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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtcttgcctgctttgctacttgcataatgaatgacaattgcactgttgagcttgactttggaatcttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT

Basic information

species Oryza sativa
transcript LOC_Os02g13300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13300.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G161299_T01 (Zea mays), 3'ss of exon 2
------gttggtcttgcctgctttgctacttgca--taatgaatgacaattgcactgttgagcttgactttggaat---cttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT
       |    ||    ||| |  | | | | |    || ||| |    |||||| |||||||||||||   |||   ||| | |||||||||||||||| ||||||||||| ||||| || |||||||||||||||||||||||||||||||||||| | || |||||||||||||| |||||||||
gtttgcctcttcctaatttgcgtgacaaatggtagtctattaataaatgatgcactcttgagcttgacttcttaattgtctttctttagGGGAAATGGAGCTAGTGTTGCTCGAATTGTCCCGTATGCAGCTTTGCATTATATGGCCTATGAAGAATACCGCCGGTGGATCATTCTTGGCTTTCCTAAT

upper sequence: LOC_Os02g13300.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G15430.1 (Glycine max), 3'ss of exon 2
gttggtcttgcctgctttgctacttgcataatgaatgacaattgcact--gttgagcttgactttggaatcttccct---------tagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT
|||  |||  | |   |||  |||   || |||| |||| ||     |  ||||   |||| ||    ||||| | |          || ||||||||||| ||||||||  ||||| ||||||| |||||| | ||||||||| ||||||| |||||| |  ||||||| || |    ||||||| ||
gtttttctgacttaagttgaaactgtgatcatga-tgaccatcattataagttgcaattgaattaaccatctttcttgatgagttgcagAGGAAATGGAGCAAGTGTTGCAAGGATTATTCCTTACGCAGCTATTCATTATATGTCCTATGAGGAATACCGCAGATGGATTATACAAACTTTTCCTCAT

upper sequence: LOC_Os02g13300.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G26180.1 (Arabidopsis thaliana), 3'ss of exon 2
gttggtcttgcctgctttgctacttgcataatgaatgacaattgcact-gttgagcttg--actttgg----aatcttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT
||  || ||| ||    || ||  ||| |  ||      | ||      | |||   ||  ||||| |      | |      || || ||||| || |||||||||||||| ||||| ||||||||| | ||||| ||||| ||||| ||||||||  ||||||| ||  ||||||| ||  | 
gtacgt-ttgtctttagtgttagatgcgttttgggatctagttcagtcagatgattctgtaactttcgttttggtttgtgaacagAGGGAATGGTGCAAGTGTTGCTCGGATAGTTCCCTATGCAGCTCTTCATTACATGGCTTATGAGGAATACAGGAGATGGATTATCTTTGGTTTCCCAGAC

upper sequence: LOC_Os02g13300.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g02470.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------gttggtcttgcctgctttgctacttgcat-aatgaatgacaattg--cactgttgagcttgactt----tggaatcttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT
                               ||| || ||    | ||   | |    | || | ||  |  |||  |     | | ||  |  |    ||| |  |      || || |||||||| ||||||||||| |||||||||||||||||  ||||||||||||| |||||  ||||| | ||||||||||| ||   ||| ||| | 
gtggaaatctgaatctctttttctacttaatttgatcctggggtcattatcattcatgtgaaagtattgcttttggccctcaataatctctatatcacgtgggacttgtatccagAGGGAATGGAGCAAGTGTTGCTCGAATTGTTCCTTATGCAGCACTGCATTATATGGCTTATGAGCAATACCGGCGATGGATCATACTCAATTTCCCTGAC

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|33677964|gb|CF306203.1|CF306203
EST:     GGATCATTTCGAACAATCTCTCGAACAGAAGGGCTTTTAGGGTTTTACAG                         GGGAATTGTTTCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTA
genomic: GGATCATTTCGAACAATCTCTCGAACAGAAGGGCTTTTAGGGTTTTACAGgttggtcttg ... cttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTA
EST: gi|300215830|gb|HO088456.1|HO088456
EST:     GGATCATTTCGAACAATCTCTCGAACAGAAGGGCTTTTAGGGTTTTACAG                         GGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTA
genomic: GGATCATTTCGAACAATCTCTCGAACAGAAGGGCTTTTAGGGTTTTACAGgttggtcttg ... cttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcataatgaatgacaattgcactgttgagcttgactttggaatcttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT
                              gcttgac  putative branch site (score: 4)
                                            tcttccctt  putative PPT
     taatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtcttgcctgctttgctacttgcataatgaatgacaattgcactgttgagcttgactttggaatcttcccttagGGGAAATGGAGCCAGTGTTGCTCGGATTGTTCCTTATGCAGCTTTGCATTATATGGCCTATGAAGAATACAGACGATGGATCATTCTTGGTTTTCCTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA