Computational Discovery of Overlapping Transcriptional Units in the Human & Mouse Genomes

Candidate UniGene cluster:UniGene Cluster Hs.171495
Description:retinoic acid receptor, beta
Best-Of-UniGene (BOU) SequenceNM_000965
Genomic Coordiantes Displayed:Bases 222000 to 243000 of contig Hs3_5919_24
BOU Orientation Along Contig:RIGHT-TO-LEFT with respect to contig
Link to JPEG of genomic mappingHs.171495.jpeg
Best sense EST/protein match:NM_000965 matched ref|NP_000956.2| (NM_000965) retinoic acid receptor, beta isoform 1; retinoic acid (E = 0.0)
Best antisense EST/protein match:No protein match with an e-value of less than 1e-10


This page provides information on exon-intron structure, mouse-human homologies, polyA signals & locations, and protein homologies of ESTs from directionally-cloned libraries that are members of a UniGene cluster that is a candidate for containing ESTs derived from distinct, overlapping sense & antisense transcripts.
The upper portion of the graph is reserved for the exon-intron mappings of ESTs oriented consistently with the Best-Of-UniGene (BOU) sequence (in gold). The lower portion of the graph is reserved for the exon-intron mappings of ESTs oriented opposite the BOU sequence (in white). Dividing these portions are the exon-intron mapping of the BOU sequence itself (in blue and green). Immedietely below the BOU are HUMMUS-defined streches of sequences highly conserved between mouse and human. The height of each bar is reflective of the % identity of human-mouse homology over a 100 base-pair window centered at a given base. At the left of the graph, the GenBank accession number of the BOU or EST sequence represented along that Y-axis position is listed, along with the UniLib identification number of the library from which that EST was derived.Below the graph, the GenBank accession numbers of each of the sense & antisense ESTs are provided, along with information on which have polyA signals and protein homologies, as determined by the NCBI.

Below are listed the same set of ESTs as is depicted above, with information of read direction, tissue type, protein similarity (P), and poly-adenylation signal (A).

ANTISENSE ESTs
  T65078 cDNA clone IMAGE:21587 brain 5' read 1.2 kb
  F11864 cDNA clone c32f02 brain
  R19027 cDNA clone IMAGE:32941 brain 5' read 1.0 kb
  R34729 cDNA clone IMAGE:37413 brain 5' read 1.2 kb
  H09455 cDNA clone IMAGE:46180 brain 5' read 1.2 kb
  F09509 cDNA clone c32f02 brain 3' read Polyadenylation signal
  H09105 cDNA clone IMAGE:46180 brain 3' read 1.2 kbPolyadenylation signal
  R49601 cDNA clone IMAGE:37413 brain 3' read 1.2 kbPolyadenylation signal
  R44014 cDNA clone IMAGE:32941 brain 3' read 1.0 kbPolyadenylation signal
  T65045 cDNA clone IMAGE:21587 brain 3' read 1.2 kbPolyadenylation signal

SENSE ESTs

  N66800 cDNA clone IMAGE:287077 ear 3' read Polyadenylation signal
  BG250945 cDNA clone IMAGE:4471412 adenocarcinoma, cell line 5' read
  AV699006 cDNA clone GKCFOE09 hepatocellular carcinoma 5' read Protein similarity
  AV695731 cDNA clone GKCFOB08 hepatocellular carcinoma 5' read Protein similarity
  AV695585 cDNA clone GKCFRE03 hepatocellular carcinoma 5' read Protein similarity
  AV683700 cDNA clone GKCFPB01 hepatocellular carcinoma 5' read Protein similarity
  T28640 cDNA clone ATCC:103088 gall bladder 5' read Protein similarity
  AV690234 cDNA clone GKCFQD03 hepatocellular carcinoma 5' read Protein similarity
  AV686874 cDNA clone GKCFQA06 hepatocellular carcinoma 5' read Protein similarity
  AV686873 cDNA clone GKCFQA05 hepatocellular carcinoma 5' read Protein similarity
  AV695583 cDNA clone GKCFRE01 hepatocellular carcinoma 5' read Protein similarity
  AA317545 cDNA clone ATCC:118055 eye 5' read Protein similarity
  BE888409 cDNA clone IMAGE:3915516 leiomyosarcoma 5' read Protein similarity
  BI837196 cDNA clone IMAGE:5229160 pooled pancreas and spleen 5' read Protein similarity