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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcgagcctccaatgtaaatttctgtttggccctatgcatgactagggtcaaaacgaagctacatcagtaggacctttatttgggtgatgaggc...

Basic information

species Oryza sativa
transcript LOC_Os09g28570.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G479068_T01 (Zea mays), 5'ss of exon 4
GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcgagcctccaatgtaaatttctgtttggccctatgcatgactagggtcaaaacgaagctacatcagtaggacctttatttgggtg-atgaggc----------------------------------------------
||||| ||||||||  |||| ||||| ||| |||||||||| |||||||| ||||| ||| |||||||| ||||||||||||||||||||||  ||     |    | |   || ||     || |  ||  |   | |  |||  |  || |   | || |     ||   | || ||   |||  |                                              
GCTGGCTTTTTCCTGGTCCAATATGCGCACCTGTGGCAAGACCATCTTGAAAAACTGTTTAACCTGTATTCCTCTGGAAAGCTAAAGgtatggttcacatttgtg-tctctcttgctacgacgcgcagtggttcctttgtttcatgaaaaaccacgaccattctctactcgttctgtgtttgtgaaaccgtactcatcttacatttttcgaacttcaactttctgcgttaacag

upper sequence: LOC_Os09g28570.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G147191_T02 (Zea mays), 5'ss of exon 16
GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcgagcctccaatgtaaatttctgtttggccctatgcatgactagggtcaaaacgaagctacatcagtaggacctttatttgggtgatgaggc-----------------------------------------------------------------------------------
||||| ||||||||  | |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||  |     |   |||  | |    |   ||||      |||   |   ||| |      |   |    ||  |  ||| |     |||||   |                                                                                   
GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgctccataattt--atgccactccaagcagggcctagcaaatggaaataatcagatgactaccttactcctaatat-tttgtgctcatgatggatcataaattcgtgcgataatttatatctataatttcaccttgtaacttaccttttcatgccataccacgatatggcgtgtaacag

upper sequence: LOC_Os09g28570.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA02G15070.1 (Glycine max), 5'ss of exon 16
GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcgagcctccaatgtaaatttctgtttggcc----ctatgcatgactagggtcaaaacgaagctacatcag-taggacctttatttgggtgatgaggc----------------------------------------
 |||| ||||||||  | || |||| ||||||||||||||| |||||||||| ||| ||| | || ||  | || ||||||||||||||| |       | | | ||  | || | ||  |        |||| | | | ||     | |   |    |  |  | |||   || || || |  | ||                                            
TCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAGgtaagttatacacattccattcatatctatggatcaataaagctat-cttcattaacagtatatttatttgatttttgctagttgctatacttagcagttgctatgctagtttgtgatccttaactttctcgtttcttcatacag

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|86881108|gb|CI339289.1|CI339289
EST:     ATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: ATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|86876432|gb|CI318417.1|CI318417
EST:     AGATCATCTTGACAAACTTTTTGACCTGTAGGCCTCTGGAAAGGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTTTAGCTTCTGCGCCTGATGC
genomic: AGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAA-GCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGC
EST: gi|88267019|gb|CI378954.1|CI378954
EST:     AGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTC-TGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88274323|gb|CI394729.1|CI394729
EST:     ATCTTGACAAACTTTTT-ACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: ATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88269934|gb|CI381232.1|CI381232
EST:     AAGATCATCTTGACAAACTTTTTGACCTTTATGCCTCTGGAAAGGTAAAG                         GTTTCCCGTGACCCGAAGAAATTCCTGGGGGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|29670808|gb|CB667083.1|CB667083
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|86865386|gb|CI330890.1|CI330890
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         CTTTCCCTTGATCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88834245|gb|CI000609.1|CI000609
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88254018|gb|CI352644.1|CI352644
EST:     TCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: TCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|13165263|gb|AU174060.1|AU174060
EST:     ACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: ACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88254109|gb|CI352735.1|CI352735
EST:     GACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: GACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|86837438|gb|CI345680.1|CI345680
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|66913912|gb|CX100760.1|CX100760
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|86907581|gb|CI296578.1|CI296578
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|33800750|gb|CF326245.1|CF326245
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|29675620|gb|CB671895.1|CB671895
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88289413|gb|CI555775.1|CI555775
EST:     CAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: CAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|87009274|gb|CI313747.1|CI313747
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGG-AAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
EST: gi|88265497|gb|CI376399.1|CI376399
EST:     AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG                         GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG
genomic: AAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCG

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: 52 (upstream exon), 72 (downstream exon)
Score: 19

GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcg ... catacaacagGTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGgtatgcctcgagcctccaatgtaaatttctgtttggccctatgcatgactagggtcaaaacgaagctacatcagtaggacctttatttgggtgatgaggc

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