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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcctgaaatttcagttagctatagagtcactctcaatggcccagcatgaaaaccaattatgtgatggttaatatcgtgcctgtgtcttgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT

Basic information

species Zea mays
transcript GRMZM5G871861_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871861_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g10340.1 (Oryza sativa), 3'ss of exon 9
aactcctgaaatttcagttagctatagagtcactctca-atggcccagc---atgaaaaccaattatgtg----atggttaatatcgtgcctgtgtcttgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT
      |||||  |    |   |||  |||    || |  ||| |||      ||  |     || ||||    || ||||||||  | | | |  ||| |||| ||||||||||| |||||||| || || || ||||| ||| |||||| ||||||||| |  |
------tgaaaaattgactg--tatcaagtactgctgatgtggtccaattttgtggtattgctttttgtgggggattgttaatattattcttataacttctcttacagAAACTTCTCTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT
















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|32834214|gb|CD973892.1|CD973892
EST:     TTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAG                         AAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTA
genomic: TTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTA
EST: gi|60341182|gb|DN208155.1|DN208155
EST:     TTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAG                         AAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTA
genomic: TTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTA
EST: gi|74240574|gb|DT648488.1|DT648488
EST:     TTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAG                         AAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTA
genomic: TTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTA

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 4 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 45 (downstream exon)
Score: 5

TCATCTCCCCACTTACATATTGTTTGACAAGGTGACTGAAGTTTCTCGGTTTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 3

TCATCTCCCCACTTACATATTGTTTGACAAGGTGACTGAAGTTTCTCGGTTTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 3

TCATCTCCCCACTTACATATTGTTTGACAAGGTGACTGAAGTTTCTCGGTTTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT


Block sizes: 48 (upstream exon), 20 (downstream exon)
Score: 2

TCATCTCCCCACTTACATATTGTTTGACAAGGTGACTGAAGTTTCTCGGTTTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAAGgttattttca ... tgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatgaaaaccaattatgtgatggttaatatcgtgcctgtgtcttgtcttgcagAAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCT
                       ggttaat  putative branch site (score: 2)
                                          tcttgtctt  putative PPT
                         ttaatat  TA-rich tract