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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtatatcattttttcagaaacttattttttgtacatacaaattttaactttttgcagacccatttcacttatttttattcaccttgctattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTTCGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCAAATCGATTACT

Basic information

species Oryza sativa
transcript LOC_Os01g16090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132465_T01 (Zea mays), 3'ss of exon 1
------catgtatatcattttttcagaaacttattttttgtacatacaaattttaactttttgcagacccatttcacttatttttattcaccttgctattttacagGATGCTTATAACTATTTTACTGTGGCCAGA--------TGATTCTACGTGTTCCTGCTTCGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCAAATCGATTACT
      |     |||  ||| ||  |||  || | ||| || || ||| | |     ||| || ||| |  ||||||||||||| ||  | |||||||||| |||||||| |||||||||||||||||||||||||        ||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||| | |        
acaaaccgcaattatgctttattgggaaggttgtcttt-gtccacacatact----gtttctg-agaactgtttcacttattttaatctatcttgctatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGTTCCTGCTTGGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCTACT--------
















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|88380409|gb|CI518779.1|CI518779
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88443063|gb|CI546635.1|CI546635
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88220083|gb|CI219643.1|CI219643
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88441562|gb|CI554786.1|CI554786
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|86853838|gb|CI329284.1|CI329284
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTA-                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88380511|gb|CI521080.1|CI521080
EST:     ATGGCANTACTCCACCAGGAGGCCCAGGAANAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCANATGATTGTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88482451|gb|CI419722.1|CI419722
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88201587|gb|CI201942.1|CI201942
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|89182955|gb|CI045713.1|CI045713
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|4715429|gb|AU056546.1|AU056546
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTG-TT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|18386536|gb|BM419734.1|BM419734
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|89175614|gb|CI042635.1|CI042635
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATGACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88985718|gb|CI016427.1|CI016427
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88973971|gb|CI002633.1|CI002633
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88515218|gb|CI442872.1|CI442872
EST:     ATGCCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|29618189|gb|CB623201.1|CB623201
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88515778|gb|CI443432.1|CI443432
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|89174986|gb|CI041064.1|CI041064
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88471888|gb|CI409159.1|CI409159
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|29674565|gb|CB670840.1|CB670840
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88501875|gb|CI429381.1|CI429381
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88283122|gb|CI404568.1|CI404568
EST:     GGCAGTACTCCANCCAGNGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: GGCAGTACTCCA-CCAG-GAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|29646424|gb|CB651431.1|CB651431
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88198208|gb|CI198058.1|CI198058
EST:     ATGNCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88440621|gb|CI552087.1|CI552087
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88507080|gb|CI434586.1|CI434586
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|6799259|gb|AU082210.1|AU082210
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTG-TT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88471076|gb|CI408347.1|CI408347
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
EST: gi|88248973|gb|CI248822.1|CI248822
EST:     ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAG                         GATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT
genomic: ATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTT

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), 75 (downstream exon)
Score: 48

GATGCCTGGTGCTGGTGGTTATTTGGGCGGCTATGGGGGTGGTGGTGGGTATGGCAGTACTCCACCAGGAGGCCCAGGAAGAAATTACATGGGTCATTAGgtaagatccg ... tattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTTCGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCAAATCGATTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactttttgcagacccatttcacttatttttattcaccttgctattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTTCGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCAAATCGATTACT
 ttttaac  putative branch site (score: 48)
                                       ccttgct  putative PPT
                   atttcacttattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtatatcattttttcagaaacttattttttgtacatacaaattttaactttttgcagacccatttcacttatttttattcaccttgctattttacagGATGCTTATAACTATTTTACTGTGGCCAGATGATTCTACGTGTTCCTGCTTCGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCAAATCGATTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
catgtat
- - - - - - - - -cagaaac
- - - - - - - - - - - - - - - - - - catacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca