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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGATGACACGCCGTGGGACGGAGgtgagacccatccgatttagtttgcctcgatctgtaattgctcaatagctggcttctgcactttgggtactgccaatttcgttagttggtgattggttga...

Basic information

species Zea mays
transcript GRMZM2G007260_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 2
GCCGGATGACACGCCGTGGGACGGAGgtgagacccatccgatttagtttgcctcgatctgtaattgctca-atagctggcttct-gcactttgggtactgccaatttcgttagttggtgattggttga-
 |||||||||||||||||||| |||||||||  ||||  || ||  ||  |||   | |||  |     | ||| || | | || |   ||  | || |      || | |   ||   | |   ||  
ACCGGATGACACGCCGTGGGATGGAGgtgag-tccatttgactt--ttccccttattttgttctgatcaagatatctagttactagtgattgtgataatttggtgtttggtgaatgaaaaattaatgtt
















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|211209634|gb|FL170002.1|FL170002
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|22521069|gb|BU079880.1|BU079880
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211209639|gb|FL170007.1|FL170007
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211212202|gb|FL170018.1|FL170018
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211209646|gb|FL170014.1|FL170014
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211416709|gb|FL320472.1|FL320472
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211209638|gb|FL170006.1|FL170006
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211209637|gb|FL170005.1|FL170005
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|149074449|gb|EE162844.2|EE162844
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211209642|gb|FL170010.1|FL170010
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|211212201|gb|FL170017.1|FL170017
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|14701443|gb|BI233861.1|BI233861
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
EST: gi|20803162|gb|BQ294212.1|BQ294212
EST:     GCCGGATGACACGCCGTGGGACGGAG                         GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC
genomic: GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTC

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: 48 (upstream exon), 49 (downstream exon)
Score: 7

GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 3

GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 11

GCCGGATGACACGCCGTGGGACGGAGgtgagaccca ... acacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA