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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATCCTGTGGCGCACATTGTACAGCTGCCGTCGCTGAGCCTCGAGAAAACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgcaataatttttcactgggtcaacaatccttgagaaattaatacaatctattcaattaaatattcactatagcatgctttttacag

Basic information

species Zea mays
transcript GRMZM2G074024_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074024_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g40260.1 (Oryza sativa), 5'ss of exon 3
AGTATCCTGTGGCGCACATTGTACAGCTGCCGTCGCTGAGCCTCGAGAAAACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgcaataatttttcactgggtcaacaatccttgagaaattaatacaatctattcaattaaatattcacta-tagcatgctttttacag
||| |||||||| ||||||||||||||||| || ||||| |||||||||||| ||||||| |||| | ||| ||||| ||||| ||||||||||||||||||||| | || || |||| ||| | || | || | |||| |||| ||| ||||||||| | | || | | |||
AGTGTCCTGTGGAGCACATTGTACAGCTGCTGTTGCTGAACCTCGAGAAAACAATGGCACTATATCAAGAAGTAGGCTCTGGGTCTGGGGACAAAATCAGgtttgcccctcatatgatt-actgt-ccaata-----tgtgtgatcag--caatttatttaataaaatattcagcacttgcggtatccatgcag
















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|76933450|gb|DV173464.1|DV173464
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|31663993|gb|CD573173.1|CD573173
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|211129102|gb|FL371420.1|FL371420
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGAAGCTTTCCCACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|29543619|gb|CB603999.1|CB603999
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|211047338|gb|FL129969.1|FL129969
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|76021288|gb|DT948458.1|DT948458
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|71420798|gb|DR805186.1|DR805186
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
EST: gi|76930470|gb|DV172399.1|DV172399
EST:     ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAG                         GGTTCAGATTACCCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG
genomic: ACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCC-TCGTCTATTTTGGGGAGCTTTCACACCAAACACG

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), 45 (downstream exon)
Score: 42

AGTATCCTGTGGCGCACATTGTACAGCTGCCGTCGCTGAGCCTCGAGAAAACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 54

AGTATCCTGTGGCGCACATTGTACAGCTGCCGTCGCTGAGCCTCGAGAAAACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 31

AGTATCCTGTGGCGCACATTGTACAGCTGCCGTCGCTGAGCCTCGAGAAAACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 82

AGTATCCTGTGGCGCACATTGTACAGCTGCCGTCGCTGAGCCTCGAGAAAACGATGGCACGGTATCGAAAAGCAGGCTTTGGGTTTGGGGACAAAATCAGgtttgctgca ... ctttttacagGGTTCAGATTACCCTCGTCTATTTTGGGGAGCTTTCACACCAAACACG