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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctacatttgaacttcatatcttctctaaactctcgtatcattcattgtattcttcctttttttggacaatgcaaaattataatctgctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG

Basic information

species Zea mays
transcript AC207890.3_FGT002
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 3
gtgctacatttgaacttcatatcttctctaaactctcgtat---------cattcattgtattctt--------------cctttttttggacaatgcaaaattataatctgctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG
|| || ||| |||| || | ||||||| | || |  | ||           ||  ||||| ||  |                |   | |   ||||| ||||||  ||  ||   |||||||||||||||||||||||||| || || ||||| ||| ||||||||||||| || |||||||| || ||||||||||||||||| |||||  ||||| |||
gtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatg---ttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTTGGTACTGTTTACCTCGGTGACAAGAATGTTGCCTACTCGATAATTGCTG
















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|67028823|gb|CO457572.1|CO457572
EST:     TCTCTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAG                         GAGGTCTCATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTC
genomic: CCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatt ... gctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTC




















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), 49 (downstream exon)
Score: 125

GCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatt ... gctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatt ... gctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatt ... gctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

GCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatt ... gctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattgtattcttcctttttttggacaatgcaaaattataatctgctgttacagGAGGTCACATTCAGAGTGGATTATACGGCTCCTAATATTGGACGAGAATTCGGAACTGTTTATCTAGGTGACAAGAATGTTGCGTACTCAGTAATTTCTG
                           aatgcaaaattataat  TA-rich tract