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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC

Basic information

species Zea mays
transcript GRMZM2G155384_T03
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T02 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 21
gtaagt--atatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC
||||||  ||| ||| || | |||  |||   | |  |  |  | |  |  ||  | | |||||    ||||   | | | |||  ||       ||  ||   ||  |||||| |||||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||| ||  | ||||| || |||||
gtaagttaataaatccacaatgatccttttaaacctgtgctccattc-tgttg--tacctggttg---tatataatgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
















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|166695594|gb|EG314197.1|EG314197
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGT                         GTTAGAATTGCCCAGGG
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTgtaagtatat ... tcgtcgtcagGTTAGAATTGCCCAGGG
EST: gi|32850124|gb|CD989805.1|CD989805
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGT                         GTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTgtaagtatat ... tcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|211100370|gb|FL070848.1|FL070848
EST:     ATTACTACAAAGAAGCTGCTCATCTGTTTTGT                         GTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: ATTACTACAAAGAAGCTGCTCATCTGTTTTGTgtaagtatat ... tcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|32867559|gb|CF007241.1|CF007241
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGT                         GTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTgtaagtatat ... tcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|211100371|gb|FL070849.1|FL070849
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGT                         GTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCYT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTgtaagtatat ... tcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC
                        cattgat  putative branch site (score: 4)
          ttataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcagGTTAGAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC