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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgggaccatctgtcgcaaatgtatctgccatgccacaataataaaaaaagagataattttgtcaatgaccatatcttctattctttttgactggctttaccttatggtctcggagagtggtttgatgctgatgcaagtctttttttcttagtaaccatgttacatttttttcatgctggtatgttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTAGGCAGTGCTCACCTCAACTCAAACAGGCCACCAATTGCTATGAAATGCC

Basic information

species Zea mays
transcript GRMZM5G884316_T03
intron # 2
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|78077326|gb|DV505760.1|DV505760
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCCAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|78111844|gb|DV530241.1|DV530241
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|76918443|gb|DV167297.1|DV167297
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|89762405|gb|DY690005.1|DY690005
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|76011704|gb|DT938874.1|DT938874
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|71431444|gb|DR812494.1|DR812494
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|76021372|gb|DT948542.1|DT948542
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|78105804|gb|DV524222.1|DV524222
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|74232780|gb|DT640694.1|DT640694
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGNTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|76911871|gb|DV164475.1|DV164475
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|78120002|gb|DV538386.1|DV538386
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|148971070|gb|EE021911.2|EE021911
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
EST: gi|71439008|gb|DR820058.1|DR820058
EST:     GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAG                         GTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA
genomic: GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTA

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 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 20

GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTAGGCAGTGCTCACCTCAACTCAAACAGGCCACCAATTGCTATGAAATGCC


Block sizes: 17 (upstream exon), 33 (downstream exon)
Score: 3

GCATAAATCGTCCCTGTTGGTGAGCTGTTCCAAAGACTCAAAGgtaatgggac ... gttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTAGGCAGTGCTCACCTCAACTCAAACAGGCCACCAATTGCTATGAAATGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttttcttagtaaccatgttacatttttttcatgctggtatgttgcatcagGTTAAAGTTTGGGACACAGTGGCTCCTTCGAGTGGTTCATCACCATGTGTAGGCAGTGCTCACCTCAACTCAAACAGGCCACCAATTGCTATGAAATGCC
           tagtaac  putative branch site (score: 3)
                   atgttacattttttt  TA-rich tract