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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatattgaatgtcattttgtttttaattgtagacagaatagaaggttatttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT

Basic information

species Oryza sativa
transcript LOC_Os08g19850.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G137615_T01 (Zea mays), 3'ss of exon 5
gttatattgaatgtcattttgtttttaattgtagacagaatagaaggttatttatctaaactt-catttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT
|||   |||||||| ||| | |  |||     |   ||||||     | |||||||||| | |  |||  ||||||||||| ||||||||||||||| | || |||||||||||||| ||||| ||||||||||| ||| |||| |||||||||||||| |||||||||||||||||||
gttcgcttgaatgttattctatcatta--cagaattagaataa----tcatttatctaaccatgtattatctgttacagCTGGATTTTCAGCTGCCCATTCGGTTCAAGCTGACTTATTCTGCTGAGGATGAAGCAAAAATTGAAAGGCCTGTGATGATACACAGGGCAATCCTAGGTT

upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 16
gttatattgaatgtcattttgtttttaattgtagacagaatagaaggttatttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT
|||   |||||||| ||| |||  | ||   |      ||||| |  |||| || |   || | |||  ||||||||||| ||||||||||||||| | || ||||||||| |||| ||||| ||||||||||||||| |||| |||||||||||||| |||||||||||||||||||
gttcccttgaatgttattctgtcatcaa--atgattgaaatagtaa-ttatctaaccttacattattatctgttacagCTGGATTTTCAGCTGCCCATTCGGTTCAAGCTGGCTTATTCTGCTGAGGATGAAGCCAAAATTGAAAGGCCTGTGATGATACACAGGGCAATCCTAGGTT

upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 15
----------gttatattgaatgtcattttgtt--tttaattgtagacagaatagaaggttat--ttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT
           | |  | || | |||||    |  || | || |  | |   |   || | ||  ||   | ||  |  || | ||   ||||| || || ||||| ||    || || ||| ||   | ||| || ||||||||||||||| ||||||| ||||| ||||| ||||| || |||||||| |
gtttgcacctttcagctggattttcattcacatgattcagttttgaataacttttcagctgatggttggatgaatgtggttgcttg---cagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATCCTAGGAT

upper sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
---------gttatattgaatgt-cattttgtt--tttaattgtagacagaatagaaggttat--ttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT
         |||    |  || | ||||   ||  || | || |  | |   |   || | ||  ||   | ||  |  || ||||   ||||| || || ||||| ||    || || ||| ||   | ||| || ||||||||||||||| ||||||| ||||| ||||| ||||| || || ||||| |
gtttgcactgttcagctagatttgcattcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctg---cagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT

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|29628276|gb|CB633287.1|CB633287
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG                         CTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
EST: gi|8956844|gb|BE230647.1|BE230647
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG                         CTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
EST: gi|33794572|gb|CF323173.1|CF323173
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG                         CTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
EST: gi|29626606|gb|CB631617.1|CB631617
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG                         CTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
EST: gi|38479117|gb|CF963250.1|CF963250
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACGG                         GTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
EST: gi|29622569|gb|CB627580.1|CB627580
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG                         CTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
EST: gi|8956784|gb|BE230587.1|BE230587
EST:     TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAG                         CTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT
genomic: TTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGAT

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: 63 (upstream exon), 75 (downstream exon)
Score: 46

ATCAATGAAGGTGATGGTGCCTTCTATGGTCCAAAAATTGATATTGGTGTGTTTGATGCCCTCAAGAGGAAATTTCAGTGTGCAACTCTACAGgttatattga ... cctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattgtagacagaatagaaggttatttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT
                              atctaaa  putative branch site (score: 46)
                                     cttcatttcctgtt  CT-rich tract
                        ttatttatctaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatattgaatgtcattttgtttttaattgtagacagaatagaaggttatttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG