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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataatccaatgttttgaagatgttgtgccttttgaagtacaacaaatcatgtaaatgtttgggctttggagtctttcatgatttgtttgtttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG

Basic information

species Zea mays
transcript GRMZM2G011575_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011575_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 2
cataatccaatgttttgaagatgttgtgccttttga-agtacaacaaatcatgtaaatgtttgggctttggagtctttcatgatttgtttgtttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG---
 || || | ||  |||  |||   |||   |||  | ||| ||  |  ||  |  |||| || |    |   |       |  |||     ||| |  |||||||| ||||||||||| |||||  || |||||||    ||||||||||||||||||| ||| |||||||||||||||  |  |   
-atgattctatccttttcagagtctgtttttttaaatagtgcactatttctcggtaatgctttgtgacttccgctacctgtttttttaaattttttgacagGCTGCTTGTGATGAAACCTCTGATAAACCAGAACAGTTGTTTCTCCAACTTCTGTTAAATTCAACTAATGGGGACAACGATAGGGAG
















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|91048056|gb|EB158474.1|EB158474
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
EST: gi|71307834|gb|DR790138.1|DR790138
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
EST: gi|211502396|gb|FK960896.1|FK960896
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
EST: gi|29167999|gb|CB411259.1|CB411259
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
EST: gi|31358140|gb|CD442497.1|CD442497
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
EST: gi|211502392|gb|FK960892.1|FK960892
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
EST: gi|148933022|gb|EE285909.2|EE285909
EST:     AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAAT                         GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT
genomic: AAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTT

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), 45 (downstream exon)
Score: 55

GATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 23

GATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 37

GATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 40

GATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAATAAATgtaagctgta ... tttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatgtaaatgtttgggctttggagtctttcatgatttgtttgtttcttgcagGCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG
                                     tttgtttgtttctt  CT-rich tract
       taaatgttt  TA-rich tract