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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagaatcaatttcatcaatgaggccttcatctctttgtgctcgcaattttagtttctgttactgtttgataaaatttacttttaattatacttaccttggcatatgcactggaaatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT

Basic information

species Oryza sativa
transcript LOC_Os03g11440.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 4
gtgaagaatcaatttcatcaatgaggccttcatctctttgtgctcgcaattttagtttctgttactgtttgataaaatttacttttaattatacttaccttggcatatgcactggaaatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT
||||| |  || || | ||| || ||    | | || || || ||    || | |||| ||||| |     ||  |   | ||||| | ||     ||  | |||    || |||||||  |||||||| |||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||| || ||||||||||| |||
gtgaaaagccagttccttcagtggggagaccttttcgttatgatcatttttattgtttttgttatttaacaattgatcattcttttgacta-----acaatagca----cattggaaataatgcagTTTGGCTGATGTCCTTGCAAATCCATTCCATGCACTGTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCT

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 4
gtgaagaatcaatttcatcaatgaggccttca----tctctttgtgctcgcaattttagtttctgttactgtttgataaaatttacttttaattatacttaccttggcatatgcactggaaatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT
||||| |   | || | ||| || || ||        ||  | |   |    ||||| |||  | ||  | ||  ||||  ||   | ||  ||  ||| ||  | |||    || ||||||    ||||||| |||||||| || ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || 
gtgaaaagctagttccttcattggggactggggaggccttctcgccatgatcatttttgttgtttttgttattcaataa--ttaggtattcttttgactaacaatagca----cattggaaaccacgcagTTTGGCTGATGTCCTTGCAAATCCATTCCATGCACTGTTTTATGTGGTCTTCATGCTGTCAGCCTGTGCTCTGTTCTCAAAGACATGGATTGAAGTTTCC

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------gtgaagaatcaatttcatcaatgaggccttcatctctttgtgctcgcaattttagtttctgttactgtttgataaaatttactt---------ttaattatacttaccttggcatatgcactggaaatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT
                                                       ||   |||      |   |   || ||||||| | |    |   ||   || ||| ||    || |  |||   ||| | |         || || |  || |  |  || | |||  |  |  | |||||| ||||||||| |    || ||||| |||||||||||||||||| | || || ||||| |||||||||||  | |||||||| |||||||||||||| |||
gtaggagaattgctgacaaattgatgttcagtgctttgtatgctgtatatatactaattgtcagccagctatgtactgctttcatctttctcatttgataaccctaatttgtgcctttgctgtatatgtttttcatctttctcatttgataaccctaatttgtgcctttgctgtatatgttttgcagCTTAGCTGATATGGCGGCCAATCCTTTCCATGCACTGTTCTATCTTGTGTTTATGCTTTCAGCTTGTGCCTTGTTCTCAAAAACATGGATTGAAGTCTCT

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 5
gtgaagaatcaatttcatcaatgaggccttcatctctttgt---gctcgcaattttagtttctgttactgtttgataaaatttacttttaatt--ata--cttaccttg-gcatatgcactggaaatgtt-gcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT
  | | || || | |   |||       ||||   ||||||   |     |  | || | || |  | |  |  |    ||| | || | |||  |||  | ||  ||| || | |||  |  | || || |||| ||||||||| |    || ||||| |||||||| ||||||||| | || || ||||| ||||| |||||  | ||||| || |||||||||||||| |||
--gtaaaagcattgttgacaaattcaagttcagtgctttgtatggtatatatatatactgtcagccagttatgtactgcattcatttctcatttgataaccctaatttgtgcctttgctttatatatttttgcagCTTAGCTGATATGGCAGCCAATCCTTTCCATGCTCTGTTCTATCTTGTGTTTATGCTTTCAGCCTGTGCCTTGTTCTCTAAAACATGGATTGAAGTCTCT

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|29627508|gb|CB632519.1|CB632519
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|86519507|gb|CI159713.1|CI159713
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|27577737|gb|CB000432.1|CB000432
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|29616183|gb|CB621195.1|CB621195
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|29627509|gb|CB632520.1|CB632520
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|699763|gb|D46054.1|D46054
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGNCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|58679189|gb|CK067876.1|CK067876
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|27554203|gb|CA998103.1|CA998103
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|29665157|gb|CB661432.1|CB661432
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|33796315|gb|CF324025.1|CF324025
EST:     CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: CATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|9864956|gb|AU100706.1|AU100706
EST:     CTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCCTCGCAAATCCCATTCCATGCACTGTTCTATGTGGTC
genomic: CTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTT-CTCGCAAAT-CCATTCCATGCACTGTTCTATGTGGTC
EST: gi|86490193|gb|CI132826.1|CI132826
EST:     GTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: GTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
EST: gi|66914888|gb|CX101736.1|CX101736
EST:     GCTCCATCAAG                         TTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT
genomic: GCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 109

ATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTGCTTACTATGTAACTGCTCCATCAAGgtgaagaatc ... aatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatttacttttaattatacttaccttggcatatgcactggaaatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT
                    tacttac  putative branch site (score: 109)
     atttacttttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagaatcaatttcatcaatgaggccttcatctctttgtgctcgcaattttagtttctgttactgtttgataaaatttacttttaattatacttaccttggcatatgcactggaaatgttgcagTTTAGCTGATGTTCTCGCAAATCCATTCCATGCACTGTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG