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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggggtctcttggcaagttctgctcctcccaatgacaagtaggacagcagtagctcccactctattggcttacacattaacttcctttgttaaaacgatgcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTTTCCCCTCCGG

Basic information

species Zea mays
transcript GRMZM2G126079_T01
intron # 9
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|50323333|gb|CO518459.1|CO518459
EST:     AGAAGCATTACCAAATCTGGGCAGTCCCGCAGTGCTGTCGCGTGCTCCAG                         TTCATCAGTACATGGTTCAGCAACATCCAGTTCAAGTACCGAATTATACTT
genomic: AGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTT
EST: gi|74243473|gb|DT651387.1|DT651387
EST:     AGAAGCATTACCAAATTTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAG                         TTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTT
genomic: AGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTT
EST: gi|71298675|gb|DR785312.1|DR785312
EST:     AGAAGCATTACCAAATTTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAG                         TTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTT
genomic: AGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTT

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: 19 (upstream exon), 31 (downstream exon)
Score: 1

TTTCCTTCTTTAACTTCTATGCAAGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTTTCCCCTCCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

TTTCCTTCTTTAACTTCTATGCAAGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTTTCCCCTCCGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 108

TTTCCTTCTTTAACTTCTATGCAAGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTTTCCCCTCCGG


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 5

TTTCCTTCTTTAACTTCTATGCAAGAAGCATTACCAAATCTGGGCAGTACCGCAGTGCTGTCGCGTGCTCCAGgtatggggtc ... gcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTTTCCCCTCCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccactctattggcttacacattaacttcctttgttaaaacgatgcatctacagTTCATCAGTACATGGTTCAGCAACATACAGTTCAAGTACCGAATTATACTTTCCCCTCCGG
                    cattaac  putative branch site (score: 5)
                               tttgttaaaa  TA-rich tract