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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattgcatcttttagttctttgaccaaagactttgaattttatcagtatgttgacatctcagagtgtttgcgctgactgatatttcatgtttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC

Basic information

species Zea mays
transcript GRMZM2G081924_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g38620.3 (Oryza sativa), 3'ss of exon 6
----acattgcatcttttagttctttgaccaaagactttgaattttatcagtatgttgacatctcagagtgtttgcgctga-ctgatatttcatgtttgtg----atagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC
      |||| ||  |||| |||||      |||  |    |||||||    |  ||   |   | |    |||| ||| | ||| |  || || ||||||    | |||||  |||||| ||||||||||||||||||| || |||||||| |||||||| ||||| |||| ||| |||||||| || |||||||||||||| || ||
ctttcaattgtattctttaattcttc-----aagttt----attttatattcaactttgtaaaaccggacatttgtgctaaactgctgattgatatttgtgtcatacagATGAAATTGAACCTGATGTTTATGTTCCTGAGGTGGATATCCTGTCAGTCTTGGATGTGCCTCCTGGCAAAATGGGGCGTGTTATTGGCAGAAAAGGATC
















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|211412951|gb|FL027551.1|FL027551
EST:     CTTAAACGACAACCAATTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTG                         ATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
genomic: CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
EST: gi|19351659|gb|BM896191.1|BM896191
EST:     CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTG                         ATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
genomic: CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
EST: gi|211331399|gb|FL462812.1|FL462812
EST:     CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTG                         ATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
genomic: CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
EST: gi|211412952|gb|FL027552.1|FL027552
EST:     CTTAAACGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTG                         ATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
genomic: CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
EST: gi|76292397|gb|DV031965.1|DV031965
EST:     CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTG                         ATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTTT
genomic: CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
EST: gi|60341483|gb|DN208456.1|DN208456
EST:     CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTG                         ATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT
genomic: CTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCT

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: 154

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 92

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

TCTTTATGGCGTCTGGCAGTTCGCAGTGAGCTGTACTGTAGGTGCTTTTGCTTAAATGACAACCAGTTTGCAGATTGGTCACCTCTTCCTCCTGTTCCTGgtcagtatat ... tttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatgttgacatctcagagtgtttgcgctgactgatatttcatgtttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC
                              gactgat  putative branch site (score: 107)
                                   atatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acattgcatcttttagttctttgaccaaagactttgaattttatcagtatgttgacatctcagagtgtttgcgctgactgatatttcatgtttgtgatagATGGCATTGAAGCTGATGTTTATGTTCCTGAAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTC

-cattgca
- - - - - - - - - - - gaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg