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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttggtttccttaggataatagatctgatgcatccagtgacctctaatggctagcacatctcttgcttgatggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA

Basic information

species Zea mays
transcript GRMZM2G040247_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 2
gtaagtttggtttccttaggataatag---atctgatgcatccagtgacctctaatggctagcacatctcttgcttgatggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA
||    ||  | || ||    ||  ||   |||  ||  |||  ||||  || ||||| | |      |||  |||       ||  ||||| |||||||||| ||||| ||||||||||| ||||| |||||| | || || ||||| |||||||| ||||||||||| ||||||||||||||||  |
gtgcacttcttctcattgtcctacaagaaaatcaaattgatctggtgatttcaaatggtt-gtgtgagtctc-ctta-----catacagGTTCTGCGTGATGGCGAAGGACCAATCCATTCTATGAAATGGAGGACAGACCTCCTTGCCTGGGCTAACGATGCAGGGGTAAAAGTGCATGATATGAAGA
















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|86470940|gb|DY237310.1|DY237310
EST:     GCCAAGTACTTGTGCTGACAAAGAAGTCTTGGGGAGGTTACCATAAGAAG                         GTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGAT
genomic: GCCAAGTACTTGTGCTGACAAAGAAGTCTTGGGGAGGTTACCATAAGAAGgtaagtttgg ... ggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGAT




















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: 48 (upstream exon), 49 (downstream exon)
Score: 146

CCCTAATTATGCCCGGAACTATAGAAGATTTGCTACTGGTGGTTTAGCAGGCCAAGTACTTGTGCTGACAAAGAAGTCTTGGGGAGGTTACCATAAGAAGgtaagtttgg ... ggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 192

CCCTAATTATGCCCGGAACTATAGAAGATTTGCTACTGGTGGTTTAGCAGGCCAAGTACTTGTGCTGACAAAGAAGTCTTGGGGAGGTTACCATAAGAAGgtaagtttgg ... ggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

CCCTAATTATGCCCGGAACTATAGAAGATTTGCTACTGGTGGTTTAGCAGGCCAAGTACTTGTGCTGACAAAGAAGTCTTGGGGAGGTTACCATAAGAAGgtaagtttgg ... ggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

CCCTAATTATGCCCGGAACTATAGAAGATTTGCTACTGGTGGTTTAGCAGGCCAAGTACTTGTGCTGACAAAGAAGTCTTGGGGAGGTTACCATAAGAAGgtaagtttgg ... ggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcatccagtgacctctaatggctagcacatctcttgcttgatggttatgtagGTTTTGCGTGATGGTGAAGGGCCAATCCATTCGATGAAGTGGAGGGCGGATCTTCTTGCTTGGGCTAATGATGCAGGGGTCAAAGTGCATGATATGAGAA
                                               ttatgta  TA-rich tract