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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA

Basic information

species Oryza sativa
transcript LOC_Os01g74350.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
------------------------------------gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaa-gtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
                                      |   || ||  |   |    ||  ||  ||    || | ||| ||     |||  ||| | |  ||     ||||| |||  |||||| ||||| ||||| ||||||||||||||||||||||| | ||||||||| |||||||||||||| || |||||||| ||||||||||
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttg--attattgatcaaccattaattgtgatgaaatt-----cagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
----------------gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
                      | || || |  ||||  | | |  ||     |  |  |    ||    |  |  |  | |  |||  |||| |||  |||||||||||| ||||| ||||||||||||||||| |||||    |||||||| ||||||||||| || || || || || ||||||||||
gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------------------gtttg-gtccctactca-acaagtgcgctttcttcagaatgaatgaaca--gattctaaagtggtaa-ggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
                                                                                  | |   |   ||   | | |  |     ||   |||      |||  |  |||     | |  |   | |   || ||||| |||  |||||| ||||| ||||| ||||||||||||||||||||||| | ||||||||| ||||||||||| || || || ||||| ||||||||||
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
-------------gtttggtccctactcaacaagtgcgctttcttcag--aatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
               |   | ||  |    ||||  | | |  ||     | ||||| |    ||    |     |  | |  | |  |||| |||  ||||||||| |||||||| ||||||||||||||||||||||| |  |||||||| |||||||| || || || || || || ||||||||||
gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaat-actgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
--gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaaca--gattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
             ||   | |  |   || ||   |  |    | |||   || |  |   ||     | || |  |||||||||  |||||| ||||| |||||||| |||||||||||||||||||||   || ||||  |||||||| || ||||| || ||||| || ||||| |
gtagaaaaagatgacaagatatatttcctctcccaattacttctaaaccttgaattaatcttgaccttgattaacacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 4
gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
          ||  |||   ||   | |||||   |  |  |       |   | ||||  |    | |   ||||| |||   || |||||||| || ||||| || ||||||||||| ||||||||||||| ||  || |||||| | ||||| |||||| |  |||| || |
---------gtag-caaagtgtttacattcttttcagcgtttc------tctaagagtgtcatctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCAGAGA

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 5
gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaa-agtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
          ||  ||| | ||   | | |||   |  |  |       |||||| ||||  |    | |   ||||| |||   || |||||||| || ||||| || ||||||||||| ||||||||||||| ||  || |||||| | ||||| |||||| |  |||| || |
---------gtag-caaaatgtttacatccttttcagcgttt-------ttctaagagtgtcatctatctgatcagGGGGAGAAGGACGATAAGATCATAGCAGTGTGCGCTGATGATCCAGAGTACAAGCATTGCACGGACATCAAGCAGCTCCCGCCTCACAGGCTAGCGGAGA

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|86478948|gb|CI121581.1|CI121581
EST:     GATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCAATGATCGATCAG                         GGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCAATGATCGATCAGgtttggtccc ... ttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTAC
EST: gi|29621784|gb|CB626795.1|CB626795
EST:     GATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCTATGATCGATCAG                         GGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCAATGATCGATCAGgtttggtccc ... ttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTAC
EST: gi|88486325|gb|CI423596.1|CI423596
EST:     GGCCATCGGTGTCATGCCAATGATCGATCA-                         GGAGAGGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTA
genomic: GGCCATCGGTGTCATGCCAATGATCGATCAGgtttggtccc ... ttttatccagGGAGA-GGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTA
EST: gi|88485439|gb|CI422710.1|CI422710
EST:     GATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCAATGATCGATCAG                         GGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTAC
genomic: GATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCAATGATCGATCAGgtttggtccc ... ttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTAC

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: 29 (upstream exon), 74 (downstream exon)
Score: 13

GAGCCAGTTATCCCAGGATGCTTCCTACGGGCAAAGGCCATCGGTGTCATGCCAATGATCGATCAGgtttggtccc ... ttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcgctttcttcagaatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA
                             ttctaaa  putative branch site (score: 13)
                                             ttttatcc  putative PPT
                            attctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA