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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcaaatgcttttttgtccttccatttctccatgctagatgtaaaaagaaaaacccattgttcttcggaacatgcctcacaaacattctatttttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG

Basic information

species Zea mays
transcript GRMZM2G402002_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 11
gtaggtcaaatgcttttttgtccttccatttctccatgctagatgtaaaaagaaaaacccattgttcttcggaacatgcctcacaaacattctatttttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG
|| |     ||||  |  | ||  | |||   |      ||     |||||| |||   || | |  ||| | |  |   | ||| | ||  | || ||||  ||||| || || || || |||||||||||  |||  ||||||| ||||||| ||||||| || ||||| || |||||||| || ||||||||||| |||||||
gtggtggtcatgccctaatttcaatgcatgcgtgtgctttatgcagaaaaagtaaatttcaat-tcgttctgtatgt---tgacacaaatattgttgttga--cagCTTGTAAAACTAAATCTCCAAGCTGACCCAAATGGTTCATATGTTGAAGTTCTTGAGCGATATGTGAACCTTGGACCCATCGTGGACTTCTGTGTGGTTG
















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|32933076|gb|CF037888.1|CF037888
EST:     ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAG                         CTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
genomic: ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
EST: gi|33093329|gb|CF053323.1|CF053323
EST:     ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAG                         CTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
genomic: ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
EST: gi|32931773|gb|CF036585.1|CF036585
EST:     ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAG                         CTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
genomic: ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
EST: gi|32931536|gb|CF036348.1|CF036348
EST:     ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAG                         CTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT
genomic: ATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATT

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: 49 (upstream exon), 49 (downstream exon)
Score: 503

TTTGAAAATTGAATACCTGGGAGAGACTTCGATTGCATCATCTATTTCGTATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG


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

TTTGAAAATTGAATACCTGGGAGAGACTTCGATTGCATCATCTATTTCGTATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

TTTGAAAATTGAATACCTGGGAGAGACTTCGATTGCATCATCTATTTCGTATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

TTTGAAAATTGAATACCTGGGAGAGACTTCGATTGCATCATCTATTTCGTATCTTGATAATGGTGTTGTTTACGTCGGTTCACGGTTTGGCGATTCACAGgtaggtcaaa ... tttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaacccattgttcttcggaacatgcctcacaaacattctatttttgaaacagCTGGTGAAGCTGAACCTCCAAGCTGATGCAAGCGGTTCATTTGTTGAAATTCTTGAACGGTATGTTAATCTTGGACCGATTGTGGACTTCTGCGTGGTTG
                          gcctcac  putative branch site (score: 267)
                                      ttctattttt  putative PPT
                                 aaacattctattttt  TA-rich tract