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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattatgttcctgttaattcttggcttgtaaacaactaaacatatcttttgcttgtatggtttgtccaggttgatatagttattgcgcgttagatt...

Basic information

species Oryza sativa
transcript LOC_Os04g42380.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42380.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G086486_T01 (Zea mays), 5'ss of exon 5
CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattatgttcctgttaattcttggcttgtaa-acaactaaacatatcttttgcttgtatggtttgtccaggttgatatagttattgcgcgttagatt-----
 | |||||  |||||||||  || || ||||||||||| || || || ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||  | ||| || ||     |||||| |  |  | |   ||     |    || |||||| | | |  | |      ||  | |   |    | |  | |     
TCCAAGAAGGCCACCAAGGTAAACAAACCTGGCAAGGGAGGAAACAGATTCTGGAAGAACATTGGCCTTGGTTTCAAGACACCCAGGGAAGCCATTGAAGgtc--agtatttttcttc---ttcttgtccagccatatcgctggtgtttctgttagcttgt-tagctcatacgaagctatgaactaggtcaatgattcactagtcc

upper sequence: LOC_Os04g42380.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G23400.2 (Glycine max), 5'ss of exon 3
CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattatgttcctgttaattcttggcttgtaaacaactaaacatatcttttgcttgtatggtttgtccaggttgatatagttattgcgcgttagatt-----
 | ||||| ||    ||||| ||||  ||||| || || |||||  | || ||||||  |||||| ||||| || ||||| ||||||||||||||||||||| |   | |  ||   || |    |  ||  || | ||       | |  |||||   | ||  ||   ||||||  | | ||   |    |||   |      
ACAAAGAAGACTGGGAAGGGAAAGAGACCTGGAAAAGGTGGGAACCGCTTTTGGAAGTCCATTGGGCTTGGATTTAAGACTCCCAGGGAAGCCATCGAAGgtatctctct-ctctcattcaccactttctcttataaaat---gtttgttctttgcg-atgtgaatttatcaggttattgttgtggatatttgtttcttcttatt

upper sequence: LOC_Os04g42380.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G11430.1 (Glycine max), 5'ss of exon 3
CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattatgttcctgttaattcttggcttgtaaacaactaaacatatcttttgcttgtatggtttgtccaggttgatatagttattgcgc-gttagatt-
 | ||||||||    ||||| ||||  || || ||||| |||||  | || |||||   |||||| ||||| || ||||| ||||||||||||||||||||| |     | |   |  |   |||  | |||||||    | |   | |    ||    | |  |  ||    |||| | ||  ||||       | |||| 
TCGAAGAAAACTGGGAAGGGAAAGAGACCCGGAAAGGGTGGGAACCGCTTTTGGAAATCCATTGGGCTTGGATTTAAGACTCCCAGGGAAGCCATCGAAGgtatctccctctcattcatctctctctg-ttgtaaaatgtttattctgtgcgatgtgaatctattaggttattgttg-tgtacatatttttttaattgatta

upper sequence: LOC_Os04g42380.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G30800.1 (Arabidopsis thaliana), 5'ss of exon 3
CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgt-ctgattatgttcctgttaattcttggcttgtaaacaactaaacatatcttttgcttgtatggtttgtccaggttgatatagttattgcgcgtta--gatt-
 | |||||| |    ||||| |||| |||||| || || || ||| | ||||||||||||||||||||||| ||||| || || || || || || |||||| ||| || | |  ||   |  |||    || |     || |    ||      ||||  ||   ||    | ||||   |  |||  |  | |    |||| 
TCGAAGAAATCTGGTAAGGGAAAGAGGCCTGGTAAAGGAGGTAATCGTTTCTGGAAGAACATTGGCCTTGGTTTCAAAACTCCAAGAGAGGCTATTGAAGgtactgtttttatgtct--cagctctcaattt-tgctttaccatgtctagaagaagctt-catttgttaaaaaagttggattctttagagaacttagaggattt

upper sequence: LOC_Os04g42380.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 5'ss of exon 3
CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattatgttcctgttaattct-tggcttgtaaaca-actaaacatatcttttgct-tgtatggtttgt-ccaggttgatatagttattgcgcgttagatt
 | |||||| |  | |||||||||| |||||| ||||| || ||  |||||||||||| ||||||| | ||||| ||||||||| | || || || |||||| ||| |   ||    || | | | ||  || ||||     ||  | |   ||||| | | |     | || |   | ||||||  |  | |    |||    
TCGAAGAAATCTGCGAAGGGGAAGAGGCCTGGGAAGGGTGGAAACCGGTTCTGGAAGAGCATTGGCTTAGGGTTTAAGACACCCCGAGACGCTATTGAAGgtttgaattcattttacttgagtttgtgaattctaaatttgatattcttgcattttggtatatcaatctagtgcttagctgatatcttactcgtttttta----

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|88378834|gb|CI681652.1|CI681652
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88396239|gb|CI598351.1|CI598351
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88347954|gb|CI636047.1|CI636047
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88363094|gb|CI616251.1|CI616251
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|29629652|gb|CB634661.1|CB634661
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|33653511|gb|CF276125.1|CF276125
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|58596533|gb|CK007061.1|CK007061
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88765515|gb|CI774609.1|CI774609
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88511630|gb|CI439136.1|CI439136
EST:     CAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|33655599|gb|CF278213.1|CF278213
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|218494166|gb|FG952748.1|FG952748
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88451487|gb|CI565540.1|CI565540
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|8404565|gb|AU091919.1|AU091919
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88329106|gb|CI658767.1|CI658767
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88722377|gb|CI745887.1|CI745887
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|58604496|gb|CK015024.1|CK015024
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|38468664|gb|CF952795.1|CF952795
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGAGACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|29629653|gb|CB634662.1|CB634662
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|29682482|gb|CB678757.1|CB678757
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|86887857|gb|CI297968.1|CI297968
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|86901952|gb|CI298599.1|CI298599
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88325214|gb|CI646636.1|CI646636
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88571463|gb|CI662836.1|CI662836
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|29682483|gb|CB678758.1|CB678758
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|27410185|gb|CA923255.1|CA923255
EST:     CCGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGT
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGT
EST: gi|163929347|gb|EG713772.1|EG713772
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88299875|gb|CI579936.1|CI579936
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88343902|gb|CI654938.1|CI654938
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
EST: gi|88827779|gb|CI778344.1|CI778344
EST:     CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAG                         GAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG
genomic: CTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGG

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), 71 (downstream exon)
Score: 77

CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattat ... cttcttgcagGAACCTACATTGACAAGAAATGCCCATTCACTGGTACTGTATCAATTAGGGGTCGTATCATAGCTGGAACATGTCATAGTGCTAAGATGAACAGGACCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTAAGAAAACCACCAAGGGGAAGAAGCCTGGCAAGGGCGGGAATAGGTTCTGGAAGAACATTGGCCTTGGGTTCAAGACACCCAGGGAAGCCATCGAAGgtctgattatgttcctgttaattcttggcttgtaaacaactaaacatatcttttgcttgtatggtttgtccaggttgatatagttattgcgcgttagatt

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC