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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcggataatatcccattggagagttcagatgttgtatgagggacatgcacatattttaccatgatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT

Basic information

species Zea mays
transcript GRMZM5G807639_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 8
gtaagg-cggataatatc-ccattggagagttcagatgttgtatg----agggacatgcacatattttaccatgata--ttgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT
|||||  |   |   |||  || | |   |  ||||| || | |     ||| ||| ||| || ||| |||||  ||  ||||||||||| ||||||||||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||  | ||||||||||||||||||||
gtaagatcaactttcatcatcaataggttgcacagatttttttttttacaggtacaagcatatctttaaccattttaatttgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT
















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|67025111|gb|CO453860.1|CO453860
EST:     AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|7031253|gb|AW461141.1|AW461141
EST:     AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|6056485|gb|AW090875.1|AW090875
EST:     GGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: GGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|211169877|gb|FL077606.1|FL077606
EST:     CAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: CAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|32834807|gb|CD974485.1|CD974485
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|67031724|gb|CO460473.1|CO460473
EST:     CGTCCCCTTCAGGAAC-ACAACTCCCCTCCAAAAGAACGGGAGCGGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAAGATTC
genomic: CGTCCCCTTCAG-AACCACAACTCCC-TCCAAAAGAACGGGAGCGG-CGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTC

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), 47 (downstream exon)
Score: 116

GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagagttcagatgttgtatgagggacatgcacatattttaccatgatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT
                               acatatttta  TA-rich tract