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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcagtttaacgtactagatctgatctggtacataatctctgcattgtgcttccttttacttgagatttgaaaaaagttctcatcaataaatttc...

Basic information

species Zea mays
transcript GRMZM2G063909_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcagtttaacgtactagatctgatctggtacataatctctgcattgtgcttccttttacttgagatttgaaaaaagttctcatcaataaatttc---------------------------------------------------------------------------------------
|||||||||||||||||||| |||||||||||||| ||| |  |  ||||||| |||||||| ||  | || ||||| || |||||||||||||||||||   ||||| |||||  ||||  ||||  |  ||  |    | |||  |  | |  | | |  ||| | ||   |    || |  ||                                                                                        
GTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAGgtatgctcagtttgttgtactggatcttctctgccacatcctg-ctaaacaaggattcactgcattgcatactcaaaatatgt---cgcagattatctttggaagaaggaacataatgttccttccatttttaaattgatattttagtgtgtgtgtgtgaactaaccatagttcacatccaatgcag

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 14
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtat--gctcagtttaacgtactagatctgatctggtacataat-ctctgcattgtgcttccttttacttgagatttgaaaaaagtt-ctcatcaataaatttc---------------------------------------
||||||||||||||||||||||||||||||||||| ||| |  |  ||||||| |||||||| ||| | || ||||| || ||||||||||  |||||||||   | ||| |||||  | ||   |||  | ||    |     | |     || |  | || ||    |  |   |  | |||  ||||                                        
GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAGgtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcag
















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|211458206|gb|FL358448.1|FL358448
EST:     CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAA                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     CATCATCTGTGAATGGGTT-GCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     CCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT

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: 46 (upstream exon), 49 (downstream exon)
Score: 285

GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA