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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataagcagcctttctcttaaccctttgatttcgtcatcgcttctatttttattcagctgtatttgaataagcccgttcttacatcatacgggatcgattttcag

Basic information

species Zea mays
transcript GRMZM2G015967_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015967_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g29370.1 (Oryza sativa), 5'ss of exon 5
TGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataagcagcctttctcttaaccctttgatttcgtcatcgcttctatttttattcagctgtatttgaataagcccgttcttacatcatacgggatcg-attttcag
|||||| ||||| |||||||| || || ||| | |||||  ||||||||||  | ||||| |||||||| || ||||||||||||||||||||||||||||| ||||    |||   ||   ||     ||   ||||   |||      |  |||   || |||||| |  || |||  |||||||||  | ||  ||||     |||||
TGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggcacagttctttcttt----tttcagtttcagaatctaccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcag
















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|13558732|gb|BG550088.1|BG550088
EST:     AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
genomic: AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
EST: gi|13558131|gb|BG549487.1|BG549487
EST:     AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
genomic: AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
EST: gi|16378290|gb|BI992374.1|BI992374
EST:     AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
genomic: AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
EST: gi|13562267|gb|BG550487.1|BG550487
EST:     ATGGTTGATGGTGATAAGGCGCCTGTATATGGGTGAAACACTTGAA                         GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
genomic: ATGGTTGATGGTGATAAGGCGCCTGTATAT-GGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
EST: gi|13558132|gb|BG549488.1|BG549488
EST:     AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
genomic: AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGA
EST: gi|161589776|gb|EY963523.1|EY963523
EST:     AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGTCGCTACAAGGCTCAAACAAA
genomic: AAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAA

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: 44 (upstream exon), 49 (downstream exon)
Score: 59

TGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 306

TGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 16

TGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 175

TGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTATGGTTGATGGTGATAAGGCGCCTGTATATGGTGAAACACTTGAAgtgagtataa ... cgattttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA