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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattcgtatccatttgtacttcactataactgctcatcaaaatgcaatagaccagttcataaataattgtcacattttcatattaacctttttgaacaaggaatttattaatttgtaatttgcattagtttgctgcattgtgttctctgtgtttaaggtggatttttttttttcatttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAGATTTAGAGGACATTGAGATGTGATAATTCCACCGTTCAGAATTGGCAAT

Basic information

species Oryza sativa
transcript LOC_Os04g56480.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56480.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G044011_T02 (Zea mays), 3'ss of exon 14
gtaagtattcgtatccatttgtacttcactataactgctcatcaaaatgcaatagaccagttcataaataattgtcacattttcatattaacctttttgaacaaggaatttattaatttgtaatttgcattagtttgctgcattgtgttctctgtgtttaaggtggatttttttttttcatttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAGATTTAGAGGACATTGAGATGTGATAATTCCACCGTTCAGAATTGGCAAT
                                                                                 |  || |||   |||   | |||       |  | | | || |||  |    ||||||||||  |      ||| |||||     | ||    |||    |||| |||||||||||||  |||||||||| || ||||||||||| |||||  | || ||  |||||||||| ||| |||||| |  ||| | ||     ||  | ||
--------------------------------------------------------------------------------atagattttattgtttggaagcaattgggaaaacattatttacttttaaaatatttgctgcatact------tgtatttaaataacacttgcccttt---cttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT
















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|89182762|gb|CI114131.1|CI114131
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86883503|gb|CI338061.1|CI338061
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88224189|gb|CI224038.1|CI224038
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88428005|gb|CI556899.1|CI556899
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88429886|gb|CI562697.1|CI562697
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86505661|gb|CI148294.1|CI148294
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88457668|gb|CI539464.1|CI539464
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86840851|gb|CI335043.1|CI335043
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86600311|gb|CI356068.1|CI356068
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86864162|gb|CI334008.1|CI334008
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88296986|gb|CI542698.1|CI542698
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88446697|gb|CI526530.1|CI526530
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86257435|gb|CI004252.1|CI004252
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86825581|gb|CI361755.1|CI361755
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86505390|gb|CI148023.1|CI148023
EST:     TGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: TGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88544532|gb|CI472636.1|CI472636
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88227542|gb|CI227022.1|CI227022
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|88286498|gb|CI524997.1|CI524997
EST:     TTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: TTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
EST: gi|86854586|gb|CI258879.1|CI258879
EST:     NTTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAAC                         AGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG
genomic: ATTCGGTGGCACAGTGCACATCTTTTCTTCAATGCATGTCTCTGGTGAACgtaagtattc ... atttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgcattgtgttctctgtgtttaaggtggatttttttttttcatttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAGATTTAGAGGACATTGAGATGTGATAATTCCACCGTTCAGAATTGGCAAT
                                 tttttttttttcattt  CT-rich tract
                                atttttttttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattcgtatccatttgtacttcactataactgctcatcaaaatgcaatagaccagttcataaataattgtcacattttcatattaacctttttgaacaaggaatttattaatttgtaatttgcattagtttgctgcattgtgttctctgtgtttaaggtggatttttttttttcatttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAGATTTAGAGGACATTGAGATGTGATAATTCCACCGTTCAGAATTGGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG