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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcttgcctttaatcattatatatttaatttcctcccatgcatctgcatgcatgcctgatgagttttgatgcatgggcggtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG

Basic information

species Zea mays
transcript GRMZM2G059836_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059836_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g32330.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------gtaatgcttgcct-ttaatcatt---atatatttaatttc----ctcccatgcatctgcatgcat--gcctgatga-gttttgatgcatgggcg----gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG
                                                               |   | | ||   |||| ||     ||| ||| | ||       ||   ||| ||| |||  ||     || ||| || ||  ||| |   |     |||  || |||||||||||||||||||||||||||||||||| || |||||| |  | ||||||| |||||||||||||||||| || |||||||||||| |||||||| 
gtgttttaattttctcgatcttgatcgatttatatatactacatgcatgcatgtttgctcaaatttcgttggctaattaagcacagagataaattaatttgtgaagttcttgtgcttcttcattaattaatttggtgatgtgtttttgcttatacaatatgtgtgtgtagACGGTGAACATCAAGGTGAAGATGGACTGCGAGGGGTGCGAGAGGAGGGTGAAGAACGCGGTGAAGTCGATGCGAGGGGTGACGAGCGTGGCGGTGAACC
















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|37385126|gb|CF629682.1|CF629682
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
EST: gi|37379696|gb|CF626596.1|CF626596
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
EST: gi|211417210|gb|FL450428.1|FL450428
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
EST: gi|18172922|gb|BM348310.1|BM348310
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
EST: gi|40335507|gb|CK369577.1|CK369577
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
EST: gi|37392554|gb|CF633529.1|CF633529
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTG

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), 41 (downstream exon)
Score: 15

TGGCCGTGGCGCCATGGGCATCCTGGACCACATGTCGCATGTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

TGGCCGTGGCGCCATGGGCATCCTGGACCACATGTCGCATGTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TGGCCGTGGCGCCATGGGCATCCTGGACCACATGTCGCATGTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

TGGCCGTGGCGCCATGGGCATCCTGGACCACATGTCGCATGTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAGgtaatgcttg ... gtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatgcatctgcatgcatgcctgatgagttttgatgcatgggcggtggttgcagACGGTGAACATCAAGGTGAAGATGGACTGCGAAGGTTGCGAGCGTCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGACGGTGAACG
                             ttttgat  putative branch site (score: 124)
                             ttttgat  TA-rich tract