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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacagataaacacttgttactgatttcttacatactgttcttcgcgagttgatttttgctcgaatttttgattcattgttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAACTTTCTTCTCTGGCCAAAGAGGTGGCGAGAGTGGAGTTGGTCAGGGATTA

Basic information

species Oryza sativa
transcript LOC_Os02g51330.1
intron # 1
splice site 3'
intron type U2

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|88451525|gb|CI565578.1|CI565578
EST:     TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACTAG                         GG-TCATAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAAC
genomic: TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAGgtatcacaga ... gttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAAC
EST: gi|58605796|gb|CK033829.1|CK033829
EST:     TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCA-                         GGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAAC
genomic: TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAGgtatcacaga ... gttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAAC
EST: gi|88314828|gb|CI608287.1|CI608287
EST:     TAATGTCCGCGGCTGCCTCGCTGCC-TGAATGCCTCCACCTCTGAACCAG                         GGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTG
genomic: TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAGgtatcacaga ... gttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTG
EST: gi|88408585|gb|CI686087.1|CI686087
EST:     AATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCNAC-TCTGAACCAG                         GGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAAC
genomic: AATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCC-ACCTCTGAACCAGgtatcacaga ... gttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAAC
EST: gi|88407783|gb|CI607917.1|CI607917
EST:     TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAG                         GGGTTACAGAAGCGGTGGAGGTTGGGAGCGAGGAG
genomic: TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAGgtatcacaga ... gttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAG
EST: gi|88414365|gb|CI691525.1|CI691525
EST:     TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAG                         GGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGC
genomic: TAATGTCCGCGGCTGCCTCGCTGCCCTGAATGCCTCCACCTCTGAACCAGgtatcacaga ... gttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgttcttcgcgagttgatttttgctcgaatttttgattcattgttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAACTTTCTTCTCTGGCCAAAGAGGTGGCGAGAGTGGAGTTGGTCAGGGATTA
                                 ttttgat  putative branch site (score: 4)
                                              ttgtttt  putative PPT
                              aatttttgattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcacagataaacacttgttactgatttcttacatactgttcttcgcgagttgatttttgctcgaatttttgattcattgttgttttagGGGTCACAGAAGCGGTGGAGGTTGGGAGCGAGGAGATGTTGTTTGAGCAACTTTCTTCTCTGGCCAAAGAGGTGGCGAGAGTGGAGTTGGTCAGGGATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG