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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaagaatcaattttctctttaataccacagcagctttagaatgctatttaaacaaatgcaactttttctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCTGATGAGAAAATTTCTGGCTGTGTGATGGAGGTAGCCTGCTGCAGCAGTA

Basic information

species Oryza sativa
transcript LOC_Os05g07070.8
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07070.8 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118344_T02 (Zea mays), 3'ss of exon 6
--------gtagaaagaatcaattttc-tctttaataccacag-cagctttagaatgctattta-aacaaatgcaacttttt------ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCTGATGAGAAAATTTCTGGCTGTGTGATGGAGGTAGCCTGCTGCAGCAGTA
         | | |||||  ||  |   |  ||| || ||||  |      || |||   | |  ||| |||| || ||| |       |||   ||||||||||||||||||| |||||| |||||| |||| ||||| ||||| |||||||| ||| ||||  ||||||||| |||| || |||||||||||  | 
gtagtaagattgtaagaaagaacctagataattagtatcacaaaccaacacaggatgtgttctgtaactaatgtaagtttctatgctgttatctgcagGAGCTGCTGGCTTTGGGAGAACGAATAGGCAATGTCAACACGGGCCTAGCTGATGAAAAACTTTCAAGCTGTGTGACGGAGATACCCTGCTGCAGCTCTG
















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|33678771|gb|CF307010.1|CF307010
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|86890276|gb|CI321453.1|CI321453
EST:     GATCCTCACT-GGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGCCTTTGGAAGAACCCATA-GCCATGTGAACACTGGCCTCGCT
genomic: GATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|109712957|gb|CI105565.1|CI105565
EST:     TCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCC
genomic: TCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|89174305|gb|CI110503.1|CI110503
EST:     ATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: ATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|88964798|gb|CI084796.1|CI084796
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|29633286|gb|CB638295.1|CB638295
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|218502858|gb|FG946692.1|FG946692
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|88243449|gb|CI244571.1|CI244571
EST:     GGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: GGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|29646727|gb|CB651734.1|CB651734
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|14981531|gb|BI306209.1|BI306209
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|86490334|gb|CI132967.1|CI132967
EST:     TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: TCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|88982886|gb|CI250490.1|CI250490
EST:     GATGACATGAGCTATGAG                         GAGCTTCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: GATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
EST: gi|86487200|gb|CI129833.1|CI129833
EST:     CACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAG                         GAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT
genomic: CACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGgtagaaagaa ... ctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccacagcagctttagaatgctatttaaacaaatgcaactttttctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCTGATGAGAAAATTTCTGGCTGTGTGATGGAGGTAGCCTGCTGCAGCAGTA
                                       ctttttctat  CT-rich tract
                      tatttaaacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaagaatcaattttctctttaataccacagcagctttagaatgctatttaaacaaatgcaactttttctatacacagGAGCTGCTGGCTTTGGAAGAACGCATAGGCCATGTGAACACTGGCCTCGCTGATGAGAAAATTTCTGGCTGTGTGATGGAGGTAGCCTGCTGCAGCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG