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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttttcttttacaaaaattcgaacaaagaattatctgcttgagaatgatgcgattgttaaccaaaggcttttacaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG

Basic information

species Oryza sativa
transcript LOC_Os03g02590.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02590.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 2
------gtatttcttttcttt-tacaaaaattcg---aacaaagaattatct--gcttgagaatgatgcgatt--------gttaaccaaagg------cttttacaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG
        | ||||   ||    |||  |    |   | |||  |||   |   | ||  |||| |   | ||         ||||||   ||      ||| ||| ||||||||||||||| |||||||| ||||| ||||||||| |||| || ||||| ||| | ||| |||| |||||   ||||
gtaaatcgacttctcccctccacacagtacactgttcatcaagaaatcccccccgtttaggaatcacagggttcgaaacgaattaacctgcgggttcttcttctacgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGGCTCGGACGAACGGGGATCGTCAAG
















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|218487592|gb|FG945521.1|FG945521
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|33662420|gb|CF293387.1|CF293387
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|313084054|gb|HO213837.1|HO213837
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|38480632|gb|CF964721.1|CF964721
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|84117673|gb|CD151440.1|CD151440
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|29687966|gb|CB684241.1|CB684241
EST:     TGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|86829554|gb|CI286745.1|CI286745
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|25798400|gb|CA754361.1|CA754361
EST:     TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
EST: gi|58585983|gb|CF984291.1|CF984291
EST:     TCAGCCCTCCTGCGGAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG                         TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG
genomic: TCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAGgtatttcttt ... acaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattatctgcttgagaatgatgcgattgttaaccaaaggcttttacaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG
                           tgttaac  putative branch site (score: 2)
                                        cttttac  putative PPT
                                         ttttacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttttcttttacaaaaattcgaacaaagaattatctgcttgagaatgatgcgattgttaaccaaaggcttttacaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC