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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaccttttttagcatattcagtttgtattaactagcattatagatttgtctcttcctgtctcttgtttgtaattcccggctgcgcttcttacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTTGAAAACGGGGGTGGTGGTGTTGATGACGAGCCTTTGAAGGTACCCATGT

Basic information

species Zea mays
transcript GRMZM2G063253_T09
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 7
-tgaccttt--tttagcatattcagtttgta-----ttaactagca-ttatagatttgtctcttcctgtctcttgtttgtaatt--cccggctgcgcttcttacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTTGAAAACGGGGGTGGTGGTGTTGATGACGAGCCTTTGAAGGTACCCATGT
 |  | |    | |    | |   | ||| |     || || |  | || | || | || ||      || |   | | | ||   | |  |    |  | || ||| |||| ||||||| ||||  | |  ||||||||| |||||||| ||||||||||||| || || ||||| |  |||||||| |||||| | |||||||| ||||
gtagcttccagtctgaattttattgcttgcaaatggttcaccattagttctggaatcgtttcaattgttcccacatatcttatcagctcttcaaaacgccatatattacagGCGAAAGAAGGCGATTCGGCTCCTTTGATCTCAGACTCTCTGAGCAAAGTTGAGAATGGAGGTGGAGTGGTTGATGATGAGCCTCTCAAGGTACCGATGT
















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|76915215|gb|DV165885.1|DV165885
EST:     TCTGCACAGTGGAGACCCAGCNNNNNNNTGTTGAAGTCTCCCCACAACAG                         GTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
genomic: TCTGCACAGTGGAGACCCAGCAAAAAAATGTTGAAGTCTCCCCACAACAGgtaactttct ... tacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
EST: gi|74245192|gb|DT653106.1|DT653106
EST:     CTGCACAGTGGAGACCCAGCNNNNNNNNTGTTGAAGTCTCCCCACAACAG                         GTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
genomic: CTGCACAGTGGAGACCCAGCAAAAAAA-TGTTGAAGTCTCCCCACAACAGgtaactttct ... tacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
EST: gi|5325129|gb|AI783320.1|AI783320
EST:     TGTTGAAGTCTCCCCACAACAG                         GTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
genomic: TGTTGAAGTCTCCCCACAACAGgtaactttct ... tacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
EST: gi|74245191|gb|DT653105.1|DT653105
EST:     CTGCACAGTGGAGACCCAGCNNNNNNNNTGTTGAAGTCTCCCCACAACAG                         GTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
genomic: CTGCACAGTGGAGACCCAGC-AAAAAAATGTTGAAGTCTCCCCACAACAGgtaactttct ... tacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
EST: gi|211497837|gb|FL444530.1|FL444530
EST:     TCTGCACAGTGGAGACCCAGCNNNNNNNTGTTGAAGTCTCCCCACAACAG                         GTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT
genomic: TCTGCACAGTGGAGACCCAGCAAAAAAATGTTGAAGTCTCCCCACAACAGgtaactttct ... tacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtctcttcctgtctcttgtttgtaattcccggctgcgcttcttacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTTGAAAACGGGGGTGGTGGTGTTGATGACGAGCCTTTGAAGGTACCCATGT
                                         ttcttac  putative branch site (score: 2)
                                      cgcttctt  CT-rich tract
                     tttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaccttttttagcatattcagtttgtattaactagcattatagatttgtctcttcctgtctcttgtttgtaattcccggctgcgcttcttacattgcagGTGAAAGAAAGCGAGGCAGGCCCTTTGATCGCAGACTCTATGAGCAAAGTTGAAAACGGGGGTGGTGGTGTTGATGACGAGCCTTTGAAGGTACCCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG