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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccattttatatgtttggaccacccagttggttcatttttgtataccataattaattcaacgtggtttactaatccttatattcgccatcctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAAACGTCGGAAACGAGAACATCTTAGAGCAGAAGAAAGCAAACCCTATTGC

Basic information

species Oryza sativa
transcript LOC_Os04g40310.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 3
-acccattttatatgtttggaccacccagttggttcatttttgtataccataattaattcaacgt---ggtttactaatccttatattcgccatcctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAAACGTCGGAAACGAGAACATCTTAGAGCAGAAGAAAGCAAACCCTATTGC
| || | | ||| | | || || || | || | | | || | | || ||||||||| || | ||| |||| ||| ||||||||||||||| | || ||||||||||||| |||||||||||||| || || || |||||| | | ||||||||||||||||||||| | ||
gagatatggaacttcttttggcgctt---ttaattaataatgtcgagtcagagtaagtttgatggtcaggcccactaatcctcg-atactgcattatgttctagGCAATGTGGGTCAGGACTACGCCATCTTTGAGCAAGGCGCTTCTGCAGGAAATGTTGGGAATGAGAACCTTGTGGAGCAGAAGAAAGCAAACCCTGTCGC

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G00500.1 (Glycine max), 3'ss of exon 2
acccattttatatgtttggaccacccagttggtt-catttttgtataccataattaattcaacgtggtttactaatccttatattcgccatcctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAAACGTCGGAAACGAGAACATCTTAGAGCAGAAGAAAGCAAACCCTATTGC
| ||| | || | | || || |||| | || | | | | || | | | |||||| || || || || |||||||| ||||||||||||||||| || ||||| |||||||| || || || | ||||||||||| ||||| ||| ||||
------------------------gtaattgaatacaaatacaataataatcgttcattctat-tgaataagaagtaaata-aatggttggtgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAAATGTCGGAAAGGAAAAGATGGTGGAGCAGAAGAAGGCAAATCCTGTTGC
















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|86504182|gb|CI146815.1|CI146815
EST:     CAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: CAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
EST: gi|29687051|gb|CB683326.1|CB683326
EST:     TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
EST: gi|29662276|gb|CB658551.1|CB658551
EST:     TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
EST: gi|86428208|gb|CI074889.1|CI074889
EST:     TTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: TTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
EST: gi|87018960|gb|CI256845.1|CI256845
EST:     TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
EST: gi|29662277|gb|CB658552.1|CB658552
EST:     TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
EST: gi|29687448|gb|CB683723.1|CB683723
EST:     TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG                         GTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA
genomic: TGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatctt ... cctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accataattaattcaacgtggtttactaatccttatattcgccatcctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAAACGTCGGAAACGAGAACATCTTAGAGCAGAAGAAAGCAAACCCTATTGC
                       tactaat  putative branch site (score: 1)
 ccatcct  putative PPT
 aattaattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccattttatatgtttggaccacccagttggttcatttttgtataccataattaattcaacgtggtttactaatccttatattcgccatcctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAAACGTCGGAAACGAGAACATCTTAGAGCAGAAGAAAGCAAACCCTATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - -accataa