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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgtagatttgatgttattctttccagataggcttcgattgctggtttgtgatgcatcttttttcattctctttcctag

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348675_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 5'ss of exon 10
AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgtagatttg----atgttattctttccagataggcttc----gattgctggtt------------------------tgtgatgcatcttttttcattctctttcctag
||||| ||||| |||||||| ||||| ||||||||||| ||||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||||||   |||  |||      |||  |   |||  || | |  |||      ||| |  ||                        | ||||   |  ||||   |    ||||||||
AAAATTGCTGAACAAGATGGTGGCCGATATGAGATGGCAGTATATGCTTTACAATGCAGTAACTTAAAGCGTATCTTGCCGATCTGTACTGACTGGGAGgtatactgtttattcagctcatgcaaacgttttgagtttgatttcttgaagttgttctttccttgactgaatgcgtgacctccatatgatatgttattttctctctgatttcctag
















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|211285653|gb|FL023028.1|FL023028
EST:     TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG                         TCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
genomic: TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
EST: gi|60349063|gb|DN216036.1|DN216036
EST:     TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG                         TCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
genomic: TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
EST: gi|60349063|gb|DN216036.1|DN216036
EST:     TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG                         TCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
genomic: TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
EST: gi|5567060|gb|AI881971.1|AI881971
EST:     TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACT-GG-G                         --AGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
genomic: TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
EST: gi|31441055|gb|CD510486.1|CD510486
EST:     TACAATGCAGTAACTTAAAGCG-GTCTTGCCAATCTGTACTGACTGGGAG                         TCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA
genomic: TACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 223

AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTAGAATTATCTCAGTACCAAACAAGTAGACCAGAAAAGCAACTTGATGACG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 52

AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTAGAATTATCTCAGTACCAAACAAGTAGACCAGAAAAGCAACTTGATGACG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 73

AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTAGAATTATCTCAGTACCAAACAAGTAGACCAGAAAAGCAACTTGATGACG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 65

AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAGgtacgttgta ... tctttcctagTCAGCTTGTTGGGCAATGGCAAGATCCTGGCTAGATGTTCAAGTGGATCTAGAATTATCTCAGTACCAAACAAGTAGACCAGAAAAGCAACTTGATGACG