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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcaaaatgcgtgtttgttctatatgctcaatcgtttagtttacccttttcttttacacattcttgtctgacataatgaatctttctgcgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTGACAAAAGAAGTGCAGCAACTAAGAAGGGAGAACCAACAGCTCAGGCAGC

Basic information

species Zea mays
transcript GRMZM2G088261_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088261_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g09470.1 (Oryza sativa), 3'ss of exon 9
atttcaaaatgcgtgtttgttctatatgctcaatcgtttagtttacccttttcttttacacattcttgtctgacataatgaatctttctgcgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTGACAAAAGAAGTGCAGCAACTAAGAAGGGAGAACCAACAGCTCAGGCAGC
 |||    ||  |  | || | |      |   | || |||||||  |  |  ||  |    | | | | |  |  |       |  || |  | |||||||||||||||| |||||| ||||| ||||| | || ||| |||||||||| ||||| ||||||||||| |||||||||||||||||||||||| ||||||
gtttgtgcatttgcatctgctatgacattttctttgtgtagtttaatccatgattcgaggactccatatttacccaaggtttaataccttcttgcaacagATGGAAATGTCGGGCGTGTTGAACCTGGTCTTAGAGAAGTTGGAAGGCCTTACAAAGGAAGTGCAGCAGCTAAGAAGGGAGAACCAACAGCTCCGGCAGC
















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|91878842|gb|EB408799.1|EB408799
EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|76280381|gb|DV019949.1|DV019949
EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|93282882|gb|EB675146.1|EB675146
EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|89251454|gb|DY623240.1|DY623240
EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|86473318|gb|DY239688.1|DY239688
EST:     ATGTGAGAAATCTCCCCATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|88755725|gb|DY539866.1|DY539866
EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|89251709|gb|DY623495.1|DY623495
EST:     ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAG                         ATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
genomic: ATGTGAGAAATCTCCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG
EST: gi|91048721|gb|EB159139.1|EB159139
EST:     CCACATGGAACTTTTAAGACAGTTTCACATGCACGAG                         AGGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCGG
genomic: CCACATTGAACTTTTAAGACAGTTTCACATGCACGAGgtaaaatttc ... cgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttttcttttacacattcttgtctgacataatgaatctttctgcgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTGACAAAAGAAGTGCAGCAACTAAGAAGGGAGAACCAACAGCTCAGGCAGC
                      gtctgac  putative branch site (score: 3)
                                     tctttctgc  putative PPT
                             ataatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcaaaatgcgtgtttgttctatatgctcaatcgtttagtttacccttttcttttacacattcttgtctgacataatgaatctttctgcgagaaacagATGGAAATGTCAGGCGTGCTGAACTTGGTCCTGGAAAAGGTGGAAGGCCTGACAAAAGAAGTGCAGCAACTAAGAAGGGAGAACCAACAGCTCAGGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - -tgtttgt
- - - - - - - - - - - - tatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctg