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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcctggattttctcaattgtggttgttgacctttgtatgtttgtttggcctaaaatatgttttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 27
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 25
gttattttcctggattttctcaattgtggttgttgacctttgta------------tgtttgtttggcctaaaatatgttttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG
||||||||| ||     |     ||||||| |   | |||   |            || || ||   | ||||| |||||||| ||   |||||||||||||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||| | |||
gttattttcttgataccttctttttgtggtggaaaaacttaacaataggttgtttttgctttttaatcttaaaacatgttttacca---gGTGTCAGTTCACAGTATTAGGTTGCCAAAGAACAGCACTGTCGGTGATGTGCTAAATGATATAAAATCAAAG
















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|61118763|gb|DN559724.1|DN559724
EST:     AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAG                         GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
genomic: AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
EST: gi|76909980|gb|DV163634.1|DV163634
EST:     AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAG                         GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
genomic: AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
EST: gi|60394863|gb|DN227732.1|DN227732
EST:     AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAG                         GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
genomic: AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
EST: gi|211394943|gb|FL031667.1|FL031667
EST:     AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAG                         GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG
genomic: AAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTG

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: 174

TTCTGATATTCTGTACTATGAAGTATTGGACATACCACTTCCAGAATTACAAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 105

TTCTGATATTCTGTACTATGAAGTATTGGACATACCACTTCCAGAATTACAAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 63

TTCTGATATTCTGTACTATGAAGTATTGGACATACCACTTCCAGAATTACAAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 121

TTCTGATATTCTGTACTATGAAGTATTGGACATACCACTTCCAGAATTACAAGCGCTGAAGACATTAAAAGTTACCTACCATCATGCCACAAAAGATGAGgttattttcc ... ttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggttgttgacctttgtatgtttgtttggcctaaaatatgttttatcatcagGTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG
                               gcctaaa  putative branch site (score: 121)
                                           ttttatc  putative PPT
                                  taaaatatgttttatc  TA-rich tract