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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaacgcaaccgcccgcgacgagctcaccttcttctcttcagacggctaatgcatatgtagtaaggtcgtctgaccatcgcctcgtccgtcctgtacatttcgcatgcaaataatgcag

Basic information

species Zea mays
transcript GRMZM2G074672_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074672_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g23300.1 (Oryza sativa), 5'ss of exon 2
GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaacgcaaccgcccgcgacgagctcaccttcttctcttcagacggctaatgcatatgtagtaag-gtcgtctgaccatcgcctcgtccgtcctgtacatttcgcatgcaaataatgcag
||| ||||||||||||||||| || ||||||||| |||| ||||||||| | |||||||| |||||||||||||| || |||   |||||  ||    |  ||    |    |  | |  |   ||            || | ||| ||   | |   |   |        |  ||| | |    |     || |    ||  |   ||||
GTATCTGGCGGCGAAGAGCGACGCCGACCACTACCACCGCGAGCTGCAGAGGGAGCAGGAGGAGATCGACACCGTGCCGGACACAGgtaattaatta-agtcggtaacagtaa-ttaatttctctcggagtttttttttactacatctgagtttattattaccacggtggtggttcgacggctgagattggtttggccccacttg--gcag
















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|211529081|gb|FL234917.1|FL234917
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|148942328|gb|EC887346.2|EC887346
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|71444738|gb|DR825788.1|DR825788
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|71444739|gb|DR825789.1|DR825789
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|211526087|gb|FL234907.1|FL234907
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|211529073|gb|FL234909.1|FL234909
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|211529076|gb|FL234912.1|FL234912
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGC
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGC
EST: gi|211529078|gb|FL234914.1|FL234914
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|76019557|gb|DT946727.1|DT946727
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|211526086|gb|FL234906.1|FL234906
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGAGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|211529074|gb|FL234910.1|FL234910
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|76020433|gb|DT947603.1|DT947603
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
EST: gi|211526085|gb|FL234905.1|FL234905
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCCGGAG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCC-GGAG
EST: gi|211526088|gb|FL234908.1|FL234908
EST:     CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG                         AGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG
genomic: CCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGG

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 19

GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGGAGTACGGCCCCGTGGTGACCTCCCTCCGCAACAACCCCAAGGCGTGGCT


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 14

GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGGAGTACGGCCCCGTGGTGACCTCCCTCCGCAACAACCCCAAGGCGTGGCT


Block sizes: 29 (upstream exon), 35 (downstream exon)
Score: 2

GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaac ... aataatgcagAGGCCGCCGAGATCGCCGACATCCTGTCGCAGTACGGGCTGGGCCCGGAGGAGTACGGCCCCGTGGTGACCTCCCTCCGCAACAACCCCAAGGCGTGGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCGgtaagcaaacgcaaccgcccgcgacgagctcaccttcttctcttcagacggctaatgcatatgtagtaaggtcgtctgaccatcgcctcgtccgtcctgtacatttcgcatgcaaataatgcag

- - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC