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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaccactaatgctctatgaagatatgtttgtcttcagacatagtgtttcttagttgtttcttctgctaaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g01700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G154278_T01 (Zea mays), 3'ss of exon 3
gtttgtaccactaatgctctatgaagatatgtttgtcttcagacatagtgtttcttagttg-tttcttctgctaaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG
||| ||   || || |||  ||  | || ||||| | ||    | |||||||   | |||  |||||| |  ||| | |||||||||| ||||||||| |||||||||||||||||  ||||||||||||||||||| || |||||||| || | |||||||||||| ||
gttggtgaaacgaacgctgcatctatatctgtttatgttgtcgcttagtgttgactcgttcctttcttgttgtaactcatagGTTCAAAGAGAGAGGCAGAGGATAAGATAGTTCCACGAGAAATCGATGCAGATGACTCCGATGTGGAGCCTAAAAGTGATGATGAGAG

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G062076_T01 (Zea mays), 3'ss of exon 3
gtttgtaccactaatgctctatgaagatatgtttgtcttcagacatagt-gtttcttagttgtttcttctgctaaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG
||| ||   |  || ||| ||| || ||  ||||   ||  | | |||| ||  |||  |  ||||||    ||| | |||||||||| ||||||| | |||||||||||||||||  ||||||||||||| ||||| || |||||||| || | ||| ||||| || ||
gttggtggaatgaacgctgtatcaatatcagtttacgttgtggcttagtagtgacttgttcctttcttgctgtaactcatagGTTCAAAGAGAGAGACAGAGGATAAGATAGTTCCACGAGAAATCGATGCTGATGACTCCGATGTGGAGCCTAAAAGCGATGACGAGAG

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G15050.2 (Glycine max), 3'ss of exon 2
--------------------------------------------------gtttgtaccactaa--tgctctatgaagatatgtttgtcttc-agacatagtgtttcttagttgtttcttctgctaaatt-atagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG
                                                     || |  | |||  |     | |||   ||  |||| ||| | |   ||| ||  ||  ||| |   ||   ||  || | ||| || | ||||||    || ||| | || |||||  |     | |||||||||||||||||||| |||  || |||||||||||| ||
gtattctatctcctaactaaaatactttgcaatggccttccatctaaaagaggtgaaaaaataagataaggaaagaaaccataattgttttctatattcagtattg-ttgattgataggtcctttatcttgacagGATCGAAGAGAGAAATGGAAGATCACATTGTTCCACGTAGTGTTGATGCAGATGATTCTGATGTTGAAGTCAAAAGTGATGATGACAG

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G15050.3 (Glycine max), 3'ss of exon 1
gtttgtaccactaatgctctatgaagatatgtttgtcttc-agacatagtgtttcttagttgtttcttctgctaaatt-atagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG
||    |      ||     | |||   ||  |||| ||| | |   ||| ||  ||  ||| |   ||   ||  || | ||| || | ||||||    || ||| | || |||||  |     | |||||||||||||||||||| |||  || |||||||||||| ||
gtgaaaaaataagataaggaaagaaaccataattgttttctatattcagtattg-ttgattgataggtcctttatcttgacagGATCGAAGAGAGAAATGGAAGATCACATTGTTCCACGTAGTGTTGATGCAGATGATTCTGATGTTGAAGTCAAAAGTGATGATGACAG

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|88420938|gb|CI620256.1|CI620256
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTT-AAGGAGAGAGGCTGAGGATAAGAT
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGAT
EST: gi|88402391|gb|CI596252.1|CI596252
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTTCAAGGAGAGAGGCTGAGGATAA
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAA
EST: gi|88573290|gb|CI664861.1|CI664861
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTA
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTA
EST: gi|88427649|gb|CI689512.1|CI689512
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAG
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAG
EST: gi|88444118|gb|CI594491.1|CI594491
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTACAAG                         GTTCACGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAG
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAG
EST: gi|88301238|gb|CI594764.1|CI594764
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTTCAAGGAGAG
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAG
EST: gi|88402420|gb|CI596281.1|CI596281
EST:     AGGAGAGAGATAGGCGGAAAAGCATAAGCCTACTCCTAGAAG                         GTTCAAGGAGAGAGGCTGAGGATAAGAT
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGAT
EST: gi|88377322|gb|CI600477.1|CI600477
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAG
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAG
EST: gi|88342051|gb|CI644388.1|CI644388
EST:     AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG                         GTTCAAGGAGAGAGGCTGAGGAT
genomic: AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGAT

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: 72 (upstream exon), 73 (downstream exon)
Score: 90

AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGgtttgtacca ... taaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtttgtcttcagacatagtgtttcttagttgtttcttctgctaaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG
                                          tgctaaa  putative branch site (score: 90)
                                ttgtttcttctgct  CT-rich tract
                                             taaattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaccactaatgctctatgaagatatgtttgtcttcagacatagtgtttcttagttgtttcttctgctaaattatagGTTCAAGGAGAGAGGCTGAGGATAAGATAGTTCCTAGAGAAATCGATGCAGATGATTCTGATGTGGAACCCAGAAGTGATGATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT