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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtactcgtagtttcttcctgtgcagtagtgatgatatttaataagaataaatttgatagttttccatgttggttgcaagctgacaaaatattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA

Basic information

species Oryza sativa
transcript LOC_Os03g01890.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G109987_T05 (Zea mays), 3'ss of exon 15
gtaagtgtactcgtagtttc-ttcctgtgcagtagtgatgatatttaataagaataaatttgatagttttccatgttggttgcaagctgacaaa-atattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA
            ||| |||| |||| |||| ||  |  |||||  | |    |||   |||| |  ||||  ||      || || || | |   ||  | ||  |||      ||| |||||||||||  | || ||||||| |||||||||||||| ||  |||  ||||||||| ||||| |||||| | | ||||||| || |||||||||| 
------------gtaatttccttcccgtgctgt--ttctgatacctcacctaaatgg-tttggttcttttttat------tgtaatctcatagctattcttttgggccccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G042250_T01 (Zea mays), 3'ss of exon 16
gtaagtgtactcgtagttt-cttcctgtgcagtagtgatgatatttaataagaataa----------atttgatagttt---tccatgttggttgcaagctgacaaa-atattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA
||||||| | | ||| ||| |||||  ||| ||  |  |||||| | | |  |||            ||||  |  |||   |   | ||  ||| || || |     ||  | ||  | |      ||| ||||||||||| || || ||||| | ||||||||||| || ||  |||  ||||||||| ||||| |||||| | | ||||||| || |||||||||| 
gtaagtgaagttgtaattttcttcccatgctgt--ttctgatatctcacataaatggtttgattcttatttatttatttatttatttatttattgtaatctcatggctattcttttggggcccaatacagCTACCATCTAGGTGTGGAATTACTCAATCAATCAGATGAAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCT

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G109987_T03 (Zea mays), 3'ss of exon 16
gtaagtgtactcgtagtttc-ttcctgtgcagtagtgatgatatttaataagaataaatttgatagttttccatgttggttgcaagctgacaaa-atattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA------
            ||| |||| |||| |||| ||  |  |||||  | |    |||   |||| |  ||||  ||      || || || | |   ||  | ||  |||      ||| |||||||||||  | || ||||||| |||||||||||||| ||  |||  ||||||||| ||||| |||||| | | ||||||| || ||||||||||       
------------gtaatttccttcccgtgctgt--ttctgatacctcacctaaatgg-tttggttcttttttat------tgtaatctcatagctattcttttgggccccaatacagctaccatctagGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCCTTTAAG

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 15
gtaagtgtactcgtagtttcttcctgtgcagtagtgatgatatttaataagaataaatttgatagttttccatgttggttgcaagctgacaaaatattattatgccgt----cgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA
                  |   |    |  ||    || | || | |   ||  |  |  |  | ||| |  | ||| ||  ||  | | |   |  | || |    |    | |||||||||||| | ||||  ||||| || ||         ||  | ||  ||     |||| || |   | |||||| |||| |||||||||||||||||||||
------------------ttgactgaaggtgttcccatta-atctcactggaccagttgaggaattttcctcttttgtttctaaaataaaattttcctgtttttgttttttcccctcagTTACCATGTTGGGGCGGAGTTGCTGAGATCTGATTCTGTGGGTGGCGATTCGGTGTTAAAAAATTTGTGGCATCACCAGGATGCTATTTTGTGCTGCTCA

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|58690834|gb|CK079521.1|CK079521
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|58653920|gb|CK042600.1|CK042600
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCGATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|218497597|gb|FG966590.1|FG966590
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|218500446|gb|FG953830.1|FG953830
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|87038321|gb|CI192943.1|CI192943
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|163918446|gb|EG711616.1|EG711616
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTATTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|163926532|gb|EG712396.1|EG712396
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|58683794|gb|CK072481.1|CK072481
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCACAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
EST: gi|58669786|gb|CK058472.1|CK058472
EST:     GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCA                         TTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA
genomic: GGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACA

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), 63 (downstream exon)
Score: 19

CTATCTCTCCCTCTCAAACTGGTCTAAATGCCGGACAGAGGATAATCTCTGGTTTCCCTGAAGCAGCAACCCTTGCTCGATGGGTTTGCCAGAGCTACCAgtaagtgtac ... cgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagttttccatgttggttgcaagctgacaaaatattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA
                       agctgac  putative branch site (score: 19)
                          tgacaaaatattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtactcgtagtttcttcctgtgcagtagtgatgatatttaataagaataaatttgatagttttccatgttggttgcaagctgacaaaatattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT