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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgcccctgccattccttcctttacgtattccaatcccgatccagtgcgcctctcgcctccctgacgaatcgtgcttccctccag

Basic information

species Zea mays
transcript GRMZM2G077669_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077669_T01 (Zea mays), 5'ss of exon 2
lower sequence: EDO98756 (Chlamydomonas reinhardtii), 5'ss of exon 4
AGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgcccctgccattccttcctttacgtattccaatcccgatccagtgcgcctctcgcctccctgacgaatcgtgcttccctccag-----------
                    |||||||||||||| |||||||| |||||||| ||||||||| ||||||||||| | ||||| ||||| |||||||| ||||  |  || ||||||   ||    |        |  |      | |||||   || |   |      || | | ||| |      |||||           
--------------------GACATCGGCCGCCTGTTCATCGCGGGCTTCGGCTCCTCCATGATCTTCGGCACCGTGGTCGGGTCCCTGGCCGACAAGCAgtgagtgcggccctgc-gctcagggcccggtccctcgccgcgggggtccagaaagc-tggggagggggtgtcaactcgggaagttgtccagcgaatgtagga
















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|78179671|gb|DV550044.1|DV550044
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|12047314|gb|BF729453.1|BF729453
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTG
EST: gi|32803871|gb|CD956107.1|CD956107
EST:     GATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211181672|gb|FL010880.1|FL010880
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|149009314|gb|EE041383.2|EE041383
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211344699|gb|FL214759.1|FL214759
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         GGGCCGCAAGAGGGCCTGCGTCACCTATTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184075|gb|FL010888.1|FL010888
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211181671|gb|FL010879.1|FL010879
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|50336619|gb|CO531745.1|CO531745
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184079|gb|FL010892.1|FL010892
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184074|gb|FL010887.1|FL010887
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184069|gb|FL010882.1|FL010882
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|149016972|gb|EE154301.2|EE154301
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184070|gb|FL010883.1|FL010883
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184080|gb|FL010893.1|FL010893
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|31354966|gb|CD439323.1|CD439323
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|8577312|gb|BE129949.1|BE129949
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184071|gb|FL010884.1|FL010884
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|148980798|gb|EE027354.2|EE027354
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCCCGCCGACAAACC                         AGGCCCGCA-GAGGGCCTGCATCCCCTACTGCATCAGCTACATCC
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCC-GCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCC
EST: gi|74236381|gb|DT644295.1|DT644295
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|149030377|gb|EE286314.2|EE286314
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|78110935|gb|DV529333.1|DV529333
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
EST: gi|211184076|gb|FL010889.1|FL010889
EST:     GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACA                         AGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG
genomic: GGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTG

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: 44 (upstream exon), 48 (downstream exon)
Score: 50

AGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

AGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

AGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 135

AGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATCCTCCATGCTCTTCGGCACCATCGTCGGCTCCCTCGCCGACAAACAgtacgcccgc ... ttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC