Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttgtttacagttatcatcctgagattctttcctgagtttgtctcacaatgcatttacactgacgttccctcattttgaatag

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 11
GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttgtttacagttatcat-----cctgagattctttcctg-agtttgtctcacaatgcattta-cactgacgttccctcattttgaatag
|| ||||||||||||||||||||||| ||||| |||||||||||  |||||||||||||||||||||| |||||||||||||| |    ||||| ||| | ||||      |||||||||   |||| | | | | |   | |   | |  ||||||   |||     | | |||||
GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctgttttcagctttcatgcaaatctgagattcacccctgcaatctttgttgtattatttctggcactgaacctcc-----tcttaatag
















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|29681301|gb|CB677576.1|CB677576
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86496217|gb|CI138850.1|CI138850
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88218075|gb|CI217924.1|CI217924
EST:     ACCACTACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86494783|gb|CI137416.1|CI137416
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86433522|gb|CI093865.1|CI093865
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|33805337|gb|CF328546.1|CF328546
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|66920288|gb|CX107136.1|CX107136
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86498360|gb|CI140993.1|CI140993
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|27554584|gb|CA998484.1|CA998484
EST:     CTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: CTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88970906|gb|CI387047.1|CI387047
EST:     CATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCCCAACAAGTAGAAAGTGATTA
genomic: CATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86889251|gb|CI315862.1|CI315862
EST:     GCAAAGACATCCATCTATCTTCACAGTCCGCAG                         G-ATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: GCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88828754|gb|CI073624.1|CI073624
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCGATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86597807|gb|CI276593.1|CI276593
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88962552|gb|CI097704.1|CI097704
EST:     ACCACAACCCTGCCACTGCAAAGACATCGATCGATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86421137|gb|CI057126.1|CI057126
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86503924|gb|CI146557.1|CI146557
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88243189|gb|CI244311.1|CI244311
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88849154|gb|CI087676.1|CI087676
EST:     TCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: TCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|33805339|gb|CF328547.1|CF328547
EST:     ACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86434209|gb|CI094552.1|CI094552
EST:     ACCACAACCCTGCCACTGCAAAGACATCTATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86494924|gb|CI137557.1|CI137557
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88849422|gb|CI089330.1|CI089330
EST:     CTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: CTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86498473|gb|CI141106.1|CI141106
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88222012|gb|CI221968.1|CI221968
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86495339|gb|CI137972.1|CI137972
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86504575|gb|CI147208.1|CI147208
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|88228888|gb|CI226739.1|CI226739
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86492322|gb|CI134955.1|CI134955
EST:     CCACTGCAAAGACATCCATCGATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: CCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86489810|gb|CI132443.1|CI132443
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|87007439|gb|CI279110.1|CI279110
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86597966|gb|CI278356.1|CI278356
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86428049|gb|CI073146.1|CI073146
EST:     ACCACAACCCTGCCACTGCAAAGACATCTATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|87015853|gb|CI279605.1|CI279605
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|89165615|gb|CI102705.1|CI102705
EST:     ACCGCAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|89198870|gb|CI003607.1|CI003607
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86431778|gb|CI085389.1|CI085389
EST:     TTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: TTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
EST: gi|86494277|gb|CI136910.1|CI136910
EST:     ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG                         GAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA
genomic: ACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTA

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: 67 (upstream exon), 57 (downstream exon)
Score: 11

GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttg ... ttttgaatagGAATCTGAGGTTAAAGGGAAGCCGAGAATCGCAACAAGTAGAAAGTGATTACATCCAGCTACGCAAAACCAAAGAGTGCACAAGAAATCATGTACATTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAGgtaatagttgtttacagttatcatcctgagattctttcctgagtttgtctcacaatgcatttacactgacgttccctcattttgaatag

- - - - - - - - - - - - - - - - - - - - - - - - GCAAAG