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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttctaatgtcttggatatccagctacagtgatgttattaaatatcaatagcttatgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA

Basic information

species Zea mays
transcript GRMZM2G011136_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011136_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 10
gtatgtttctaatgtcttggatatcc--------agctacagtgatgttattaaatatcaatagctta-------tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA
|||||||||| || | |||| ||||| | || || || || | ||||| || |||| | ||||||||||||| || |||| || ||||||||||||||||||||| |||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||
gtatgtttctgatcttttggctatccctgcatgcaactctagcaatattttactatatcgatcccttacccttggtcccttgcagGTCACTTTATTTGGTTCCCTTGAAATGCCAAAGGCTGATATATGGGTTGTCATAGCAATCTTGTCGGGTGTGATTGGATATTGTGCTAAGATCTACTTCA
















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|6227171|gb|AW155700.1|AW155700
EST:     TAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTG                         GTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTA
genomic: TAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTA
EST: gi|32850036|gb|CD989717.1|CD989717
EST:     TAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTG                         GTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTA
genomic: TAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTA
EST: gi|32839351|gb|CD979032.1|CD979032
EST:     TAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTG                         GTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTA
genomic: TAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTA

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), 49 (downstream exon)
Score: 125

CCAGAGAAGAAAAATCCGTCACTAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

CCAGAGAAGAAAAATCCGTCACTAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

CCAGAGAAGAAAAATCCGTCACTAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 169

CCAGAGAAGAAAAATCCGTCACTAACACCAATGGATTGGGTCAAGTTTCTCATTTCTGCTGTTATCGGTTTGgtatgtttct ... tgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggatatccagctacagtgatgttattaaatatcaatagcttatgacttgcagGTCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCA
                        ttattaaatatcaata  TA-rich tract