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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccccctcgccttctccccgccgccgcctccaacctgacctcactgcgtgcccagttcctcccgggattcaccgctgatcatctcagcacccgcgagtctttccgtttcctcgtcgttctcgctttttttttttttattttttttgagttttctcctggacgagttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC

Basic information

species Oryza sativa
transcript LOC_Os07g47580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 1
gtaagtccccctcgccttctccccgccgccgcctccaacctgacctcactgcgtgcccagttcctcccgggattcaccgctgatcatctcagcacccgcgagtctttccgtttcctcgtcgttctcgctttttttttttttattttttttgagttttctcctggacgagt-tggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC
||||| |||| || |||| | ||    || | ||| ||  |||   | || | |||||        ||     |  |  |   ||||||||| |  | |   | ||||| ||  |||||                   |||  |||||| |        | || |||| | |||||||||||||||||||||||||| ||||| ||||||||||||||||||  |||||||||| |||| ||||||||||||||||| | ||| ||||||||||||| ||
gtaagcccccgtcccctttttccga--gcggtctcgaatttgagacctctccttgccc--------ccctagctagctcccattcatctcagtattccccgctgtttccattaactcgt-------------------tttgattttttcg-------ccgtgcacgactgtggctgcagCCGCAGGGAGATCACATCGAGCTGCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAAGAGCGCAAGCGCAAGCGCGAGGCCCGCGAGGTGCACAGGC

upper sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 1
gtaagtccccctcgccttctccccgccgccgcctccaacctgacctcactgcgtgcccagttcctcccgggattcaccgctgatcatctcagcacccgcgagtctttccgtttcctcgtcgttctcgctttttttttttttattttttttgagttttctcctggacgagt-tggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC
||||| ||||| || |          ||||||||| | |||  |    |    ||||    || |||| |   |  ||  | |                    |||    |||  |||   || |   || |     ||   |  |  ||   ||  | | || |||||| | |||||||||||||||||| ||||| ||||||||||||||||||||||||  |||||||||| |||||||||||||||||||||| | ||||||||||||||||| ||
gtaagccccccgcggcc--------acgccgcctcgagcctagcgctcccatatgcctcaatcttccctgctcttcccattta--------------------cttgtttttttttcgcgattttgttttctacaagttccgtgctgatt---ttcccccgtgcacgagtgttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAGGAGCGCAAGCGCAAGCGCGAGGCGCGCGAGGTGCACAGGC
















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|87008746|gb|CI302901.1|CI302901
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|58689868|gb|CK078555.1|CK078555
EST:     CAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33653812|gb|CF276426.1|CF276426
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88395389|gb|CI611306.1|CI611306
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88302583|gb|CI668429.1|CI668429
EST:     TCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: TCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33688902|gb|CF317141.1|CF317141
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|86848058|gb|CI290577.1|CI290577
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88394705|gb|CI622579.1|CI622579
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACAAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|12622982|gb|AU173195.1|AU173195
EST:     CTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGNAGNATCACATAGNAGCTTCACCAGAAGCGCCATGGCCGGCGC
genomic: CTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGG-AG-ATCACATAG-AGCTTCACCAGAAGCGCCATGGCCGGCGC
EST: gi|88351380|gb|CI627396.1|CI627396
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33813020|gb|CF332400.1|CF332400
EST:     CTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGAT-ACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|87011090|gb|CI287767.1|CI287767
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33814059|gb|CF332914.1|CF332914
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCG-CATG                         CCG-AGGGAGAT-ACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|58681353|gb|CK070040.1|CK070040
EST:     GCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: GCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88333766|gb|CI643798.1|CI643798
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGGGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88570881|gb|CI662254.1|CI662254
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGGGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33658076|gb|CF280690.1|CF280690
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|58661138|gb|CK049818.1|CK049818
EST:     CCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACCATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCT
genomic: CCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCA-CATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCT
EST: gi|88330377|gb|CI633584.1|CI633584
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCACCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88364720|gb|CI612535.1|CI612535
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33657881|gb|CF280495.1|CF280495
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|86887864|gb|CI297975.1|CI297975
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88851570|gb|CI671010.1|CI671010
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|38469043|gb|CF953174.1|CF953174
EST:     CAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33692111|gb|CF320350.1|CF320350
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88399306|gb|CI618496.1|CI618496
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|58678013|gb|CK066700.1|CK066700
EST:     GCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCAGCAGAAGCGCCATGGCCGGCGCCTG
genomic: GCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|33809375|gb|CF330567.1|CF330567
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
EST: gi|88330904|gb|CI638312.1|CI638312
EST:     CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATG                         CCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG
genomic: CCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTG

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), 52 (downstream exon)
Score: 107

CCTCCTTTCCTCCTCCCCCACCCAAAGCTCGAGCTCCCGCTAGGGTTTCGCCGCCGCCATGgtaagtcccc ... ttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgctttttttttttttattttttttgagttttctcctggacgagttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC
     ttttttttttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccccctcgccttctccccgccgccgcctccaacctgacctcactgcgtgcccagttcctcccgggattcaccgctgatcatctcagcacccgcgagtctttccgtttcctcgtcgttctcgctttttttttttttattttttttgagttttctcctggacgagttggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG