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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgcaatctaaactagtatcatgcctgtaatgtttggattctgaaatataatcactgatgtatgttgtttttcctttttgtag

Basic information

species Oryza sativa
transcript LOC_Os07g42450.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G159237_T03 (Zea mays), 5'ss of exon 2
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatact--cgcaatctaaactagtatcatgcctg-taatgtttgg-attctgaaatataa-------------tcact-gatgtatgttgtt--tttcctttttgtag
||||||||| |||||||||||||| || |||||||| || ||| | ||||| ||||||||||| ||||||||||| |||||||||||||||||  |||||||| |||     |||||||||||||  | | |||   ||||| |   |||   ||| | ||             ||||| | || ||  || |  |||||  |||| ||
CAAGGGGAAACAGAGCATTGGTTGTCTGTTCTGGCTGCTCGCCCGAATGGTCCTCCAGATGCGCGGTACAATTCTTCCAGGACACAAGTGGGACATCATGgtaaactgatataatctaaactagttccttccctaacaatgtctaacatttataaacaaaacaaatactttttttcactcgttgaatcatgctcgtttcccatttgcag

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G01460.1 (Glycine max), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgcaatctaaactagtatcatgcctgtaatgtttggattctgaaatataatcactg-atgtat-gttgttt--ttcctttttgtag-------------
|||||| || || ||||||||||| || || ||||| ||||| ||||||||  | |||||| | |||||||||| ||| || | ||| ||||||||||||||| |      || || | |  | ||   | | | |   | |||||||||| | || ||  || |  |||   |||||  | |||  ||   |             
CAAGGGAAAACACAGCATTGGTTGTCTCTTTTGGCTCCTTGCAAGGATGGTATTGCAGATGAGGGGTACAATTCGCCCTGGCCTCAAATGGGATGTCATGgtaaa------atatatatttttttctgccttttcaaagtaggattctgaactgtattcggtgcacttattactgtttgatgcctgatttctgagataaaatagga

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G42150.1 (Glycine max), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgcaatctaaac-tagtatcatgcctgtaatgtt----tggattctgaaatataatcactgatgtatgttgttttt-cctttttgtag------------------------------------------------------------
 ||||||||||| ||||||||||| || ||||||||  | || |||||||| || |||||||| ||||| ||||  ||||| |||||||||||||| |||||| |  |    | | |   |  |||    | ||  | | |    |   ||   | || |    | |  |||  |   ||  |  | ||  || |                                                            
TAAGGGGAAGCATAGCATTGGTTGTCTCTTCTGGCTATTAGCTAGGATGGTACTGCAGATGCGGGGTACTATTCGTCCAGGTCACAAGTGGGATGTAATGgtaaatacttgttatgattgttttatagctcttgagaagatatagtctgttagtagatgtctgtattcttgtgagaaattagtatcattgggtgggggggggggggctgtaagttcttagattagtatctaattatctcaagttttgttatgcag

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G04890.1 (Glycine max), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtata-------ctcgcaatctaaacta-gtatcatgcctgtaatgtttggattctgaaatataatcactgatgtatgttgtttttcctttttgtag------
|||||| || || ||||||||||| || |||||||| ||||| ||||||||  | |||||| | ||||| |||| ||| || | ||| ||||||||||||||| |        | ||   |    ||| |||  || ||    || ||  |   |     ||| |    |  ||| || ||| |  | | |  ||        
CAAGGGCAAACACAGCATTGGTTGTCTCTTCTGGCTCCTTGCAAGGATGGTGTTGCAGATGAGGGGTACCATTCGCCCTGGCCTCAAATGGGATGTCATGgtaaaatatttttttgctgccatttctaagtaggattccaaccatattcag---cgtgcttattactttttgtgtttgatgtctgacttatgagttaaaatat

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgta---tactcg---caatctaaactagtatcatgcctgtaatgtttggattctgaaatataatcactgatgtat-gttgtttttcctttttgtag-----------------------------------------
 ||||||||||| ||||||||||| || || |||||  | || |||||||| || |||||||| || || ||||  ||||| |||||||||||||| ||||||   |||| |   |  |    | ||| ||  ||  |   |||| || ||||    | | ||| | |  | | | |  |  ||||||    |                                            
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgcaatctaaactagtatcatgcctgtaatgtttggattc-tgaaatataatcactgatgtatg--ttgtttttcctttttgtag------------
|||||| ||||| |||||||| ||||| ||||||||||| ||  | ||||| || ||||||||||| || |||    | ||||| ||||||||||||||||||        ||         | | |     | || |  |   ||| | ||| |   || ||| |   ||  |   |||| | | | |||             
CAAGGGAAAGCACAGCATTGGGTGCCTTTTCTGGCTTCTGGCTCGCATGGTCCTTCAGATGCGTGGAACCATTGCTGCTGGACAGAAGTGGGATGTCATGgtaagaatatcattcttggagctcttagattagaaaggcatctgttcattaaaaactttccctgtttattgactgaatttttcatatggtatggtgttgtgcag

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G04770.2 (Arabidopsis thaliana), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgcaatctaaactagtatcatgcctgtaatgtttggattctgaaatataatcactgatgtatgttgtttttcctttttgtag
|||||| || || |||||||||||| | ||||||||| | ||  | ||||||||||| |||||||| || |||||| |||  || || ||||||||||||||| ||||        || || ||||| | ||    |||||    ||  | |   |  ||  ||| | ||   | ||||  || |||||
CAAGGGAAAACACAGCATTGGTTGCTTGTTCTGGCTTTTGGCTCGTATGGTTCTCCAAATGCGTGGAACCATTCTCGCAGCTCAGAAATGGGATGTCATGgtaaactc-----tagaaatactatcaggactt--gtgttt---ctccaacac-cagacaaagatct-tgacttgtttctgttgtgtag

upper sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 5'ss of exon 3
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgta----tactcgcaatctaaactag----tatcatgcctgtaatgtt--tggattctgaaatata--atcactgatgtatgttgtttttcctttttgtag----------------------------------------------------------------------------------------------
|||||| ||||| |||||||| || || ||||||||  | || ||||||||||| ||||||||| | || |||   || ||||||||||||||||| ||||||    ||   | || | |   | |    |||  | | |  | | ||  | | ||||||| |     || ||  || ||    |||||| |  | |   |                                                                                              
CAAGGGAAAGCACAGCATTGGCTGTCTGTTCTGGCTGTTGGCAAGGATGGTTCTGCAGATGCGTCGCACTATTGCTCCCGGACACAAGTGGGATGTGATGgtaaagatatcagaaaaccattttgggttttatagttcatacagtattatttgcttctgaattgacgcatgacgaatttacaa-gtttttgcactgtactgaggtttacatttttgagtttgatgatttagcttgccccctggtggatgattacttgatgattttgacttaccatgatctttcctcgatatgtag

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|86821489|gb|CI266865.1|CI266865
EST:     TGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|218493254|gb|FG945789.1|FG945789
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|29680688|gb|CB676963.1|CB676963
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|88956487|gb|CI092733.1|CI092733
EST:     AGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGTAAGCGAAGGAGCAAGAGGAA
genomic: AGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|2312443|gb|C28598.1|C28598
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|58681997|gb|CK070684.1|CK070684
EST:     GGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: GGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|87038852|gb|CI193474.1|CI193474
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|86255009|gb|CI017129.1|CI017129
EST:     CACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: CACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|66915310|gb|CX102158.1|CX102158
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAAGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGG
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGG
EST: gi|29680643|gb|CB676918.1|CB676918
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|89175022|gb|CI041100.1|CI041100
EST:     CTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: CTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|218496598|gb|FG964018.1|FG964018
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|25801336|gb|CA757297.1|CA757297
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAG
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAG
EST: gi|87038900|gb|CI193522.1|CI193522
EST:     TTCTCCAGATGCGTGG-ACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|86530972|gb|CI171178.1|CI171178
EST:     AGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: AGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|88984221|gb|CI020139.1|CI020139
EST:     ACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: ACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|218498639|gb|FG958416.1|FG958416
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|87028612|gb|CI266011.1|CI266011
EST:     GTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: GTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|8857538|gb|AU094856.1|AU094856
EST:     TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGAAATCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: TTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
EST: gi|86854195|gb|CI254140.1|CI254140
EST:     ACAAGTGGGATGTCATG                         GTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA
genomic: ACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAA

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: 73 (upstream exon), 70 (downstream exon)
Score: 90

CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgc ... ctttttgtagGTTGATCTGTTCTTCTACAGGGACCCAGAGGAAGCGAAGGAGCAAGAGGAAGAAGAGGCGGCTCTGGTGGCTCCTGATTATGGTGCGGTTGCGGAATATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgtatactcgcaatctaaactagtatcatgcctgtaatgtttggattctgaaatataatcactgatgtatgttgtttttcctttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG