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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatttttattatagttgcattgtatccacattacatggagttgttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG

Basic information

species Oryza sativa
transcript LOC_Os09g13870.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024615_T02 (Zea mays), 3'ss of exon 3
ttttatttttattatagttgcattgtatccacattacatggagt--tgttattataactctagttactcactttgct--ttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGAT-GTTACACTATAAAGTCCCATGGAACCAAAGTGGCGA--GACTTCACATGTACGACT--GGATAATACTTCTACTCCTTG
           |||  ||   |    |   | ||  |||||| |  | ||   |  | |  |  |       | | |  | ||| |  |  ||| | |   |  |||    ||    || |  | | |   || |||  |   ||    |||||   |  ||  ||  ||||| | || | | |    ||  |||||     |   |||
----------gttagggtcttac-acaattagatcccatggaatgatattggcaagattacacatgtatgactggataatacttctcctccttgctgtc--atagACGGGCTGTTGAATATAATTGAACCATTTCACCGTTTTGT----TGGAAAAGACATGATGACCGACTTGAGATATCCTATGAAGGGCAATACAGTGCCATTTTG

upper sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G050658_T02 (Zea mays), 3'ss of exon 2
---ttttatttttattatagttgcattgtatccacattacatggagttgttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
   |   |||  | ||  ||| ||  || | ||       |  || |||    | | | | ||  | ||   ||| || ||||  | | |||||| |||| |||| |||||||||||    ||||| | ||||||||| |  ||||||||||  | | |||| ||  | |||||||| ||||||||||||||||| |||||||
tagtaacattgatcttgcagt-gctgtgaagcccttgagaactgaattgcagctgttattgtaact-ctggattttctctcttactctctttgtt-tttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATGATATTGGCAAGGTTGCACATGTATGACTGGATAATACTTCTCCTCCTTG

upper sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024615_T01 (Zea mays), 3'ss of exon 2
-ttttatttttattatagttgcattgtatccacattacatggag--ttgttat-tataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
 |  || |   |    ||    ||||| | |||  |  | | |   || | || |  |||| || | |||   |||    ||| || |   ||||| |||| |||| |||||||||||    ||||| | |||||| || |  ||||||||||  | | |||| ||| | |||||||| ||||||||||||||||| |||||||
atactaatggaacctgagaactattgt-tgcaccctgtacgaaagattatcatgtgcaactttactcactggtttt-tgctctcgt-actcttgtt-tttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATGATATTGGCAAGATTACACATGTATGACTGGATAATACTTCTCCTCCTTG

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|88355849|gb|CI626290.1|CI626290
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29642303|gb|CB647310.1|CB647310
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|700788|gb|D47079.1|D47079
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88454303|gb|CI569875.1|CI569875
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|88407270|gb|CI583728.1|CI583728
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29640276|gb|CB645285.1|CB645285
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29642638|gb|CB647645.1|CB647645
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|29671233|gb|CB667508.1|CB667508
EST:     TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: TCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
EST: gi|300215590|gb|HO088216.1|HO088216
EST:     CGAGGAGCCGCTCGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT                         GACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC
genomic: CGAGGAGCCGCT-GGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACC

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: 60 (upstream exon), 16 (downstream exon)
Score: 1

GGTGGTTCTTGGTGCAGAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCTgtgagttctt ... ttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
                 tactcac  putative branch site (score: 1)
                                    ttatgtttgttattt  TA-rich tract