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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatactccaatctgtgttcatatatttttcatggctttggcactgtacacttgttgcttcaatttattgacatagcttcatacttacacttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAGCCTGGAAATGCTGGTTTACTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G098042_T01 (Zea mays), 3'ss of exon 2
taaatactccaatctgtgttcata--tatttttcatggctttggcactgtacacttgttgcttcaatttattgacatagcttcatacttacacttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAGCCTGGAAATGCTGGTTTACTTGG
    |   | |||     ||  ||  |||| | | |  | ||       |     | |||||     ||  |    ||   |  || ||     |  | ||||||| || |||||||||||| |  || |||  ||||||| |  ||||||||||||||||||| |||||||||||
--tgtttactaatgcaaattagtaactattctactttacctttctgtattgtcaattttgctcttcctttgttctctaatgttttagttttgtgtcctatagCTTAATACGGGAGACAACAGGGTGGCTGAAAGTACTGGTGTTAAGTTAAAGCCTGGAAATGCAGGTTTACTTGG

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 18
-------------------------------------------------taaatactccaatctgtgttcatatatttttcatggctttggcactgtacacttgttgcttcaatttattgacatagcttcatacttacacttattgt-----agCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAGCCTGGAAATGCTGGTTTACTTGG
                                                 || ||   | ||| |   ||  || || ||  |   ||||| |  | |  |||  |   ||   | |    |  | |  | ||| ||  | ||  |||     |||||| ||  ||||||||||| |  || |||  ||||||| |  ||||||||||||||||||| |||||||||||
gttaaaatgtttttagagcctctcctttttgttataaggtcatctgctgtacatttactaatgtaaattagtaaatattcta---ctttgcctttctgtactgttgattttgctcttcctatgttgtctaatattttaattttgtgtcctatagCTTAATACAGGAGACAACAGTGTGGCTGAAAGTACTGGTGTTAAGTTAAAGCCTGGAAATGCAGGTTTACTTGG
















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|29656612|gb|CB652887.1|CB652887
EST:     TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
genomic: TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
EST: gi|701421|gb|D47712.1|D47712
EST:     CCAGGCTACTGATCAATTCTTGCAAATAGGCAAAACAACATCATGAAAAG                         CTTACTATGGGNGACAACAGCG-AGCCGA
genomic: CCAGGCTACTGATCAATTCTTGCAAATAG-CAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGA
EST: gi|109974420|gb|DT806899.1|DT806899
EST:     TCCAAGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACAACAGC
genomic: TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGC
EST: gi|58603390|gb|CK013918.1|CK013918
EST:     ATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACGACGGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
genomic: ATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
EST: gi|701323|gb|D47614.1|D47614
EST:     TCCAGGCTACTGATCAATTCTTGCAAATAGCAAACCACCATCATGAAAAG                         CTTACTATGGGNGGACAACAGCGCAGCCGAAGGCTACTGGTATCCAGTTTA
genomic: TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAG-ACAACAGCGCAGCCGAAG-CTACTGGTATCCAGTT-A
EST: gi|300215776|gb|HO088402.1|HO088402
EST:     TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
genomic: TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
EST: gi|426538|gb|D22359.1|D22359
EST:     TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACAACAGCGCAGCCGGAAGCTACTGGTATCCAGTTAAA
genomic: TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCG-AAGCTACTGGTATCCAGTTAAA
EST: gi|29640582|gb|CB645591.1|CB645591
EST:     TCCAGGCTACTGATCGATTCTTGCAAATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
genomic: TCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
EST: gi|33675788|gb|CF304027.1|CF304027
EST:     CAATTCTTGCAAATAGCAAAACAACATCATGAAAAG                         CTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
genomic: CAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAG
EST: gi|58607870|gb|CK035903.1|CK035903
EST:     CCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAACAAG                         CTTACTATGGGCAGACAACAGCGCAGCCGAAGCTACTG
genomic: CCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAA-AAGgtatgcacat ... cttattgtagCTTACTATGGG-AGACAACAGCGCAGCCGAAGCTACTG

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: 54 (upstream exon), 73 (downstream exon)
Score: 24

TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAGgtatgcacat ... cttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAGCCTGGAAATGCTGGTTTACTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacacttgttgcttcaatttattgacatagcttcatacttacacttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAGCCTGGAAATGCTGGTTTACTTGG
                                     tacttac  putative branch site (score: 24)
                 aatttattgacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatactccaatctgtgttcatatatttttcatggctttggcactgtacacttgttgcttcaatttattgacatagcttcatacttacacttattgtagCTTACTATGGGAGACAACAGCGCAGCCGAAGCTACTGGTATCCAGTTAAAGCCTGGAAATGCTGGTTTACTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - tttcatg
- - - - - - - - - - - - - - - - - - - - - - ctgtaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcat