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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctctggattgcctttacatatctacactctgagatcttcaagagatagtaaatgcttgttgactattatgcttaaatgtttttccttttccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA

Basic information

species Zea mays
transcript GRMZM2G409265_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------atctctggattgcctttacatatctacactct-gagatcttcaagagatagtaaatgcttgttgactatta--tgcttaa-atgtttttccttttccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA
                                                  | | |  |||   |||    ||      ||| |||||||  |  || |  |  ||     ||    | ||    | ||  || | |||  ||| || || |||||||| ||||||||||| ||||||||| |||| ||||| |||||||||||||||||||| |||||||||||||| || || | ||||||||| || ||||
gtacaaattcttcactggaggcaaaactcttatgcatattttctctccattttttccattatgtttgtgcatgcttggtctagagatctggagaaggtgttggatatccttttgtcaataaacacctatcatttatttattttgccatggcagGTTACGACAACAATTAATAACCTTATCATTGGCCGAGTCTATTGCCATCACCATGGCACGATGAACATAAGTGGAAACAGGCAATATTCATGTAAGCTGA
















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|60346794|gb|DN213767.1|DN213767
EST:     GTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAG                         GTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCAC
genomic: GTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCAC
EST: gi|60344714|gb|DN211687.1|DN211687
EST:     GTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAG                         GTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCAC
genomic: GTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCAC
EST: gi|60344453|gb|DN211426.1|DN211426
EST:     GTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAG                         GTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCAC
genomic: GTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCAC

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), 47 (downstream exon)
Score: 118

CAATCTAAAGAGCAAATTCTGGGGACAATCCATTCGACTGGATCCTAATGGTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 53

CAATCTAAAGAGCAAATTCTGGGGACAATCCATTCGACTGGATCCTAATGGTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

CAATCTAAAGAGCAAATTCTGGGGACAATCCATTCGACTGGATCCTAATGGTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

CAATCTAAAGAGCAAATTCTGGGGACAATCCATTCGACTGGATCCTAATGGTGTGCTAACTTTAGAGTTTGATGATGGAGAAACTTTCCAATGGAGTAAGgtataatttt ... tccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagtaaatgcttgttgactattatgcttaaatgtttttccttttccttgtcagGTTACAACAACAATTAACAACCTTATCCTTGGTCGAGTATATTGCCATCACCATGGCACAATGAACATAAGTGGGAATAGACGATATTCATGCAAACTGA
             tgttgac  putative branch site (score: 95)
                                 tgtttttccttttcct  putative PPT
                    tattatgcttaaat  TA-rich tract