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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgtgccgccacgcttatagtcgaagcaagggagaggattggtaatgttcatgcactcttgaatgaaactagtttctgttctgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG

Basic information

species Zea mays
transcript GRMZM2G133959_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133959_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g72870.1 (Oryza sativa), 3'ss of exon 4
gtccgtgtgccgccacgcttatagtcgaagcaagggagaggattggtaatgttcatgcactcttgaatgaaactagt------ttctgtt-ctgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG
    || |   | ||| || |   |||  |  |      |  |||  | || ||||| |    | | |||    | |      | ||||| |||||  | ||| |||| ||| || || ||||||| ||| || | ||||||||| ||||||||||| ||||||||||||||||
----gt-tagtggcacactgaagatcggtgagaattgatgtgttg-cattgctcatgaaagagt-attgaggtcattggagaatcctgttgctgtttggcagGTATCGTTGCATTCTACAAGGACTTTGTTGAAGAGCTCTATGAGAACCTCGGTGGGCAAGCATCTATTACAG
















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|78080387|gb|DV508799.1|DV508799
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
EST: gi|76290047|gb|DV029615.1|DV029615
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
EST: gi|76015724|gb|DT942894.1|DT942894
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
EST: gi|71431549|gb|DR812599.1|DR812599
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
EST: gi|50336059|gb|CO531185.1|CO531185
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACC
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACC
EST: gi|89764029|gb|DY690985.1|DY690985
EST:     AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAG                         GCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG
genomic: AAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCG

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), 40 (downstream exon)
Score: 12

CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG


Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 9

CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 12

CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 15

CTTTGCGACGGAACTGCTCGAGATAAGGTCCAAAGAGCCGTCCCTCCACGTGCTGCTTATTGCTGGGAACCCAGgtccgtgtgc ... tgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggtaatgttcatgcactcttgaatgaaactagtttctgttctgttctgtagGCATCGCTGCGTTTTATAAGGACTGTGTCGAGGCGCTCTATGAAAACCTCGGTGGCCAAGCATCTATTACAG
                                    tttctgttctgttct  CT-rich tract
      taatgtt  TA-rich tract