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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatagttcacacttgttgaaaaagaatttattttttttctacgacggttattaacttatctctgttctttgttgcag

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 20
CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatagttcacacttgttgaaaaagaatttattttttttctacgacggttattaacttatctctgttctttgttgcag
|||||| || || ||||||||||| ||||| || ||||||||||| ||||||||||||| ||| || |||||||| ||||| | ||| |  |  || |    | |||||| |     || |  |          | ||| |||| | ||    |   | ||| |||
CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtgttctttta----ttttgaaagatggcatactact----------gattactaacct-tcaacatctctggtttcag
















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|32930909|gb|CF035721.1|CF035721
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGA-G---                         GCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTTCTCCTTTTAA
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGAC-TCCCCTTTTAA
EST: gi|6022040|gb|AW066983.1|AW066983
EST:     GACAAGGGAGTGGTTTACACCCCCAAGGATCTTCCTTTGCAATGA-G---                         GCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTTCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|60344250|gb|DN211223.1|DN211223
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|211181077|gb|FL441225.1|FL441225
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTTCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|101391685|gb|EB817779.1|EB817779
EST:     GACAAGGGAGTGGTTTACACCCCCAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|149066719|gb|EE286860.2|EE286860
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
EST: gi|67017479|gb|CO446228.1|CO446228
EST:     GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA                         --A--TAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG
genomic: GACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAG

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 129

CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAGTACCCTTTTCTTTTATTCCATGCTACAAAGTTTGGTGTCGTAACAAGCA


Block sizes: 37 (upstream exon), 46 (downstream exon)
Score: 3

CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAGTACCCTTTTCTTTTATTCCATGCTACAAAGTTTGGTGTCGTAACAAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 548

CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAAgtaataatag ... tttgttgcagGCAAATAACCTCCGTTGTGGTCGTAACGAATGGCTGGACTCCCCTTTTAAGTACCCTTTTCTTTTATTCCATGCTACAAAGTTTGGTGTCGTAACAAGCA