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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggactattagcccttacctatttacctcacacaaggacaacaatcatatgagtttattccttatccagtataaatgtttgctgttaatgtcttatg...

Basic information

species Zea mays
transcript GRMZM2G457881_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G457881_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g49730.2 (Oryza sativa), 5'ss of exon 13
GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggactattagcccttacctatttacctcacacaaggaca-acaatcatatgagtttattccttatccagtataaatgtttgctgttaa-tgtcttatg
|| |||| ||||||||||| || |||||||||||||| ||||||||||| ||||||||||||||||||||| || |   || ||   |  ||| |         | | |        | |     ||| || ||||||||||   || ||  ||   | | | |  
GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaatacttttccctattcacctacttactgtgttcatatatcgcggagtaacaactttcattgtccagtataagctttggcctttggctatttca--
















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|89755657|gb|DY686001.1|DY686001
EST:     TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATG                         GTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
genomic: TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
EST: gi|211477964|gb|FL457116.1|FL457116
EST:     TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATG                         GTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
genomic: TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
EST: gi|149023563|gb|EE154541.2|EE154541
EST:     TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATG                         GTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
genomic: TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
EST: gi|71322958|gb|DR798156.1|DR798156
EST:     TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATG                         GTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA
genomic: TTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGA

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: 46 (upstream exon), 47 (downstream exon)
Score: 42

GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGATATACTTAAAGTAACACATGGCGTAAAATCCCAGTTCATGAAAGAGCTC


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 20

GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGATATACTTAAAGTAACACATGGCGTAAAATCCCAGTTCATGAAAGAGCTC


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 29

GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGATATACTTAAAGTAACACATGGCGTAAAATCCCAGTTCATGAAAGAGCTC


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 17

GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggacta ... tctgttgtagGTTGCTTGAGTTCACAGAGGATGCACTAAAATCTTTAACCAGAGCAGCAGATATACTTAAAGTAACACATGGCGTAAAATCCCAGTTCATGAAAGAGCTC