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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGATGATACGCCGTGGGACGGTGgtgagattcccagctctcagctctgagcctctgaccccttctcttatctgttgctcatttggtgcttgctgtgtggtcgttacttgcttgaaggtagttt...

Basic information

species Zea mays
transcript GRMZM2G074479_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 2
GCCGGATGATACGCCGTGGGACGGTGgtgagattcccagctctcagctctgagcctctgaccccttctcttatctgttgctcatttggtgcttgctgtgtggtc-gttacttgcttgaaggtagttt--------------
|||||||||||||||||||||||| ||||||  |  |     |  | | ||               |||  |||||| |||  ||| ||| ||    ||||||    || || ||||  | | |||               
GCCGGATGATACGCCGTGGGACGGAGgtgaggcttgctcggtttggttttg---------------ctccgatctgtagctggtttagtgattaggttgtggtttactaattccttggggatggttcgatgtggaaattgg
















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|18964126|gb|BM660824.1|BM660824
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGC
EST: gi|19351561|gb|BM896093.1|BM896093
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
EST: gi|211348190|gb|FL266275.1|FL266275
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
EST: gi|18964589|gb|BM661093.1|BM661093
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTAC
EST: gi|9824941|gb|BE575038.1|BE575038
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
EST: gi|166601500|gb|EG166657.1|EG166657
EST:     CCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAAACAAGCCA
genomic: CCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAA-CAAGCCA
EST: gi|18964591|gb|BM661094.1|BM661094
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCA
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCA
EST: gi|161593037|gb|EY963949.1|EY963949
EST:     CGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: CGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
EST: gi|211348193|gb|FL266278.1|FL266278
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
EST: gi|18964127|gb|BM660825.1|BM660825
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCA
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCA
EST: gi|211353005|gb|FL266309.1|FL266309
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
EST: gi|211280163|gb|FL132357.1|FL132357
EST:     GCCGGATGATACGCCGTGGGACGGTG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC
genomic: GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCAC

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: 29 (upstream exon), 46 (downstream exon)
Score: 3

GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGATTTGTCTCTAGGATGTTTCATCCAAATA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 21

GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGATTTGTCTCTAGGATGTTTCATCCAAATA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 19

GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGATTTGTCTCTAGGATGTTTCATCCAAATA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 9

GCCGGATGATACGCCGTGGGACGGTGgtgagattcc ... acatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGATTTGTCTCTAGGATGTTTCATCCAAATA