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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttacttacacagcttcatgatttgatctactctaaggaagtaaggatacacaactaaagaaaaataactattacttccatttttacatgtaaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG

Basic information

species Zea mays
transcript GRMZM2G028307_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028307_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g33420.1 (Oryza sativa), 3'ss of exon 1
tttacttacacagcttcatgatt--tgatctactctaagg-aagtaaggatacac-aactaaagaaaaataactattacttccatttttacatgtaaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG
    |     |||||| |   |   || || |  ||  |  ||   ||   |  | ||  |||  ||   ||   |||| || | |  | | | || |||||||||| ||||||||||| ||  || |||  ||   ||| || |||||||| ||||| || |||||||| ||||||||||| || || |||||| ||||| ||
----caactccagcttgactgtcgctgttccatcctttgacaaccgagcccattcgaagcaaaagaaggaaaggcttacgtctactcatgcttttacatttcagGGGCACTTCCGAGGCTAATGAACAACTTGCTGAGTTTCCACCAAGAGGCTGGAATTCCTATGATTCCTTTTCATGGATAGTTGATGAAAATACATACATG
















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|211005860|gb|FL395309.1|FL395309
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACGAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|71436528|gb|DR817578.1|DR817578
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|211079341|gb|FL392675.1|FL392675
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAATGAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|50328271|gb|CO523397.1|CO523397
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|71444847|gb|DR825897.1|DR825897
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
EST: gi|74237284|gb|DT645198.1|DT645198
EST:     AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTG                         GGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG
genomic: AGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTG

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: 257

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 83

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG


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

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

TGTCCGGCTGGAAGGCCATGGGGGCTAGGGCTACCTCCCCTCCGCCATGGAGGCGTCACTGCCTCTGCCGCGCCCTCCACTTCCTCGTTCTCTTGCTCTGgtcagtacgc ... taaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacacaactaaagaaaaataactattacttccatttttacatgtaaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG
                 aaataac  putative branch site (score: 324)
       aactaaagaaaaataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttacttacacagcttcatgatttgatctactctaaggaagtaaggatacacaactaaagaaaaataactattacttccatttttacatgtaaatttcagGGGTACTTCCGAGGCAAACAAAGAACAGGCCATGTTGCCTCCAAGAGGGTGGAACTCGTATGATTCTTTTTCATGGATTGTAGACGAAAATGCATACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - cagcttc
- - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - -caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata