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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactgcaaccgctgatgttaagttcttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG

Basic information

species Zea mays
transcript GRMZM2G702490_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G702490_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 1
--atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactg-caaccgctgatgttaagttctt-at----gtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG---------------------------------------------------------
   | ||| ||||| | |  |||||| | | ||   ||||    | ||  ||||    ||||||||||| |  || | | ||||| ||  || || ||     || |||||||||| || | ||||||||| ||||||||||||||||  |                                                         
ttgtttcaatatctgataagatggcccacatta--gacttacagttgt--ctgt----cttgttctagaatatcagctgttgatggtaccttttttatttcaataaagCTTGCAGGATCTGGTGTTTATGAGGAAGCATTACCATCAGGGGGCATAATAACTGGCATAGGACCTGTCCATGGACGATTATGTATGTTTGTGGCCAATG
















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|28910501|gb|CB331470.1|CB331470
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGG
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGG
EST: gi|211131177|gb|FL293576.1|FL293576
EST:     CACTCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCA
genomic: CA-TCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCA
EST: gi|211131173|gb|FL293572.1|FL293572
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGG
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGG
EST: gi|211125177|gb|FL001727.1|FL001727
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGG
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAGG
EST: gi|149110095|gb|EE293910.2|EE293910
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG
EST: gi|211131175|gb|FL293574.1|FL293574
EST:     GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAG                         CTTGCAGGCTCAGATGTTTATGATGAAGCATTACCA
genomic: GCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 75

CGAGGCGGTGAGGCGGAACGCGGCGCGGGGGAAGCTGCTCCCGCGGGACCGCATCGACCGACTGCTCGACCCCGGCGCGTCCTTCCTCGAGCTCTCGCAGgtttcgctcg ... ttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgtacttcttgttctagactgcaaccgctgatgttaagttcttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG
                             cgctgat  putative branch site (score: 75)
                                          ttcttat  putative PPT
                                  atgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtcagtatctaagagcatggcctagaatataaacttgttttcgttactgtacttcttgttctagactgcaaccgctgatgttaagttcttatgtacagCTTGCAGGCTCAGATGTTTATGATGAAGCATTACCATCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC