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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcagagttcaatcatcatcttttagttttgtttgtctttttgcactaacaggaggaatatcaggataatttatttatgtattttccgatggacttctatgcatgggtggttggttaaccttctatttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 3
gttaatcagag-ttcaatcatcatctttta-------gttttgtttgtctttttg-cactaacaggaggaatatcaggata------atttattta--------tgtattttccgatggacttct-atgcatgggtgg---ttggttaaccttctattttt-----atcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG
|||||||||   |||||      |||||||       | ||||||||    ||||  |       ||      |  || |        |||| |||        |||||||   | |     | | ||   ||||||    |||  | ||  ||| || ||       |||||||| |||||  ||||||||||||||||||||||||||||||||||||||||||||
gttaatcagttcttcaaaacatttcttttatactcgtgatttgtttgatactttgatatgtgtgtgaaagcccttcggttttcaaatgtttacttaatgattattgtatttcatggttcttgtttgatatgtgggtgtggtttgactcactatctgttgtttctatgccagCTTGGGTACACAGAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 15
gttaatcagagttcaatcatcatcttttagttttgtttgtctttttg-cactaacaggaggaatatcaggat----aatttatttatgtattttccgatggacttctatgcatgggtggttggttaaccttctatttttat--cagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG
|||||||||   |  |  |   |  ||| |   | ||  | | ||||  |   |   ||      | ||| |    ||| |||||   |  ||   | | ||  | |  |  ||| |   |   | | ||  | ||| |||  |||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||
gttaatcagttcttcagaacatttcttttgaactcttgatttgtttgatatgtatgtgaaagcccttaggttttcaaatgtattt-catggttcttgtttgatatgtgggtgtggttttattcattatctgttgtttctatgccagCTTGGGTACACAAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
gttaatcagagttcaat-catcatctttta-gttttgtttgtctttttgcactaa-------caggaggaatatcaggat--aatttatttatgtattttccgatg---gacttctatgcatgggtggt-tggttaaccttctatttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG
|||| | |    ||| | |||||     |  |   | ||||| || || || |         ||  |    | ||   ||  ||| |||   || |||||   |||   || | |  |   |      | |||||  | || | |||    |||||||| ||||| || || |||||||| || ||||| ||||||||||||||| | |||
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttca--cagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG

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|29657562|gb|CB653837.1|CB653837
EST:     GAAATGCGGAAAG                         CTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACT
genomic: GAAAAGCGGAAAGgttaatcaga ... tttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACT
EST: gi|58652777|gb|CK041457.1|CK041457
EST:     GGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG                         CTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACT
genomic: GGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAGgttaatcaga ... tttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACT
EST: gi|33795777|gb|CF323758.1|CF323758
EST:     CAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG                         CTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACT
genomic: CAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAGgttaatcaga ... tttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttccgatggacttctatgcatgggtggttggttaaccttctatttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG
                                ggttaac  putative branch site (score: 3)
                                      ccttctatttttatc  CT-rich tract
                                        ttctatttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcagagttcaatcatcatcttttagttttgtttgtctttttgcactaacaggaggaatatcaggataatttatttatgtattttccgatggacttctatgcatgggtggttggttaaccttctatttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA