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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtactggagaacattcactaacattcatgtccttggttttcttgcttctaaaacatggttgctttgcttgtaatttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG

Basic information

species Zea mays
transcript GRMZM2G069758_T01
intron # 11
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|18166331|gb|BM336170.1|BM336170
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|33097992|gb|CF057952.1|CF057952
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     GGAACTGGAGATTTGGCAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|8102609|gb|AW927412.1|AW927412
EST:     AGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: AGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAAT                         AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG
genomic: GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTG

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: 45 (upstream exon), 49 (downstream exon)
Score: 35

GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 172

GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 225

GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 100

GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactg ... atttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtccttggttttcttgcttctaaaacatggttgctttgcttgtaatttacacagAAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG
                  ttctaaa  putative branch site (score: 100)
                                        ttgtaattta  TA-rich tract