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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccatcttcctttagcttgaacggtccactatgaatttgataatttgacagcactcaagcttgaattcgttctttcag

Basic information

species Oryza sativa
transcript LOC_Os06g07760.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07760.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G007683_T02 (Zea mays), 5'ss of exon 4
GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccatcttcctttagcttgaacggtccactatgaatttgataatttgacagcactcaagcttgaattcgttctttcag
| || |||||||| |||||||| ||||||||||||||||| |||||||| || |||||||||||||| || || ||||| || |||||||| ||| |||  || ||||||| |||||| |   |||| | |  | ||    | ||||  |||||  | ||| | || | ||||||||
GCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCGCTGCAAAGTTCGCCGTGGGACAAAGGAAACACTGAGgcgagagcaccttccttcagcttggat--tccatttttgaatt----acttgat-gcact-gaacttcagtttgctctttcag

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G02350.1 (Glycine max), 5'ss of exon 4
GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagccca--tcttcctttagct----tgaacggtccactatgaatttgat--aatttgacagc-actcaagcttgaattcgttcttt-cag
|||| || || |||||||||||||||||||| |||||||| || ||||| || ||||| |||||| | || || || || ||||| ||  |||||| ||   |  | |||  ||| ||    || |  ||  |   ||| |  |||  |  ||  ||||   |  |  ||   |||    ||| |||
GTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAgttaagatgttctgttaactcttttgtaaagtatag-gtgactcagattcatattctcagccgattgattttcgtttcacattttgcag

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0011g01620.t01 (Vitis vinifera), 5'ss of exon 4
GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccatcttcctttagcttgaacggtccactatgaatttgata-atttgacagcactcaagcttgaat---tcgttctttcag-------
||||||| || ||||| || || || || |||||||||||||| ||||| || || || |||||||| || || || |||||||||||| | ||||  |   ||||||     || | || |  | | |   |||||  |  || |   | ||       |   ||    |||  |||||        
GTTTTTCCGGTTGTCATCGGTACGAAGCACACCAGCGCCTAGGGCTCCCAACAATTCGTTGCAAAGTTCGACGAGGAACGAAAGAAACATTGAGgtttgtt-atcttct----gcatcaatgccctaatgccaattttttctatgtattatcatctgttttctcatgttccgtgttttcatgttgcag

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|87031893|gb|CI268122.1|CI268122
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88664093|gb|CI490467.1|CI490467
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|25798058|gb|CA754019.1|CA754019
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88986727|gb|CI033870.1|CI033870
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|117232192|gb|CT859987.1|CT859987
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88273375|gb|CI393781.1|CI393781
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88324654|gb|CI506038.1|CI506038
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|86841916|gb|CI337538.1|CI337538
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATAGCTACTTCAGTCAGAAAGT
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATA-CTACTTCAGTCAGAAAGT
EST: gi|38474848|gb|CF958981.1|CF958981
EST:     CCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88567828|gb|CI498545.1|CI498545
EST:     CTCCCGACTATCCGCTGCAAAGTCCTTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88567353|gb|CI498070.1|CI498070
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|88569011|gb|CI499728.1|CI499728
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|38477761|gb|CF961894.1|CF961894
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
EST: gi|58592631|gb|CF990939.1|CF990939
EST:     CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG                         GCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG
genomic: CTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTG

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: 65 (upstream exon), 75 (downstream exon)
Score: 20

GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccat ... gttctttcagGCACCATATGCGATGAAATTGGAATGGACATACTACTTCAGTCAGAAAGTGATAATCTGTGTACCTTTGTGTTCATATGCTATACTCCTGTAATTGTAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAGgtgagcccatcttcctttagcttgaacggtccactatgaatttgataatttgacagcactcaagcttgaattcgttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA