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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g51029.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G126361_T03 (Zea mays), 5'ss of exon 4
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaa---tgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttac---atggtttgcag---
|||||||||||||||||||||||||||| || ||||| || ||||||||||||||||||||||| || |||||||||||||| ||||| |||||||| |||||   |||    | |   ||||||| ||||| | |||   || ||| || || ||| | |  || |||||| ||  | |    ||||||||| |   
GTGGACTCACATTCTTTGCTCCAAGCGAAGAAAGGCTAGAATCTGGATTGTACAGCAGGAGCTATCTTGAGAACCAAATGGCTGTAGCCCTTGGTGGCAGgtgctctttctgcatactctgttcatttctgcat-cattgactgttgctgctgcgcatattgatggactgtgagatgtaatcttatggtttgctgcag

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag---------------
|||| |||||||| |||||||| || || |||||||||||||||||||||||||| || || ||||| || || || ||||| || ||  | ||||||||||  ||   |    ||  | || |  | |   | |||   ||| | | | |  | | |    |    |     |||| ||       |                
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtgg-aacacaacatgcacagttac---cttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta-gtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgt--gtgagcttacatggtttgcag----------
|||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||| || || ||||| || || || ||||| || || || ||||||||||  ||   | ||| |   ||  | | |  |  | || | | |||   || |||||    || |    |     | ||    | |||  ||           
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattactttgtttgatcttg-gattttgacatt-tgcaagtcattcattctttaacaaactccacttgttgtcaattggctaatg

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtga-aatgttcatatctgcgtacatgtgctattgtt--gttgtgca---aagtcttgaactgtgtgagcttacatggtttgcag------------------
|||| ||||| || |||||||||||||| || || |||||||||||||||||||| ||||||||||| ||||| |||||||| || || ||||| |||||||  ||  |||| |     | ||   ||    |||   || | | ||    | | ||   |||  || || | ||| |    |  |   |  | |                  
GTGGGCTCACTTTTTTTGCTCCAAGCGAAGAAAGACTTGAGTCTGGATTGTACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAGgttagt--tagtaatggcctccacgcctcgtcacaaaagccagtctttgaatatacagagaagggtttaattatgttaaaccatctctatctctgttgtgttggctatgtcag

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagct-tacatggtttgcag---
|||| ||||| || || ||||| ||||| |||||||| ||||| |||||||| ||||| |||||||| |||||||||||||| || || ||||||||||||| | ||  |    ||      ||   |  |  || | | |  || ||  |    ||| || |||  |||    | |   |    |   |   
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttacaactgaaa--ctgtactggttttgatttacaagagtagtctt--cgagtgttaaacaatgtttattgtgtttcacctatggtag

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtt--ttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagt---cttgaactgtgtgagcttacatggtttgcag--------
|||| || || || ||||||||||| || ||||| || ||||||||| ||||||| || || ||||| ||||| || ||||| || || || ||||||||||  |||  ||| |   || | ||   |  |  ||| ||| |  |||| | || |  |||    || ||    |  |  ||    |  |   |         
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggacccc--acaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ31931 (Selaginella moellendorffii), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag
| ||  | || || || || || ||||||||||| |||||||| || || |||||| | |||||| | |||||||| ||||| || ||||||||||||||||  |   |  |  ||  |||  || | | |   ||   ||    ||   | | |                                  
GAGGTTTGACCTTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGTGGAAGgtacg---tgatctaaacttcccattttctt---tgctttaagcgtgcgattccag---------------------------------

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ37923 (Selaginella moellendorffii), 5'ss of exon 3
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag
| ||  | ||||| || || || ||||||||||| |||||||| || || |||||| | |||||| | |||||||| ||||| || |||||||| |||||||  |   |  |  ||| |||  || | | |   ||   ||    ||   | | |                                  
GAGGTTTGACATTTTTCGCACCCAGCGAGGAGAGACTTGAGTCAGGTTTATACAGCCGAAGCTACTTGGAGAACCAGATGGCGGTGGCTCTTGGGGGAAGgtacg---tgatctaatcttcccattttctt---tgctttaagcgtgcgattccag---------------------------------

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|4715109|gb|AU056226.1|AU056226
EST:     TACA-CAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|38477226|gb|CF961359.1|CF961359
EST:     GGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: GGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|58593271|gb|CF991579.1|CF991579
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|38476029|gb|CF960162.1|CF960162
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|86851309|gb|CI312710.1|CI312710
EST:     CAGCAGGAGGCTACCTAGAGAACCCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: CAGCAGGA-GCTACCTAGAGAA-CCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|58594309|gb|CF992617.1|CF992617
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|88989328|gb|CI043827.1|CI043827
EST:     GCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: GCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|2801137|gb|AA754431.1|AA754431
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTSCCGAAGAGGTGATCTTTCGGCCAAGAAAATGTGACAACTGGGGCCY
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTT-GGCCAAGAAAATGTGACAACTGGGGCCT
EST: gi|38473350|gb|CF957482.1|CF957482
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|38470910|gb|CF955041.1|CF955041
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|29668700|gb|CB664975.1|CB664975
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|58657689|gb|CK046369.1|CK046369
EST:     CGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGCCCAAGAAAATGTGACAACTGGGGCCTC
genomic: CGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|38481226|gb|CF965315.1|CF965315
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTC
EST: gi|8956776|gb|BE230579.1|BE230579
EST:     TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAG                         GGTTGCCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCT
genomic: TACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCC-GAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCT

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: 74 (upstream exon), 74 (downstream exon)
Score: 143

GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtttta ... tggtttgcagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTCCAACGATTTTATGCAGGTTTCACGTGTTGCAAGACAAATGGTTGAAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggttttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagtcttgaactgtgtgagcttacatggtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG