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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttttgttccacctatataccccctttcagctttatttctctgaatttaatcacaaggacctgggcctaactatacgaatgctgtgccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACCATTAATAAATAAGGTTCCGGCACAGTTGATCCGTTCAGATTCGTAGCCT

Basic information

species Zea mays
transcript GRMZM2G036902_T01
intron # 3
splice site 3'
intron type U2

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|40337056|gb|CK371126.1|CK371126
EST:     AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAA                         TGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
genomic: AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
EST: gi|89249591|gb|DY621377.1|DY621377
EST:     AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAA                         TGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
genomic: AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
EST: gi|37397514|gb|CF636057.1|CF636057
EST:     AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAA                         TGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
genomic: AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
EST: gi|6626443|gb|AW257975.1|AW257975
EST:     AAAGATCTGAATCCTCTAGTAGCCGGATTAATTGAATCTTGCTGGGCCAA                         TGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC
genomic: AAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACC

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: 46 (upstream exon), 49 (downstream exon)
Score: 69

GTGGTTGCTGCTGTAGGTTTCAAAGGAAGAAGGCTTGAAATCCCAAAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACCATTAATAAATAAGGTTCCGGCACAGTTGATCCGTTCAGATTCGTAGCCT


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 44

GTGGTTGCTGCTGTAGGTTTCAAAGGAAGAAGGCTTGAAATCCCAAAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACCATTAATAAATAAGGTTCCGGCACAGTTGATCCGTTCAGATTCGTAGCCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 72

GTGGTTGCTGCTGTAGGTTTCAAAGGAAGAAGGCTTGAAATCCCAAAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACCATTAATAAATAAGGTTCCGGCACAGTTGATCCGTTCAGATTCGTAGCCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 33

GTGGTTGCTGCTGTAGGTTTCAAAGGAAGAAGGCTTGAAATCCCAAAAGATCTGAATCCTCTAGTAGCCGTATTAATTGAATCTTGCTGGGCCAAgtatgtattt ... ccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACCATTAATAAATAAGGTTCCGGCACAGTTGATCCGTTCAGATTCGTAGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttaatcacaaggacctgggcctaactatacgaatgctgtgccttctgtagTGAACCATGGCGAAGACCCTCGTTTGCAAATATTATGGACACTTTGAAACCATTAATAAATAAGGTTCCGGCACAGTTGATCCGTTCAGATTCGTAGCCT
                       gcctaac  putative branch site (score: 33)
                                           tgccttct  putative PPT
                          taactata  TA-rich tract