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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagctgtcgtgccgaccaaacgtttcatgtgagctgtgcagcctgcggtggatttgtaattttcttcttcctttgtttctctgtag

Basic information

species Zea mays
transcript GRMZM2G104632_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104632_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 5'ss of exon 3
TGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagctgtcgtgccgaccaaacgtttcatg--tgagctgtgcagcctgcggtggatttgtaattttcttcttcctttgtttctctgtag
||| |||||| | ||||||||||| |||||||| || ||||| ||||||||| | ||||||||||  |||   | || | |||| || | ||    ||  ||||||| | || |   |||||    ||  | |||  | | | | |||||||
TGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCACgtaagtgtctggtttcccaaacaaatgtgtaataatagaattgtgcaggcagcagc--atttga---ttattcctttttgtttctgtctgtag
















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|9961539|gb|BE644327.1|BE644327
EST:     CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCAC                         AATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
genomic: CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
EST: gi|15632381|gb|BI679474.1|BI679474
EST:     CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCAC                         AATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
genomic: CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
EST: gi|6564069|gb|AW231691.1|AW231691
EST:     CTGCCATGCCAC                         AATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
genomic: CTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
EST: gi|32799643|gb|CD951879.1|CD951879
EST:     CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCAC                         AATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
genomic: CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
EST: gi|32796951|gb|CD949187.1|CD949187
EST:     CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCCGCCATGCCAC                         AATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
genomic: CCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
EST: gi|91869745|gb|EB400519.1|EB400519
EST:     CTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCAC                         AATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
genomic: CTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG

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), 39 (downstream exon)
Score: 307

TGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 155

TGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 76

TGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 207

TGCGAGGAACCTCGAGCCGCTGAGGGCGATAGCCACGCAGGCGCCCCCTGCCATGCCACgtaagtagct ... ttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG