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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttaccaagtctcgttgtaacagtagtggtatttgaattttaaatggtcatttccatggcttacctttgtggaatgttttttctatactctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG

Basic information

species Zea mays
transcript GRMZM2G039263_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 5
gtgtgttac-caagtctcgttgtaacagtagtggtattt-gaattttaaatggtcatttccatggcttacct---ttgtggaatgtttttt----ctatactctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
||| |||   ||  ||    |  | | | |||   ||||   |||| ||| |    || |    ||  |||    |||   ||  | ||||      ||   || ||||||||||||||||||||| |||||||||||||| |||||||| || ||||||
gtgagttttgcacttcataattcagctgcagtacaatttcagatttaaaacgaatgttccagctgcaaacccacattgcttaacatgttttaccatcatttactaccagCTTGCTATGCGTGAAGCTTGCAAATATGTTGAAGAAAAGTTGGCTGTCAAG
















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|19058770|gb|BM737437.1|BM737437
EST:     ATCTTGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGG                         CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
genomic: ATCTTGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGGgtgtgttacc ... actctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     TGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGG                         CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
genomic: TGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGGgtgtgttacc ... actctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
EST: gi|33092579|gb|CF052573.1|CF052573
EST:     ATCTTGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGG                         CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
genomic: ATCTTGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGGgtgtgttacc ... actctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     ATCTTGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGG                         CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
genomic: ATCTTGTGAAGAATAAGATCCATCCAACCTCTATAATCAGTGGCTACAGGgtgtgttacc ... actctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggtcatttccatggcttacctttgtggaatgttttttctatactctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG
                ggcttac  putative branch site (score: 3)
                                   ttttttctatactct  putative PPT
                               aatgttttttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttaccaagtctcgttgtaacagtagtggtatttgaattttaaatggtcatttccatggcttacctttgtggaatgttttttctatactctgccagCTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC