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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgcaaaggagatattatctacagtgggaatatttgttctatctggttaaatggatgtgttttcaggacacatactgatatgtcatgtctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG

Basic information

species Zea mays
transcript GRMZM2G116196_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 8
--------caatg-caaaggagatattatctacagtgggaatatttgttctatctggttaaatggatgtgttttcaggacacatactgatatgtcatgtctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG
         | ||     | | || |||| |   |||| |  | |   | |  | | |||      |  ||||  || |    ||||||| | ||    |||| | ||| ||||||||||| ||||||||||||||||| |||||||||||| ||||    ||||| ||| | || ||||||||||| ||||||||||| |||| ||||
tgtttttttattggtcttgaatatcttatatttggtggaatgaatctatattccagcttac-----tacgtttcaagaatggctactgatgtttc----ctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATCAGAAAGGTGGTTGCCAGAACTGAGAAACGCAGTTCAAGAGGCTCAAAGG
















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|37394434|gb|CF634491.1|CF634491
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|67012513|gb|CO441262.1|CO441262
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGTGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|32943202|gb|CF048021.1|CF048021
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|76287604|gb|DV027172.1|DV027172
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|60398088|gb|DN230904.1|DN230904
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|211028058|gb|FL201182.1|FL201182
EST:     ACCCGTGTTT-GCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCNTAAAATTAGCTGGCGAAACA-GAAAAG-TGGTG
genomic: ACC-GTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAA-TTAGCTGGCGAA-CAAGAAAAGGTGGTG
EST: gi|94477850|gb|EB706808.1|EB706808
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|32832662|gb|CD972340.1|CD972340
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
EST: gi|91878608|gb|EB408565.1|EB408565
EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAG

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: 93

TATCAAAATCTATCAACTTGGTGCACACACGGAGAAATCTTGTTGAGAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 20

TATCAAAATCTATCAACTTGGTGCACACACGGAGAAATCTTGTTGAGAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 19

TATCAAAATCTATCAACTTGGTGCACACACGGAGAAATCTTGTTGAGAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 17

TATCAAAATCTATCAACTTGGTGCACACACGGAGAAATCTTGTTGAGAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgca ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttaaatggatgtgttttcaggacacatactgatatgtcatgtctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG
                             tactgat  putative branch site (score: 17)
                                          tgtcttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgcaaaggagatattatctacagtgggaatatttgttctatctggttaaatggatgtgttttcaggacacatactgatatgtcatgtctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcatg