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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggtttttgtttcttgtattctctaataactttgtttttcgaatgtatatatcggtttaaagtgtacaatttgttgatgtag

Basic information

species Zea mays
transcript GRMZM2G001713_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001713_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 5
TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggtttt-tgtttcttgtattctctaataactttgtttttcgaatgtatatatcggtttaaagtgtacaatttgttgatgtag
|||||||||||||||||||||||| ||||| ||||||||| ||||||||||||||||  | || || | ||| |||||| ||| ||||||||| ||||||||||||  | | | |  |   |||| || |   || |   || ||    || | |   || |   ||| ||              
TGAAGGAGAAGGTGGTGAAATTGTGTTTGGAGGAATGGATCCTAGCCACTACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctgtttctgctaagttctgtagtgttttcgacatttgatgtaatgtttgcattgactttgtgcag-------------
















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|211224723|gb|FL222441.1|FL222441
EST:     ACAAGGGCGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|31361595|gb|CD445952.1|CD445952
EST:     GTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: GTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|211222666|gb|FL222431.1|FL222431
EST:     ACAAGGGCGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|32807856|gb|CD960090.1|CD960090
EST:     ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|211224720|gb|FL222438.1|FL222438
EST:     ACAAGGGCGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG

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), 17 (downstream exon)
Score: 334

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 707

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG


Block sizes: 49 (upstream exon), 17 (downstream exon)
Score: 453

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 351

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG