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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgccctctcccggccggtctccccacttccgtccctccttctctcgcgccacgttactgaccgaccgaccccacttctcttccctttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGT

Basic information

species Zea mays
transcript GRMZM2G010044_T01
intron # 1
splice site 3'
intron type U2

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|91051662|gb|EB162080.1|EB162080
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211185231|gb|FL072185.1|FL072185
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|31355882|gb|CD440239.1|CD440239
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211185239|gb|FL072193.1|FL072193
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         -A-A-GGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211187626|gb|FL072195.1|FL072195
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|71772889|gb|DR970812.1|DR970812
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211187638|gb|FL072207.1|FL072207
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211185236|gb|FL072190.1|FL072190
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211185238|gb|FL072192.1|FL072192
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCG--C-A----CA-                         -AGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211190029|gb|FL072209.1|FL072209
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         -A-A-GGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211187639|gb|FL072208.1|FL072208
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|76909966|gb|DV163627.1|DV163627
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211185232|gb|FL072186.1|FL072186
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211185235|gb|FL072189.1|FL072189
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|148958467|gb|EC904705.2|EC904705
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTGGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|31354069|gb|CD438426.1|CD438426
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|76012112|gb|DT939282.1|DT939282
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGT-C--                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|148955521|gb|EC901145.2|EC901145
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         CAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
EST: gi|211187634|gb|FL072203.1|FL072203
EST:     CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAG                         -A-A-GGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG
genomic: CCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGG

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 2 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 5

TCGCAGGGTGTTCGACCCTTCGCCCGCGCGCCCTCACGACATGGCCTCCTCCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGT


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 5

TCGCAGGGTGTTCGACCCTTCGCCCGCGCGCCCTCACGACATGGCCTCCTCCGTCTCCGCCGCCGCCAAGGCCGCCGCGGCGTTCGCGCACAAGGTCCAGgtccgccctc ... ttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcgcgccacgttactgaccgaccgaccccacttctcttccctttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGT
              tactgac  putative branch site (score: 5)
                        ccgaccccacttctct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgccctctcccggccggtctccccacttccgtccctccttctctcgcgccacgttactgaccgaccgaccccacttctcttccctttcccgccagCAGAAGGAGCTGGCCGCGCCGGCGCAGCGCCGCGCGGGCTTGACCCGCCGGACCAAGCCGTGCAGCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCGCCG