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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatttctataacttctttttcaactatgcacggaattggcttcccatttcttctcttagtgatgcctgtgcttttgctaattatgtaatcatttcttagGAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTGCTAGAGGTGAAGAACGTATGCTTGACTCTTGTGCATAAGAAG

Basic information

species Zea mays
transcript GRMZM2G137968_T03
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|101387982|gb|EB816005.1|EB816005
EST:     TGCCTCGCGGCAAGTCCCCCTCCGCTACGTTCGCCATGGCTCGCAACAGG                         GAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTG
genomic: TGCCTCGCGGCAAGTCCCCCTCCGCTACGTTCGCCATGGCTCGCAACAGGgtgcgttctc ... catttcttagGAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTG
EST: gi|88752186|gb|DY536327.1|DY536327
EST:     TGCCTCGCGGCAAGTCCCCCTCCGCTACGTTCGCCATGGCTCGCAACAGG                         GAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGAAGTGCTG
genomic: TGCCTCGCGGCAAGTCCCCCTCCGCTACGTTCGCCATGGCTCGCAACAGGgtgcgttctc ... catttcttagGAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTG
EST: gi|89250569|gb|DY622355.1|DY622355
EST:     TGCCTCGCGGCAAGTCCCCCTCCGCTACGTTCGCCATGGCTCGCAACAGG                         GAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTG
genomic: TGCCTCGCGGCAAGTCCCCCTCCGCTACGTTCGCCATGGCTCGCAACAGGgtgcgttctc ... catttcttagGAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcttctcttagtgatgcctgtgcttttgctaattatgtaatcatttcttagGAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTGCTAGAGGTGAAGAACGTATGCTTGACTCTTGTGCATAAGAAG
                              tgctaat  putative branch site (score: 2)
                                            tcatttctt  putative PPT
                                 taattatgtaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatttctataacttctttttcaactatgcacggaattggcttcccatttcttctcttagtgatgcctgtgcttttgctaattatgtaatcatttcttagGAAGTGGTGATTTTGCTGTTGGATGTTGGGCCTTCGATGCATGGAGTGCTGCTAGAGGTGAAGAACGTATGCTTGACTCTTGTGCATAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - atgcacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgct