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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgtcttcgatatttattggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactatttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 7
--------gtatggtgtcttcgatatttattggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactat---ttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
         |    | |||| |    || | || | |||| || |||     || |    |   | || |  |  ||    |  |||||||    | |   ||| ||||||| ||||||| |||||||||||||| |||||||| || ||||||||||||
gtaagcggctggattttctttgcacattttggggaagtttgttgttt---accaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacagCCTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG
















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|213187425|gb|FM190443.1|FM190443
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|213187001|gb|FM192338.1|FM192338
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32830913|gb|CD970591.1|CD970591
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32830394|gb|CD970072.1|CD970072
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGTCAT                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCGAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32831124|gb|CD970802.1|CD970802
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 225

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 87

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacaaaaaaagtcttttgaagttcacattttcttacaagaactatttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
                               ttcttac  putative branch site (score: 92)
                                           ctatttc  putative PPT
     aaaaaaagtctttt  TA-rich tract