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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggacgtacattagtctacattacattcttcttgttggtttccttgattatttatctgttattttttggttgttcacccttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC

Basic information

species Zea mays
transcript GRMZM2G048067_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 16
gtatgtggacgt---acattagtctacattacattcttcttgttgg-----------tttccttgattatttatctg-ttattttttggttgttcacccttggaat-agCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC---
|||||||| |     ||| || | ||||||||||| ||  | ||||           |||   |||||| | || || ||    ||    |||       ||| || |||||||||||||||||| | |||||||||||| ||||||||||||||||||||||| |||||| || | || ||||||||||||||||| || ||||||||   
gtatgtggccaagcaacactattttacattacatttttgctattggagttctatttatttatctgattaatgatatgcttccccttcttctgtgtgttggtggcattagcagCTTGCAAGATGACCAGCCAAATTGCTAGCTGGGATACGAGGTTTGAGTTGGGTACAAAAGCATCATTGTTGTTGCCATTTTCTCCTATTGTTGTTGCTGC

upper sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 15
gtatgtggac---gtacattagtctacattacattcttcttgttgg-----------tttccttgattatttatctg-ttattttttggttgttcacccttggaat-agCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC---
|||||||| |     ||| || | ||||||| ||| ||  | ||||           |||   |||||| | || || ||    ||    |||       ||| || |||||||||||||||||| | |||||||||||| ||||||||||||||||||||||| |||||| || | || ||||||||||||||||| || ||||||||   
gtatgtggcctagcaacactattttacattatatttttgctattggagttctatttatttatctgattaatgatatgcttccccttcttctgtgtgttggtggcattagcagCTTGCAAGATGACCAGCCAAATTGCTAGCTGGGATACGAGGTTTGAGTTGGGTACAAAAGCATCATTGTTGTTGCCATTTTCTCCTATTGTTGTTGCTGC
















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|30087149|gb|CB885357.1|CB885357
EST:     AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCT                         C---TTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
genomic: AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
EST: gi|28576038|gb|CB281930.1|CB281930
EST:     AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCT                         C---TTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
genomic: AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
EST: gi|31558447|gb|CD527659.1|CD527659
EST:     AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCT                         C---TTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT
genomic: AGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 130

CCTCTTTTAATTGGCTCTGATGATAACGAAGAGGCAAATGCTAGAAGGGAAGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 86

CCTCTTTTAATTGGCTCTGATGATAACGAAGAGGCAAATGCTAGAAGGGAAGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 76

CCTCTTTTAATTGGCTCTGATGATAACGAAGAGGCAAATGCTAGAAGGGAAGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 80

CCTCTTTTAATTGGCTCTGATGATAACGAAGAGGCAAATGCTAGAAGGGAAGAGAGAGAACGACTTGCACTAGATTATATCGCTAAGTGCCAGCGCTCCTgtatgtggac ... cttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggtttccttgattatttatctgttattttttggttgttcacccttggaatagCAGCTTGCAAGATGACAAACCAAATTGCTAGTTGGGATACGAGGTTTGAGTTGGGAACAAAAACAGCTTTATTGTTGCCATTTTCTCCGATCGTTGTTGC
        ccttgat  putative branch site (score: 80)
                                       ttcaccctt  putative PPT
          ttgattatttatctgt  TA-rich tract