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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcctacctcctagccgagcagcttagttccctttcgtcccttttcccttgtcgtgctgtgttttttactggatttggatggtattggtgtgcggtgcag

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g13820.2 (Oryza sativa), 5'ss of exon 2
GGCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcctacctcctagccgagcagcttagttccctttcgtcccttttcccttgtcgtgctgtgttttttactggatttgga--tggtattggtg--tgcggtgcag
|| || |||||||||||||||||||||||||||||||||||||| ||  |||||||||| | | | |||      |  ||     ||      |  || ||| | | |     | | ||  ||  | |||||||   ||||  |||||  || |||||||
GGGGCGGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCCGTGCTGgtgagctcgtgc-tactactactactactactacccgacaactagctcttcgcctatttccattttttgattcttagatttgggggtggtggtggtgcttggggtgcag
















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|149108497|gb|EE292808.2|EE292808
EST:     GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTG                         CCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
genomic: GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
EST: gi|211132360|gb|FK982427.1|FK982427
EST:     GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTG                         CCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
genomic: GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
EST: gi|71773971|gb|DR971859.1|DR971859
EST:     GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTG                         CCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
genomic: GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
EST: gi|211286765|gb|FK982431.1|FK982431
EST:     GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTG                         CCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
genomic: GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
EST: gi|148945776|gb|EC891060.2|EC891060
EST:     GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTG                         CCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG
genomic: GCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAG

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), 48 (downstream exon)
Score: 81

GGCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GGCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 94

GGCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 44

GGCGCTGGCAAGTCGGCCGTGCTGAACAGCCTCATCGGCCACCCGGTCTTGgtgagctcct ... tgcggtgcagCCGACGGGGGAGAACGGGGCGACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCA