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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagaagcataaagtacaccctatttgaacattggtatgtgcactgatttgcctcagattttataatcaacacctttgactgtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG

Basic information

species Zea mays
transcript GRMZM2G161337_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g15780.1 (Oryza sativa), 3'ss of exon 5
-------------gtatagaagcataaagtacaccctatttg-aacattggtatgtg----cactgatttgcctcagattttataatcaacacctttgactgtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG
              |         |  | |     || |||  |||||| ||||  |     ||| |     || |  | | |||||  ||   | |||   |||  ||||||||||||||||||  |||| || |||||||| ||||||||||| || || || |||
gtatatttacactatgcgcttattttgactggtatctgtttctaacatttgtataagataatactaaacgctcttatgtataataatatactattatga---tct-cttagGCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTGAGGAAG
















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|31364516|gb|CD448871.1|CD448871
EST:     ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
EST: gi|5901211|gb|AW042311.1|AW042311
EST:     ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
EST: gi|116816802|gb|EC859574.1|EC859574
EST:     CGAGCATTACGGATTGTGAATCCATA-CCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: CGAGCATTACGGATTGTGAATCC-TAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
EST: gi|71448131|gb|DR829181.1|DR829181
EST:     ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
EST: gi|211345789|gb|FL266262.1|FL266262
EST:     ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
EST: gi|67024314|gb|CO453063.1|CO453063
EST:     ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
EST: gi|211282582|gb|FL175928.1|FL175928
EST:     ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAG                         GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC
genomic: ATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTC

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), 49 (downstream exon)
Score: 319

TTTAAGCCAGAGGTTCGAGAGACGAACATATGCCAACCCATTTGAGGTTTATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1204

TTTAAGCCAGAGGTTCGAGAGACGAACATATGCCAACCCATTTGAGGTTTATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1846

TTTAAGCCAGAGGTTCGAGAGACGAACATATGCCAACCCATTTGAGGTTTATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

TTTAAGCCAGAGGTTCGAGAGACGAACATATGCCAACCCATTTGAGGTTTATCGAGCATTACGGATTGTGAATCCTAGCCCATACATGGCGTATGTACAGgtatagaagc ... gtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgcactgatttgcctcagattttataatcaacacctttgactgtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG
                                              tctattt  CT-rich tract
                   agattttataatcaa  TA-rich tract