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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactttgatcacctgagttataatagttccattatcacgcattggcctaaccgcgtaaacatgctttcgatttttctaacgattgccttcctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGATTGTTTTATCCAAACCACTCACCTATCCAGCTTCGTCATTTAGGCTGTGC

Basic information

species Oryza sativa
transcript LOC_Os08g33076.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33076.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G045944_T02 (Zea mays), 3'ss of exon 9
-------ttactttgat-cacctgagttataatagttccattat-cacgcattggcctaaccgcgtaaacatgctttcgatttttctaacgattgccttcctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAA-CACCGAAATGACAACGATTGTTTTATCCAAACCACTCACC-TATCCAGCTTCGTCATTTAGGCTGTGC
       |  | | ||| |  |||| || |   | |    |||  || || ||    | | |   || |  |  | |  || ||| ||         |   |||| |||||||||||| ||||||||||||||||| ||||| ||||  |  || | |     ||||    | |  ||  |   | | || | | ||  |||   | |   
ttatgcatctcatggatgcctctgaattgtctcaatgtagttacacaggctttattttcatcatatagagctcttattcatgttttta---------tctttctcacagGTACTGTGAGGGAGCATTCTCTACAGATTAGAAGCACCAGAGGGAGATCTTAGCTTTTCCATACATTACCTATTATGTACATCCT-GTTTTTTTCCCAGCT-
















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|86251673|gb|CI016962.1|CI016962
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88553660|gb|CI483788.1|CI483788
EST:     TTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: TTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|12405341|gb|AU166942.1|AU166942
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88295611|gb|CI530174.1|CI530174
EST:     CGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: CGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|86852887|gb|CI323196.1|CI323196
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|89173484|gb|CI041377.1|CI041377
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88260238|gb|CI362531.1|CI362531
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|86853468|gb|CI327946.1|CI327946
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88506650|gb|CI434156.1|CI434156
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88519426|gb|CI447080.1|CI447080
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|29621123|gb|CB626134.1|CB626134
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|29625221|gb|CB630232.1|CB630232
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|86600119|gb|CI258459.1|CI258459
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|86878614|gb|CI340540.1|CI340540
EST:     GGTGAAACACTTCTTTATGCATCTACTCCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|89175427|gb|CI042448.1|CI042448
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88281365|gb|CI402761.1|CI402761
EST:     TTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: TTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|29662693|gb|CB658968.1|CB658968
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88478721|gb|CI415992.1|CI415992
EST:     GGTGANACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
EST: gi|88545131|gb|CI474671.1|CI474671
EST:     GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAG                         GTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT
genomic: GGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGAT

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: 74 (upstream exon), 58 (downstream exon)
Score: 33

TTGCTAAAGTTACCCGAGGAAGAGAACTTTATATGGCGTTAGAGAAGGCTGGTGAAACACTTCTTTATGCATCTACTGCCATCGAGAAGTTTAGCAACAGgtatatttac ... cctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGATTGTTTTATCCAAACCACTCACCTATCCAGCTTCGTCATTTAGGCTGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctaaccgcgtaaacatgctttcgatttttctaacgattgccttcctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGATTGTTTTATCCAAACCACTCACCTATCCAGCTTCGTCATTTAGGCTGTGC
                             ttctaac  putative branch site (score: 33)
                                      ttgccttcctctctc  putative PPT
                         atttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactttgatcacctgagttataatagttccattatcacgcattggcctaaccgcgtaaacatgctttcgatttttctaacgattgccttcctctctcagGTACTGTGAAGGAGCATTCTCTACAGACTAGAACACCGAAATGACAACGATTGTTTTATCCAAACCACTCACCTATCCAGCTTCGTCATTTAGGCTGTGC

- - - - - cacctga
- - - - - - - - - - - - - - - - - - cacgcat