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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctcacccccctcgctgtttccctaccttctcttcttccatccgtccgctgatgatttggacccgccttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG

Basic information

species Zea mays
transcript GRMZM5G871262_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 1
-----------------gtaacctcacccccctcgctgtttccctaccttctcttcttccatccgtccgctga------tgatttggacccgcct--------tccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG
                   |    ||| |    | || |  |  | |    ||| || | |  |   | ||||      |   ||||| |||  |        | |||||||||| || |||||||||||||   |||| ||| | ||||||| ||  |||||||| || ||||||||| ||||||||||||||||||
gtaagtagtatacatatacatttccactctttcctctatcccattgcgca-tctgctgctaaactctcactgaatgttgttgattggatccgtgtgttgttgcttcctgcagGTCAGTGGGGAAGAGGCTCACCTCCGCTCTCCTGTGGGTCGCCGTCTCCGCGGTGGTTTGCGGCCTCATCCTCGGCATCCTATACG
















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|149015378|gb|EE045218.2|EE045218
EST:     TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAA                         GTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC
genomic: TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC
EST: gi|211082082|gb|FL165096.1|FL165096
EST:     TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAA                         GTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC
genomic: TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC

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: 46 (upstream exon), 48 (downstream exon)
Score: 123

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 126

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 142

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaccttctcttcttccatccgtccgctgatgatttggacccgccttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG
                        cgctgat  putative branch site (score: 133)
                                       cccgccttccctgc  putative PPT
                             atgattt  TA-rich tract