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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGGCAGGTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagctccgagcgcgaagcctcattgctcagctctccttgtctctgcgtcgccgctaagcgggtctgttgttgcttctgattgcag

Basic information

species Zea mays
transcript GRMZM2G066362_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066362_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g07720.4 (Oryza sativa), 5'ss of exon 1
CCAGGCAG-GTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagctccgagcgcgaagcctcattgctcagctctccttgtctctgcgtcgccgctaagcgggtct---gttgttgcttctgat-tgcag
  || |   | || ||  | |||| ||| ||||| ||||||| || |||||| |||| |||||||| |||||||||||||||||||||| |||||||||||||  ||| |    |||         |   |||     ||||| | |   ||  | |  || |  |  |||   ||  |||||||   | |||||
-GAGTCGTCGCCGCCGTCCGACCGTAGGCCGCTCCACTTCGCGGCGTTCCTGCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacc----agcatctttttcctccgctt--tcctcctagccatcgcagctcacctcacggtttcttgcgtgcttgcttcgattctgcag
















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|78111543|gb|DV529940.1|DV529940
EST:     GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCCTACATGTCCCAG
genomic: GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG
EST: gi|211401320|gb|FL428497.1|FL428497
EST:     GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCCTACATGTCCCAG
genomic: GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG
EST: gi|211146265|gb|FL418222.1|FL418222
EST:     GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCCTACATGTCCCAG
genomic: GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG
EST: gi|78090317|gb|DV518691.1|DV518691
EST:     GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCCTACATGTCCCAG
genomic: GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG
EST: gi|211043010|gb|FL421674.1|FL421674
EST:     GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCCTACATGTCCCAG
genomic: GGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG

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), 35 (downstream exon)
Score: 90

CCAGGCAGGTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG


Block sizes: 43 (upstream exon), 35 (downstream exon)
Score: 76

CCAGGCAGGTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 84

CCAGGCAGGTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 89

CCAGGCAGGTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagct ... ctgattgcagATACCAAGATCGACTGGGACGCCTACATGTCCCAG