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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttaactgtcttggtgatgtttcacattcctgaaactacagcgtaaacaccgttcacgactttttaatttttgctatgttaaactatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGAAGTAACAGAAGAGAGTTTCAGACTAAAGGCCTGGCCGGCCGTGCCCATC

Basic information

species Oryza sativa
transcript LOC_Os01g12080.1
intron # 8
splice site 3'
intron type U2

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|88662568|gb|CI469125.1|CI469125
EST:     CTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: CTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|9457331|gb|AU064041.2|AU064041
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88482599|gb|CI419870.1|CI419870
EST:     GGCCTCAGACTCCGACATTTTAGTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCNACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|4880376|gb|AU064675.1|AU064675
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGA-GAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|29616787|gb|CB621799.1|CB621799
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|29613834|gb|CB618847.1|CB618847
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88525030|gb|CI453998.1|CI453998
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAGCGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88484884|gb|CI422155.1|CI422155
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCANACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|29683452|gb|CB679727.1|CB679727
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|7332593|gb|AU085939.1|AU085939
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|29684396|gb|CB680671.1|CB680671
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|58605925|gb|CK033958.1|CK033958
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|29683451|gb|CB679726.1|CB679726
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGAT
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGAT
EST: gi|88555899|gb|CI486189.1|CI486189
EST:     CAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCCACGGGCCTTCACAATCAGACGAAGAGA
genomic: CAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88473860|gb|CI411131.1|CI411131
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATNCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88516994|gb|CI444648.1|CI444648
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGGTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|38480244|gb|CF964333.1|CF964333
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|12622673|gb|AU172886.1|AU172886
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88468406|gb|CI514888.1|CI514888
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
EST: gi|88374496|gb|CI515980.1|CI515980
EST:     GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAG                         TTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA
genomic: GGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGA

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: 61 (upstream exon), 65 (downstream exon)
Score: 22

ACTTGGAAGCACTTGAGAACTACGCAGGTACTCCTTTCCTGGCCTCAGACTCCGACATTTTACTTGATTCCCCAGACCAGAATGACATAGgtaactttaa ... ctatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGAAGTAACAGAAGAGAGTTTCAGACTAAAGGCCTGGCCGGCCGTGCCCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgtaaacaccgttcacgactttttaatttttgctatgttaaactatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGAAGTAACAGAAGAGAGTTTCAGACTAAAGGCCTGGCCGGCCGTGCCCATC
                       ttttaat  putative branch site (score: 22)
                      tttttaatttttgcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactttaactgtcttggtgatgtttcacattcctgaaactacagcgtaaacaccgttcacgactttttaatttttgctatgttaaactatgtccagTTGAGTACTTTGCTGATGCCATCAACGGGCCTTCACAATCAGACGAAGAGAAGTAACAGAAGAGAGTTTCAGACTAAAGGCCTGGCCGGCCGTGCCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA