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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaaatgttcacagtgcgtgaacactctggaatctggataccaccagactaggatactctgatgtcttccatcatcgcagtgaccatgcctttgtgacatttactactaaagctttgggattgccagtgcccttttatgtctatttcatgttaatggtgtgcttgaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG

Basic information

species Zea mays
transcript GRMZM2G421655_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421655_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g30980.1 (Oryza sativa), 3'ss of exon 26
gtactgaaatgttcacagtgcgtgaacactctggaatctggataccaccagactaggatactctgatgtcttccatcatcgcagtgaccatgcctttgtgacat-ttactactaaagctttgggattgccagtgccctttta-tgtctatttcatgttaatggt----gtgcttgaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG
                                                                                  ||    || |  | || ||||| ||| | || || |  |   ||||  | |||  |  || |||  |||||||||| |   |     ||||||  |||||||||  ||||||| |||||||||||  |||| |||||||||||||||||||||
---------------------------------------------------------------------------------taggagtcagga-tctgagacatgttagttctgaaacagtc--attggtattgcattgctactgtacatttcatgttcagtctatctatgcttgccttttcagATTGGTTTTGTTATTGATGAACGTTTACGAGGTAAAGGATACAAGCGCAAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211145564|gb|FL475598.1|FL475598
EST:     ATTGGGGCAAGAAGCAGGCATTTCAAAATCCAAAGAGATTACTTGAAAAG                         ATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG
genomic: ATTGGGGCAAGAAGCAGGCATTTCAAAATCCAAAGAGATTACTTGAAAAGgtactgaaat ... gaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 63

GTTTGATATTGATGATAGATCGGTAGTCTCACATATATTTCATCATTGGGGCAAGAAGCAGGCATTTCAAAATCCAAAGAGATTACTTGAAAAGgtactgaaat ... gaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG


Block sizes: 43 (upstream exon), 36 (downstream exon)
Score: 2

GTTTGATATTGATGATAGATCGGTAGTCTCACATATATTTCATCATTGGGGCAAGAAGCAGGCATTTCAAAATCCAAAGAGATTACTTGAAAAGgtactgaaat ... gaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 8

GTTTGATATTGATGATAGATCGGTAGTCTCACATATATTTCATCATTGGGGCAAGAAGCAGGCATTTCAAAATCCAAAGAGATTACTTGAAAAGgtactgaaat ... gaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgccagtgcccttttatgtctatttcatgttaatggtgtgcttgaattttcagATCAGTTTTGTAATTGATGAACGCCTACGTGGTAAAGGATACAAGCGCAAG
                             tgttaat  putative branch site (score: 8)
                                                ttttc  putative PPT
             ttttatgtctattt  TA-rich tract