Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgctcaattatgagttctgtagccttgtcaactaataccttgaatcgtgagtcatgacatttatctttgttctgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG

Basic information

species Zea mays
transcript AC234528.1_FGT005
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 8
gtattgctcaattatgagttctgtagccttgtcaactaataccttgaatcgt-gagtcatgacatttatctttgttctgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG
|||  ||||||   ||| ||||   ||||| | | |||   | ||| || || |  |    |||||| | ||||||||      |||||||||||  | || || ||||| || |||||| ||||||| ||||| |||||||||||||| ||||||||||| ||||||||||| |||||||| ||||
gtaaagctcaaccctgaattcttatgccttattatctagctctttgtatagtagcatttacacattt-tatttgttct----ttcagCAAATAATAAGGCCCCTGGACAACCCAATCAAATCAACTGGTCATATACAAATACTTTATGGCAATCTTGCACCAGAAGGTTCTGTAGCAAAAATTACTG

upper sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 8
gtattgctcaattatgagttctgtagccttgtcaactaataccttgaatcgtgagtcatgacatttatctttgttctgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG
       | || |     ||     |  | |  |   |||      |  | ||  ||      |||| || | || |  |    ||||||||||  ||||  | |  || || || ||    ||||| ||  | ||||   | ||||||||||||||||| || |||||||| |||||||| ||||
------gtgaaatgcacatttcactgtttagatataaaatgaacatacgcatgtttctcattgttta-ctgtcttttttcttctagCAAATAATAAGACCGTTGGCAAACCCCATAAAGAAGACTGGACACCTCCAAACTTTATATGGAAATCTTGCACCAGAGGGTTCTGTTGCAAAAATTACTG
















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|31363513|gb|CD447870.1|CD447870
EST:     AAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAAGGGCAG                         CAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAA
genomic: AAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAGGGGCAGgtattgctca ... tgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAA
EST: gi|31358397|gb|CD442754.1|CD442754
EST:     AAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAAGGGCAG                         CAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAA
genomic: AAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAGGGGCAGgtattgctca ... tgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAA

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), 48 (downstream exon)
Score: 193

TTACTGGTAAAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAGGGGCAGgtattgctca ... tgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 112

TTACTGGTAAAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAGGGGCAGgtattgctca ... tgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

TTACTGGTAAAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAGGGGCAGgtattgctca ... tgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 62

TTACTGGTAAAACTCTAGCTGAGAATGCTAAAATCTTCCCTCCTCTGTCTGAGGGGCAGgtattgctca ... tgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaactaataccttgaatcgtgagtcatgacatttatctttgttctgacacacagCAAATAATTCGACCACTTGACAATCCTATCAAACCAACTGGCCATATTCAAATACTTTATGGAAATCTTGCACCGGAAGGTTCTGTCGCAAAAATAACTG
                                          ttctgac  putative branch site (score: 62)
                                tttatctttgttct  CT-rich tract
                               atttatcttt  TA-rich tract