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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcagaatcaatcgtcattgattttgtttccagaattttctgtaccagaagttcagtaatttgcagctttgttaaaaccatgttttaatgtggaatgacagATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGATGCTATCTCCCCCAAAGCTCTCAGAAGTTACATACAACATCCTAAGTTGA

Basic information

species Zea mays
transcript GRMZM2G171354_T04
intron # 4
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|6695723|gb|AW288801.1|AW288801
EST:     CCAATGGTGAAGAAAAATTTATTACTTATGCCAAACCGAAGCACCATTCA                         ATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGAT
genomic: CCAATGGTGAAGAAAAAATTATTACTTATGCCAAACCGAAGCACCATTCAgtaagtttca ... ggaatgacagATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGAT
EST: gi|160481332|gb|EY254266.1|EY254266
EST:     CCAATGGTGAAGAAAAAATTATTACTTATGCCAAACCGAAGCACCATTCA                         ATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGAT
genomic: CCAATGGTGAAGAAAAAATTATTACTTATGCCAAACCGAAGCACCATTCAgtaagtttca ... ggaatgacagATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGAT
EST: gi|71447517|gb|DR828567.1|DR828567
EST:     CCAATGGTGAAGAAAAAATTATTACTTATGCCAAACCGAAGCACCATTCA                         ATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGAT
genomic: CCAATGGTGAAGAAAAAATTATTACTTATGCCAAACCGAAGCACCATTCAgtaagtttca ... ggaatgacagATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagttcagtaatttgcagctttgttaaaaccatgttttaatgtggaatgacagATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGATGCTATCTCCCCCAAAGCTCTCAGAAGTTACATACAACATCCTAAGTTGA
                                    ttttaat  putative branch site (score: 3)
                     tttgttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcagaatcaatcgtcattgattttgtttccagaattttctgtaccagaagttcagtaatttgcagctttgttaaaaccatgttttaatgtggaatgacagATGCGAGGGAGTGACACATCAACTGCTGAGTCTGGCTCAGAAGCTGACGATGCTATCTCCCCCAAAGCTCTCAGAAGTTACATACAACATCCTAAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT