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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaggggaaatcttggcgatgcaatataatactcaaaattcctcctctgaaacctgtagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG

Basic information

species Zea mays
transcript GRMZM2G126900_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126900_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 5
----------------------------------gtaagcaaggggaaatcttggc-gatgcaat-----ataata-ctcaaaat---tcctcctctgaaacc---tgt-----agctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG
                                  |  | |     ||||  |   | ||| ||       | |||| || || ||   |||  ||||||| |    |||     | |||||||||||||||||||||||||||||||||| |||||| ||||||||||||||||||
gtaagaaacaaacaacagaagcaaacagcttattgccatctcactgaaacttcttcagattcagctaggaacaatagctgaacatccatccatctctgaatctgaatgtctttgacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCAAG
















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|31363556|gb|CD447913.1|CD447913
EST:     GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|78119916|gb|DV538300.1|DV538300
EST:     GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|60396286|gb|DN229155.1|DN229155
EST:     GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|154130490|gb|EC872226.2|EC872226
EST:     GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|15554177|gb|BI644175.1|BI644175
EST:     GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|15057218|gb|BI361190.1|BI361190
EST:     CCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: CCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|76923453|gb|DV169495.1|DV169495
EST:     GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
genomic: GGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCA
EST: gi|211354362|gb|FL217076.1|FL217076
EST:     GCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAAYG-CNCACTTC
genomic: GCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTC-CACTTC

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: 47 (upstream exon), 47 (downstream exon)
Score: 20

ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 726

ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 326

ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 409

ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaagg ... tagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggcgatgcaatataatactcaaaattcctcctctgaaacctgtagctttcagGTGACACCTTCCCCGTCGGCTGCGCATACGACGAGTGCAACGTCCACTTCAAG
                                                ctttc  CT-rich tract
           aatataatactcaaaa  TA-rich tract