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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtttatctgatatcttctaatgacatatatgaggtcaggaatagttggatcctgtttcttgccaaattactaagtgtgcattttgtttacctgacagGGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGGATCAGGCTGTTCAAAGTTACCACAAGAGAATTCTTGTCGTCCTCTATCT

Basic information

species Oryza sativa
transcript LOC_Os10g21890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g21890.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G028501_T01 (Zea mays), 3'ss of exon 3
gtacagtttatctgatatcttctaatgacatata-tgaggtcagg-aatagttggatcctgtttc--ttgccaaattactaagtgtgcattttgtttacctgacagGGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGGATCAGGCTGTTCAAAGTTACCACAAGAGAATTCTTGTCGTCCTCTATCT
     |||  |||    |  ||| |       |  | |||||  | ||| |     | ||| |||  | ||||   || |  || ||||   ||  |   |  ||||   ||||||| || || |||||||| || |||||  | ||| |||||||||||| ||| |||||||||||| | |||||||||   |||||||||||||
-----gttgctctttatttatctgagtttggctgctcaggtcgcgcaattgcgttgtgctgcttcgctcgccacgctaat--gtttgcacggtgaatggttagcagGATGTGGATAAAGCTGAAAAGACTATCGCGTACACTGACCAGCATGGTCGGATCAAGCTATTCAAAGTTACCGCCAGAGAATTCGGTTCGTCCTCTATCT
















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|29622297|gb|CB627308.1|CB627308
EST:     TGGGCGCAAGGGTCCCGGGAGCTGTCCTGGATGCCACAAT                         GGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGG
genomic: TGGGCACAAGGGTCCCGGGAGCTGTCCTGGATGCCACAATgtacagttta ... tacctgacagGGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGG
EST: gi|58654848|gb|CK043528.1|CK043528
EST:     TGGGCGCAAGGGTCCCGGGAGCTGTCCTGGATGCCACAAT                         GGCATGGAGTAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCG
genomic: TGGGCACAAGGGTCCCGGGAGCTGTCCTGGATGCCACAATgtacagttta ... tacctgacagGGCATGGA-TAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCG
EST: gi|29622320|gb|CB627331.1|CB627331
EST:     TGGGCGCAAGGGTCCCGGGAGCTGTCCTGGATGCCACAAT                         GGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGG
genomic: TGGGCACAAGGGTCCCGGGAGCTGTCCTGGATGCCACAATgtacagttta ... tacctgacagGGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttggatcctgtttcttgccaaattactaagtgtgcattttgtttacctgacagGGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGGATCAGGCTGTTCAAAGTTACCACAAGAGAATTCTTGTCGTCCTCTATCT
                                      ttttgttt  CT-rich tract
                     aaattactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtttatctgatatcttctaatgacatatatgaggtcaggaatagttggatcctgtttcttgccaaattactaagtgtgcattttgtttacctgacagGGCATGGATAATGCCGATAAGACTATTGCTTACACGAATCAGGATGGTCGGATCAGGCTGTTCAAAGTTACCACAAGAGAATTCTTGTCGTCCTCTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA