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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccacatttcttgttctgcatgtaccttctgctgctttcagttgatttgtgtacagataatacaaataatgtgtccccaacttttcaaaaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCTTGCAGGTGTTATTTGACACATTAAGAAACCATGGTCATCTCTTCTCCTT

Basic information

species Oryza sativa
transcript LOC_Os03g14260.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 9
--------gtaaccacatttcttgtt-ctgcatgtaccttctgctgctttcagttgatttgtgtacagataatacaaataatgtgtccccaacttttc----aaaaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCTTGCAGGTGTTATTTGACACATTAAGAAACCATGGTCATCTCTTCTCCTT
        |||       || ||||| ||     ||  ||||||||  | | |||||  |   || |  |       ||   ||      | |||||     ||||| |||||||| | |||||||||||||| ||| || |||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| ||||| |||||  |
gtaattatgtattttttctttttgtttctatggctattttctgctgtatgctgttgaaattattatatttccagagcatgtggtaatgttagcttttatatgaaaactttgcagGACTGTCTGAACTTACCTTTGACTTAAGACCAGAAATCAGGAAAAGTGCTTTGCAAGTGTTATTTGATACATTAAGAAACCATGGCCATCTTTTCTCTCT
















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|29682831|gb|CB679106.1|CB679106
EST:     TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
EST: gi|29635728|gb|CB640737.1|CB640737
EST:     TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
EST: gi|58598098|gb|CK008626.1|CK008626
EST:     TCTTGTTGATAAGGGTGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
EST: gi|58653430|gb|CK042110.1|CK042110
EST:     TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
EST: gi|29628227|gb|CB633238.1|CB633238
EST:     TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
EST: gi|88576067|gb|CI670212.1|CI670212
EST:     TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
EST: gi|58658144|gb|CK046824.1|CK046824
EST:     TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAG                         GATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT
genomic: TCTTGTTGATAAGGATGATACTATACACTTTTGGTTTCCTTTATTAGCAGgtaaccacat ... aaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgtgtacagataatacaaataatgtgtccccaacttttcaaaaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCTTGCAGGTGTTATTTGACACATTAAGAAACCATGGTCATCTCTTCTCCTT
 agttgat  putative branch site (score: 5)
           agataatacaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccacatttcttgttctgcatgtaccttctgctgctttcagttgatttgtgtacagataatacaaataatgtgtccccaacttttcaaaaccttgcagGATTATCTGAACTTACCTTCGACCTACGACCTGAAATCAGGAAAAGTGCCTTGCAGGTGTTATTTGACACATTAAGAAACCATGGTCATCTCTTCTCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA