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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgattgcctgactagctattctgtgtcttttagcatggattattgccttcccaacttcatattattgtttgttgcgcttgtcatatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAAGGTCGACCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G085747_T02 (Zea mays), 3'ss of exon 8
gtattttgattgcctgactagctattctgtgtcttttagcatggattattgccttcccaacttcatat--tattgtttgttgcgcttgtcatatccaa--tagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAAGGTCGACCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAG
||||  |||||     ||||  ||||  ||   || |       |   ||  ||  |||  || ||||  |||||||||  | |||| || |||  ||  ||||||||||| |||||||||||||| ||||||||||| ||||| |||||||| || || || |||   |||||||| || || |||||||| || |||||||
gtatcctgattcttaaacta-ttattacgtaatttattctggaaagctttttctgaccagttttatatattattgtttgacgggcttatcctatttaaaatagGGGACAGCTGGAGTTGCTCTAGCAGGCCTACTTGGTGCTGTTAGAGCACAGGGCCGTCCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAG
















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|58687567|gb|CK076254.1|CK076254
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTT
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTT
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58665242|gb|CK053928.1|CK053928
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58694574|gb|CK083261.1|CK083261
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58659006|gb|CK047686.1|CK047686
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29664101|gb|CB660376.1|CB660376
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29656255|gb|CB652530.1|CB652530
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCANGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTG
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTG
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58604291|gb|CK014819.1|CK014819
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattgccttcccaacttcatattattgtttgttgcgcttgtcatatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAAGGTCGACCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAG
                 ttcatattattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttgattgcctgactagctattctgtgtcttttagcatggattattgccttcccaacttcatattattgtttgttgcgcttgtcatatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAAGGTCGACCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG