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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatcctgttgcattaaaagatataatattcttttctataggtttggttatacaaattgttcaagaattaatgttctgatgcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG

Basic information

species Zea mays
transcript GRMZM2G009591_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009591_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g26570.1 (Oryza sativa), 3'ss of exon 11
----gttag-atcctgttgcattaaaagatataatat-tcttttctataggtttggttataca-aattgttcaagaattaatgttctgatgcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG
     |||| || |        | |  | | |||  | ||   |||||        ||||| | |||  ||    ||  |||| |   ||| ||| ||||||| |  | ||| ||||||| |||||||||||||||||||||||| | ||| |||| || || ||||||||||| ||||||
gagtattagtataccacatagatcattgctgtaagctatccagtctatcatccactttatatataataattatgtaagaaatgctgcaatgtattatcagGAACATCTGCAACAGTCAAACGCAACTGATGCATCAGGGAACATGATCCTTGGTGATATCGGCGTGCACCTTCATCAGAAG
















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|92088053|gb|EB484284.1|EB484284
EST:     TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
genomic: TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
EST: gi|78119430|gb|DV537814.1|DV537814
EST:     CAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
genomic: CAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
EST: gi|67014533|gb|CO443282.1|CO443282
EST:     TAGAGACCAAGGGATTTGCTCTGGTTTGTGTTGCTGAAGGAGCANGACAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCANGGAACATGGTTCTT
genomic: TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
EST: gi|160481643|gb|EY254213.1|EY254213
EST:     TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
genomic: TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
EST: gi|160481647|gb|EY254217.1|EY254217
EST:     TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAAAATGGTTCT
genomic: TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCT
EST: gi|5713662|gb|AI943654.1|AI943654
EST:     CAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGCCAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTNTT
genomic: CAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
EST: gi|91056415|gb|EB166833.1|EB166833
EST:     TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAG                         GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
genomic: TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTT
EST: gi|211370273|gb|FK995942.1|FK995942
EST:     TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAG                         GAATACTTTCAAAAGCCAAATGC
genomic: TAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGC

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), 47 (downstream exon)
Score: 44

ATTCACTGTTGATGGACCGAATGGAGTTCTTCGACATCTCGAACACCTGATAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG


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

ATTCACTGTTGATGGACCGAATGGAGTTCTTCGACATCTCGAACACCTGATAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

ATTCACTGTTGATGGACCGAATGGAGTTCTTCGACATCTCGAACACCTGATAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

ATTCACTGTTGATGGACCGAATGGAGTTCTTCGACATCTCGAACACCTGATAGAGACCAAGGGATTTGCTCTGGTTTGCGTTGCTGAAGGAGCAGGACAGgttagatcct ... gcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataggtttggttatacaaattgttcaagaattaatgttctgatgcattttcagGAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG
                                      ttctgat  putative branch site (score: 87)
                                              cattttc  CT-rich tract
            ttatacaaattgtt  TA-rich tract