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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagggatattttaaccaaatttatgcgcttatattaattcttctattgtccttactttgcccttgtttgttgctttccccccattttactttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT

Basic information

species Zea mays
transcript GRMZM2G078826_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078826_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 2
--aaaagggatatttta-accaaatttatgcgcttatattaattcttctattgtccttactttgcccttgtttgttgctttccccccattttactttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT
  |  |   |  ||||  |   || ||||      ||||| |   |    || ||||||   |     ||| || |  |  |    |   ||  |||    |||||||||||||||||||| |||| ||||| || |||||||| |||||||||||||||||  ||||   ||||||||| ||||||||||||||||| ||||
ctactactaaagttttggagggaaattatagctacatatttacgatatccttatccttatccttattgtgtctgcttttgccatttccccttgttttc---agATACAACGTGCTGGATTCTCAAGTCCAACGCCAATCCAAGCTCAGTCATGGCCAATTGCCTTGCAGTGTCAAGATGTTGTAGCTATTGCAAAGACAGGAT

upper sequence: GRMZM2G078826_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g36860.2 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------aaaagggatatttta-accaaatttatgcgcttatattaattcttctattgtccttactttgcccttgtttgttgctttccccccattttactttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT
                                               |  |   |  ||||  |   || ||||      ||||| |   |    || ||||||   |     ||| || |  |  |    |   ||  |||    |||||||||||||||||||| |||| ||||| || |||||||| |||||||||||||||||  ||||   ||||||||| ||||||||||||||||| ||||
gtacgatatcttaagttggactcatgcactgttgattctttgtttctactactaaagttttggagggaaattatagctacatatttacgatatccttatccttatccttattgtgtctgcttttgccatttccccttgttttc---agATACAACGTGCTGGATTCTCAAGTCCAACGCCAATCCAAGCTCAGTCATGGCCAATTGCCTTGCAGTGTCAAGATGTTGTAGCTATTGCAAAGACAGGAT
















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|71432409|gb|DR813459.1|DR813459
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
EST: gi|211052643|gb|FL223131.1|FL223131
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATC
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATC
EST: gi|148937722|gb|EC881924.2|EC881924
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
EST: gi|26558502|gb|CA830737.1|CA830737
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
EST: gi|67039356|gb|CO465611.1|CO465611
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
EST: gi|211049693|gb|FL223127.1|FL223127
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
EST: gi|87157670|gb|DY402459.1|DY402459
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
EST: gi|22472616|gb|BU037096.1|BU037096
EST:     CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAG                         ATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG
genomic: CAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGG

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), 48 (downstream exon)
Score: 284

GGGGATAATGTGCCGACTCCAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GGGGATAATGTGCCGACTCCAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GGGGATAATGTGCCGACTCCAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 142

GGGGATAATGTGCCGACTCCAATAACTTCATTTGAGGCTGGTGGCTTCCCGTCAGAAATTCTGAAGGAGgtatgattca ... ctttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtccttactttgcccttgtttgttgctttccccccattttactttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT
     tccttac  putative branch site (score: 142)
                cccttgtttgttgctt  putative PPT
                                       attttactttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagggatattttaaccaaatttatgcgcttatattaattcttctattgtccttactttgcccttgtttgttgctttccccccattttactttttgtagATACAACGTGCTGGATTCGCAAGCCCAACACCTATCCAAGCCCAGTCATGGCCAATTGCTATGCAAAATCAAGATGTAGTAGCTATTGCAAAGACTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - aaccaaa