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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtttgcaccttcttttgcaacgcaggacatgagctccggtgtgcttgctcgctactagatgcatttgagcaattgagacttactcatgtaatatatgttttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATAATGGGGCCTGAGAGACTGCAGGAAGTTGGTTCCTGCCTAACACTGGACA

Basic information

species Oryza sativa
transcript LOC_Os03g48300.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 29
lower sequence: GRMZM2G022997_T02 (Zea mays), 3'ss of exon 4
gtgatgtttgcaccttcttttgcaacgcaggacatgagctccggtgtgcttgctcgctactagatgcatttgagcaattgagacttactcatgtaatatat-gttttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATAATGGGGCCTGAGAGACTGCAGGAAGTTGGTTCCTGCCTAACACTGGACA
                 |  |||   |  |||||| |  || | || |||||||| | | ||||      ||||          ||||| |   ||| | | | || ||||||||| ||||||||||||| | ||||||||||||||||||||||| |||| ||||||||||| |||||||||||||||||||| |||||||| ||  ||||||
----------------gtgatgct-tgttggacataaaatcagctgagcttgctcccaagtagagttgcctgagtt-------tttactaactgaatgtgttggttgggtccagGACAAAACCAGTGAAAGTTCTTCCTTGCTCCAGGAGCACACCTTGCCCATAATGGGGCCCGAGAGACTGCAGGAAGTTGGGTCCTGCCTGACCATGGACA
















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|218481023|gb|FG950412.1|FG950412
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|58605143|gb|CK033176.1|CK033176
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88255510|gb|CI354334.1|CI354334
EST:     CGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCGTGCTCCAGGAGCACACCCTGCCGATA
genomic: CGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|218492736|gb|FG956091.1|FG956091
EST:     CGGATTGAAATGACA-TTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGAT
genomic: CGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGT-GAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGAT
EST: gi|29672858|gb|CB669133.1|CB669133
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88463148|gb|CI524458.1|CI524458
EST:     TGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGGAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88381303|gb|CI528283.1|CI528283
EST:     TTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88974007|gb|CI002669.1|CI002669
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|89168931|gb|CI020471.1|CI020471
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86827434|gb|CI272827.1|CI272827
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88844694|gb|CI021269.1|CI021269
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|29674286|gb|CB670561.1|CB670561
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|29640071|gb|CB645080.1|CB645080
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|29645913|gb|CB650920.1|CB650920
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|29645535|gb|CB650542.1|CB650542
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88839229|gb|CI000701.1|CI000701
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86887378|gb|CI313281.1|CI313281
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|89191284|gb|CI393137.1|CI393137
EST:     GATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: GATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86598393|gb|CI355010.1|CI355010
EST:     TCCCGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86902835|gb|CI312212.1|CI312212
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86869891|gb|CI316619.1|CI316619
EST:     GGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: GGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86252520|gb|CI003856.1|CI003856
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|86885163|gb|CI316923.1|CI316923
EST:     CCGGAGTGAAATGACATTTAGGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: CCGGATTGAAATGACATTTA-GTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
EST: gi|88260411|gb|CI362704.1|CI362704
EST:     TTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACAGCCCTGCCGAT
genomic: TTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACA-CCCTGCCGAT
EST: gi|88252278|gb|CI350706.1|CI350706
EST:     TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG                         GATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA
genomic: TCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 32

GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAGgtgatgtttg ... tttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATAATGGGGCCTGAGAGACTGCAGGAAGTTGGTTCCTGCCTAACACTGGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagatgcatttgagcaattgagacttactcatgtaatatatgttttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATAATGGGGCCTGAGAGACTGCAGGAAGTTGGTTCCTGCCTAACACTGGACA
                       gacttac  putative branch site (score: 32)
                                atgtaatatatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgtttgcaccttcttttgcaacgcaggacatgagctccggtgtgcttgctcgctactagatgcatttgagcaattgagacttactcatgtaatatatgttttggtccagGATAAAACCAGTGAAAATACTTCCTTGCTCCAGGAGCACACCCTGCCGATAATGGGGCCTGAGAGACTGCAGGAAGTTGGTTCCTGCCTAACACTGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG