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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatttttagtgtttcatttaagatcttaactaaatgactagttttttcttcttctcccttttccttcacattggcag

Basic information

species Zea mays
transcript GRMZM5G869572_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G869572_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 24
ATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtg-atttttagt--gtttcatttaagatcttaactaaatgactagttttttcttcttctcccttttccttcacat----tggcag
||||||||||||||  | |||||||| ||||| |||||||| |||||||| || ||| ||||||| || ||||| | || ||||| |||   | ||||      | |||    | |||  | ||        | |  | | |  | | ||||    |  |||
ATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAGgtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacag
















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|31363389|gb|CD447746.1|CD447746
EST:     TGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCACAGAG                         GGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTT
genomic: TGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTT
EST: gi|211163359|gb|FK967902.1|FK967902
EST:     TGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAG                         GGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTT
genomic: TGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTT
EST: gi|60338787|gb|DN205760.1|DN205760
EST:     TGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAG                         GGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTT
genomic: TGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTT

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: 47 (upstream exon), 48 (downstream exon)
Score: 62

ATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTTAGCTGGGTGTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 38

ATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTTAGCTGGGTGTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

ATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTTAGCTGGGTGTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 31

ATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAGgtgagtgatt ... acattggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTTAGCTGGGTGTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC