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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttatttatgctaatacttttttgtgattcacatgtatcactatcactttctgcactaattttcttccaaaaaagattgacagttgctactgttgttgctgacatgattttctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT

Basic information

species Zea mays
transcript GRMZM2G099328_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099328_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 13
gtaatttatttatgctaatactttt--ttgtgattcacatgtatcactatcactttctgcactaattttcttccaaaaaagattgacagttgctactgttgttgctgacatgattttctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT
|||  ||   | |||| ||  || |       | |||  || |   | || ||||  |||        | ||||       ||     |||  ||   |  ||  |       || ||||| | ||||||| ||    ||||||  | |||||||||||||||| ||||||||||| |||||| ||||| | ||||| || ||||||  ||||||||||| | || |
gtacatttactctgctcattgttctggcaaacaatcatgtgcacttccattacttcatgccacctccatgttccctttccaatcagt-gttagtaacatctttttt-------ttctctctctctagGATTTCGGTCTCTTAGTCCTCAGGTTGAAGAAGGCATATGCCAAGTTCTTTCCCACATGTGGCTCGAGTCAGAGATCATCTTTGGTTCTAGTATCGACAT
















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|14203375|gb|BG837052.1|BG837052
EST:     TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
EST: gi|211535560|gb|FL475981.1|FL475981
EST:     TGGTCCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
EST: gi|32859029|gb|CD998710.1|CD998710
EST:     TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTTTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
EST: gi|44900705|gb|CK827250.1|CK827250
EST:     TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTTTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
EST: gi|71773668|gb|DR971565.1|DR971565
EST:     TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTTGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTTTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
EST: gi|76910058|gb|DV163680.1|DV163680
EST:     TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
EST: gi|31362847|gb|CD447204.1|CD447204
EST:     TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG                         GATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT
genomic: TGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTAT

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: 48 (upstream exon), 45 (downstream exon)
Score: 29

ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 174

ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 218

ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT


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

ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAGgtaatttatt ... ctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaaaaagattgacagttgctactgttgttgctgacatgattttctctttttagGATTCCGAAACCTTAGTATTGAGGTTGAAGAAGGCATCTGCCAAGTTCTATCCCACCTGTGGTTAGAGTCGGAAATCATCGCTGGTTCTAGTAGCAACGT
                              tgctgac  putative branch site (score: 110)
                                      tgattttctcttttt  CT-rich tract
                                        attttctcttttta  TA-rich tract