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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttacatacttgcatttagttataatctgttttccacttattgaagctttgtggagttagtcaagtactaagttttgtttagtcagatggttgctaaaagattattacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAAGTCTTG

Basic information

species Oryza sativa
transcript LOC_Os05g04340.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 6
gtatgttacatacttgcatttagttataatctgt-tttccacttattgaagctttgtggag--ttagtcaagtactaagttttgtttagtcagatggtt-gctaaaagattattacttc--cagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAAGTCTTG
                  | ||||  |||| | | |||  | | ||| | |     |  |   ||||| || |  ||||    | ||   |||||||||   |  ||   ||||  | |  ||||| || || ||||| |||||||| ||||| |||||||| ||||||||||||||  ||
-----------------gtatagtagtaatttctgtttgaattcattaaggagaaattcatctttagttaaattataagcgcagctt---cagatggtttaatgcaattctatttgtgcaacagGTTAATCCTCATACCCATCAGCTAAAATTGTGTGACTTTGGCAGCGCGAAAGTTCTG
















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|88742984|gb|CI766492.1|CI766492
EST:     ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG                         GTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
genomic: ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
EST: gi|58679859|gb|CK068546.1|CK068546
EST:     CAACACCATTGGCGTGTGTCACAGGGGATATCAAGCCACAAAATCTTCTG                         GTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
genomic: CAACACCATTGGCGTGTGTCACA-GGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
EST: gi|58671594|gb|CK060280.1|CK060280
EST:     ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG                         GTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
genomic: ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
EST: gi|66928190|gb|CX115038.1|CX115038
EST:     ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG                         GTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
genomic: ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
EST: gi|29630931|gb|CB635940.1|CB635940
EST:     ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG                         GGGAACC-ACATACTCATCAGC
genomic: ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGC
EST: gi|58690705|gb|CK079392.1|CK079392
EST:     ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG                         GTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
genomic: ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
EST: gi|88356165|gb|CI627613.1|CI627613
EST:     ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTG                         GTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA
genomic: ACAACACCATTGGCGTGTGTCACAGGGATATCAAGCCACAAAATCTTCTGgtatgttaca ... ttacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaagtactaagttttgtttagtcagatggttgctaaaagattattacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAAGTCTTG
                                tgctaaa  putative branch site (score: 2)
                                             ttacttcc  putative PPT
                                   taaaagattattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttacatacttgcatttagttataatctgttttccacttattgaagctttgtggagttagtcaagtactaagttttgtttagtcagatggttgctaaaagattattacttccagGTGAACCCACATACTCATCAGCTGAAATTATGTGACTTCGGCAGCGCGAAAGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA