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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATATGAAGATGAAGAGTTTTATCATGAGTCAGAAGATGAATATGTTGACGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcaccattcatgtagtgtaatatggcactactactatccttgttttgtttatgtgattgatttattaatattggtttgctatttcag

Basic information

species Zea mays
transcript AC213600.3_FGT002
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC213600.3_FGT002 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g16970.3 (Oryza sativa), 5'ss of exon 7
AAATATGAAGATGAAGAGTTTTATCATGAGTCAGAAGATGAATATGTTGACGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcaccattcatgta--------gtgtaatatggc-acta-ctactatccttgttttgtttatgtgattgatttattaatattggtttgctatttcag--------
               || || |  ||||| ||||| ||||||||||| || || |||||||||||||||| ||| ||||| ||||||||||| || |||||| || |||||||| |||         |||||  || | |||| ||    || |||  |  ||| |||  ||| || ||  || ||  |||  | |||           
---------------GACTTCTCACATGAATCAGATGATGAATATGTCGATGATCATGATGAGCATGTTGCGTCATACAAGTCTGATGATGATCAGAAAGGTGATGACCATTCAGgtatatggttcatgtaacctgcccactatctctcttctttgactcctttctgtatttggtt-atcgatttttcttttttcttttgttctgtcag
















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|211164201|gb|FL365727.1|FL365727
EST:     CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG
genomic: CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG
EST: gi|67033121|gb|CO461870.1|CO461870
EST:     CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG
genomic: CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG
EST: gi|60340820|gb|DN207793.1|DN207793
EST:     CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG
genomic: CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG
EST: gi|32857890|gb|CD997571.1|CD997571
EST:     CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAG                         ATTTAACTGAGCCAGGACATGCATCGGGGTTGGACAAAGTTCAGCAGACTG
genomic: CGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTG

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: 166

AAATATGAAGATGAAGAGTTTTATCATGAGTCAGAAGATGAATATGTTGACGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTGTACAAAATGTTTTCCAAAAATTCAACTCTTTTAAGACCCCTGTAGATTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 215

AAATATGAAGATGAAGAGTTTTATCATGAGTCAGAAGATGAATATGTTGACGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTGTACAAAATGTTTTCCAAAAATTCAACTCTTTTAAGACCCCTGTAGATTT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 230

AAATATGAAGATGAAGAGTTTTATCATGAGTCAGAAGATGAATATGTTGACGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTGTACAAAATGTTTTCCAAAAATTCAACTCTTTTAAGACCCCTGTAGATTT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 260

AAATATGAAGATGAAGAGTTTTATCATGAGTCAGAAGATGAATATGTTGACGACCATGATGAGCATGTTGAGTCCTACAAATCTGATGATGACCAAAAAGgttatcacca ... gctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTGTACAAAATGTTTTCCAAAAATTCAACTCTTTTAAGACCCCTGTAGATTT