAGGAC 002560 002561 GAGGGGTCTC TGTACCCGAC GCTGCCACTG GCCCAAAGGA ATTTTACCCG CGAGCGCCCA CCCCACCCTA GCTTGATGCT 002640 002641 TACGCCCGCA ACAAAACAGG AAACCAGGAC TGGGCAGTGC ATTCTTTAAG TCAACAAATA CACTGAAGAC TTCGAGCGTT 002720 002721 TGAAGGAAGG AGGGGGTTTG CACGTAAGCC TGGCCCCGCC GGGCTCGGCT TTCTCGCTGA GAAAGCGGCG CAGGCAGCCA 002800 002801 GGCGGCCTGG GCCCGCGGGG GTCCATCTCG CCCTAGACTC CTAAGAACTC CCACGGCCCT GTTCCCAGCT GCGAATTCTT 002880 002881 AATGCACAAC GCGACGGAGG GAAGGAAATT CACCAGCGCA GCGACGAGGA AGGGGAACTC AGGACCCCTT CAAGTACACA 002960 002961 CTGAGGTGTG ATCAGAGTTT TATGGGCACT TTATATGCTG TAATCATAAC GATGTGTGTG CCTTGATATG CACGCATATT 003040 003041 CACGCATCAA ACGTGCATAC ACACACAGAG TGAATGTGCG CATCCAATGT CATGTGGGTG AAATACAAGC ATCATACCCA 003120 003121 GCCCTACGAA AAAAAAATTC ACCCTGTCGG ACCAGGCTGG TGACATACTT CGCTGGCGCA TCTCCTTACT CACTCTTACT 003200 003201 TTTCCGACCC CTCACCATTC CCTCTCCTGT GGCTTGGTAA ATACACCTGC CCTCCGTGGA AGGTGAGTCC TGGACTGGCG 003280 003281 TTGCCAGGTT CGCATGTCCT CCCCAGAACC TCCGTCTGGC TCCAGGGACT CTCACTGAGC GGGTCTAGAG CACCCAGCAC 003360 003361 TTTTCAAGGA ACAGCCGCGG TTCCTTTGTC CCGCGGCTCC AGCCCCGTTC GGCCCAGCTC TCAGGGAAAC GAAGCGCTCA 003440 003441 GTAAGAACTT TTGATATTAG TTTGTATGGG TATTTACACT CTGGTGAGGG GAGCTGAGTA CGGAAGTTCC ATTAATCATA 003520 003521 CTCCAACCTT GGGTTTAGAT ATTCAGTTTA TGGGTTGGGA GAGGGAGTTT GCCGGAAAGA AAGCATCAAG GTTGGCCGCT 003600 003601 GACTCCAGAG AAATGAAAAG GGAGGTCGTT TTCTGTTTCT GGAAATCAAG AATTAGGAAT GGGCAACTAC AGGTGCTAAC 003680 003681 CAACAGACCA CTTTTTTGTT TTTTGGTAGC CCTTTGGCAG GGATAGTTTT TCCACCTTTG CCCGATACAA TTTAAAAAAA 003760 003761 AAAA

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