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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtcaacctttcaaacatagcttacaacagcaccgctagagttcaaaggcatatgcttagatttcaaaaaccaggacaatcctgttcaaccatttcctgtcgacttcactacctgttgtgtaaaagggaggagagcatttctgtctctatttgacacttgtaaataacatttcactgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG

Basic information

species Zea mays
transcript GRMZM2G177631_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 10
gtactgtcaacctttcaaacatagcttacaacagcaccgctagagttcaaaggcatatgcttagatttcaaaaaccaggacaatcctgttcaaccatttcctgtcgacttcactacctgttgtgtaaaagggaggagagcatttctgtctctatttgacacttgtaaataacatttcactgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG
                                                                                                  |  ||||  |||  ||| |  ||||   |||      |  | |           |  | ||| |   || | | || |  || | || |||| ||||| |  || || || ||||| || ||||||||||| ||||| ||||||||||||||||||||||||||||| ||||||||  | ||||| || ||
-------------------------------------------------------------------------------------------------gtattgtcagcttgtctaacaattgtc--aaataacataaggtaacataagaaaaacatcacagtaa-aactcaaatgtttctttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG

upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 11
gtactgtcaacctttcaaacatagcttacaacagcaccgctagagttcaaaggcatatgcttagatttcaaaaaccaggacaatcctgttcaaccatttcctgtcgacttcactacctgttgtgtaaaagggaggagagcatttctgtctctatttgacacttgtaaataacatttcactgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG
                                                                      ||||||| ||  |     |||||    ||  | ||      | | | | |||  ||| |          ||||    | | |   | ||   |     ||  |||| |||||  |  |||   ||| |  |||||| |    ||  |   | |   |||| | |||||||| |||||||||||| |||| ||||| |||||||| ||||||||| | ||
----------------------------------------------------------------------aaaaccatgattac----ttcaatttgttgttatca--catattcctttttgcataata----------cattc---tatttgcctcacttctaattttattatttaactgtcatatagGGATTGAGAGTGAGAAGTCAACTATGTTGTCTGAGACGAAATTGGAGAAGAAGTTTGGGCAGTCTCCTGTGTTTGTTGCATCAACTCTTCTTGAGGATGG
















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|32834499|gb|CD974177.1|CD974177
EST:     GTGAAATTGATGAAGGTGCTCCAG                         GTGCTGATATCGAGAAGGCCGGAATTGTAAATCAACAGAAACTAGAGAAGA
genomic: GTGAAATTGATGAAGGTGCTCCAGgtactgtcaa ... tgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGA




















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: 169

ACAAAACCAAAGACGGAGAAGAAGAAAAGATTATTTTTCAAGAAAGCAGAAAACCCATCTCCTGCATATGCTTTGGGTGAAATTGATGAAGGTGCTCCAGgtactgtcaa ... tgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

ACAAAACCAAAGACGGAGAAGAAGAAAAGATTATTTTTCAAGAAAGCAGAAAACCCATCTCCTGCATATGCTTTGGGTGAAATTGATGAAGGTGCTCCAGgtactgtcaa ... tgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

ACAAAACCAAAGACGGAGAAGAAGAAAAGATTATTTTTCAAGAAAGCAGAAAACCCATCTCCTGCATATGCTTTGGGTGAAATTGATGAAGGTGCTCCAGgtactgtcaa ... tgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 369

ACAAAACCAAAGACGGAGAAGAAGAAAAGATTATTTTTCAAGAAAGCAGAAAACCCATCTCCTGCATATGCTTTGGGTGAAATTGATGAAGGTGCTCCAGgtactgtcaa ... tgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagcatttctgtctctatttgacacttgtaaataacatttcactgttctccagGTGCTGATATCGAGAAGGCCGGAATCGTAAATCAACAGAAACTAGAGAAGAAATTTGGGCAGTCTTCTGTTTTTGTCGCATCAACACTTCTTGAGAACGG
                               aaataac  putative branch site (score: 369)
                                       tttcactgttctcc  CT-rich tract
                           ttgtaaataacattt  TA-rich tract