Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatgttcaaatgagtaatccagtaacactatataggcagcaacaatcatactatgtaaaaagcagcacaagttttagagaaagagactcttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAACATTGTGCTCAGCGCAGAGTGCCTTCACCAACTTGACGTAATCTGGCTGG

Basic information

species Zea mays
transcript GRMZM5G813987_T01
intron # 2
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|8577145|gb|BE129782.1|BE129782
EST:     GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAG                         CCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
genomic: GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
EST: gi|88749830|gb|DY533971.1|DY533971
EST:     GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAAAGTCAATCTTGCAAAG                         CCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
genomic: GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
EST: gi|113667940|gb|DW814894.1|DW814894
EST:     GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAG                         CCCGGCCCACTCGCCAAGAGTCTTAGCG
genomic: GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCG
EST: gi|7162229|gb|AW519836.1|AW519836
EST:     TTGCCCTCAGAGTCAATCTTGCAAAG                         CCCGGCCCACTCGCCAAGAGTCTTCGCGGCAGGANCAGTGACCAGGTGAAC
genomic: TTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
EST: gi|78112080|gb|DV530476.1|DV530476
EST:     GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAG                         CCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
genomic: GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
EST: gi|32852317|gb|CD991998.1|CD991998
EST:     GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAG                         CCCAGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
genomic: GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAAC
EST: gi|4688381|gb|AI637051.1|AI637051
EST:     GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAG                         CCCGGCCCACTCGCCAAGAGTCTT
genomic: GAGCAGCCTACAACCTTCCTTGCCTTGCCCTCAGAGTCAATCTTGCAAAGctgcaagggg ... cttaactcacCCCGGCCCACTCGCCAAGAGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatactatgtaaaaagcagcacaagttttagagaaagagactcttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAACATTGTGCTCAGCGCAGAGTGCCTTCACCAACTTGACGTAATCTGGCTGG
                                            tcttaac  putative branch site (score: 2)
                                           ctctt  CT-rich tract
        tatgtaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatgttcaaatgagtaatccagtaacactatataggcagcaacaatcatactatgtaaaaagcagcacaagttttagagaaagagactcttaactcacCCCGGCCCACTCGCCAAGAGTCTTAGCGGCAGGAACAGTGACCAGGTGAACATTGTGCTCAGCGCAGAGTGCCTTCACCAACTTGACGTAATCTGGCTGG

tgaatgt
- - - - - - - - - - - - -aacacta
- - - - - - - - - - - - - - - - - - -gcagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagaga