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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagatcctgttttccacaaatgactatcgataatgttctcatatggtttactttctactcggataaagttttcatcagttggtctctgtctatgtctacgtctgatggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG

Basic information

species Zea mays
transcript GRMZM2G412899_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412899_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 6
gtatgtagatcctgttttccacaaatgactatcgataatgttctcatatggtttactttctactcggataaagttttcatcagttggtctctgtctatgtctacgtctgatggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG
|||||||  |  |||| | |||  ||| ||           ||||  || || |   |      |  |||    | | ||   || ||  || | | |   ||       | | || |||||||||||| || |||||||||| |||||||| ||||||||||||||||||||||||||||||||  ||||||| || || |||||||||||||| || |
gtatgtaattggtgttatgcacctatgcct--------caatctctgattgtctgtat------caaatattaatcttattcatttgtacctttttct---tataatcccttggatccagGTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCAACCTGCCTTGGAATCGTAGTATCTCTCCTAATTGGTACACCTGTGAAGG
















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|211253183|gb|FL345481.1|FL345481
EST:     GAACAGGGATGGGATTGGGTCCACCAGTAGCTTCACTTTATATAACGGAG                         GTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCA
genomic: GAACAGGGATGGGATTGGGTCCACCAGTAGCTTCACTTTATATAACGGAGgtatgtagat ... tggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCA




















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: 45 (upstream exon), 49 (downstream exon)
Score: 161

TGCTCTCTCCAATAGTTTGGAGGGTATGCTCCTTGGAAGATTTTTGGTAGGAACAGGGATGGGATTGGGTCCACCAGTAGCTTCACTTTATATAACGGAGgtatgtagat ... tggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 108

TGCTCTCTCCAATAGTTTGGAGGGTATGCTCCTTGGAAGATTTTTGGTAGGAACAGGGATGGGATTGGGTCCACCAGTAGCTTCACTTTATATAACGGAGgtatgtagat ... tggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 119

TGCTCTCTCCAATAGTTTGGAGGGTATGCTCCTTGGAAGATTTTTGGTAGGAACAGGGATGGGATTGGGTCCACCAGTAGCTTCACTTTATATAACGGAGgtatgtagat ... tggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 163

TGCTCTCTCCAATAGTTTGGAGGGTATGCTCCTTGGAAGATTTTTGGTAGGAACAGGGATGGGATTGGGTCCACCAGTAGCTTCACTTTATATAACGGAGgtatgtagat ... tggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataaagttttcatcagttggtctctgtctatgtctacgtctgatggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG
                                       gtctgat  putative branch site (score: 163)
     aagtttt  TA-rich tract