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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGCATCCCGAGCAAGCAAGCCGCCGCCGCCGACGACCTAGCTCCCCGATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagcccccatactcgatccccgcccgccgccgtggtttcctccggctctcgctgacgacggccgcgggttgttgttggtgtgtgtgtgcctgcag

Basic information

species Oryza sativa
transcript LOC_Os09g32800.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G074386_T01 (Zea mays), 5'ss of exon 1
-----CGCCGCATCCCGAGCAAGCAAGCCGCCGCCGCCGACGACCTAGCTCCCCGATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagcccccatactcgatccccgcccgcc-gccgtggtttcctccggctctcgctgacgacggccgcgggttgttgttggtgtgtgtgtgcctgcag
       | |   | | | ||  | |||  ||   || |    || |   |||||| | | |||||||||||||||||||||||||||||||||||||||||||||||  | |||     |  ||||  | |||| || |    |  |    |   || || |||| || |   | ||| |  ||  |               
CTAACTCCGGTGGCTCCACCA--CTAGCAACCCGTGCAGCGAGCCCA---CCCCGACCACTGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtagcctccctgcggccttcccacctcgcctgctggccgtatcctatgtgttctctaacgagggtct--gtttggtcctgcag---------------

upper sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G817037_T02 (Zea mays), 5'ss of exon 1
CGCCGCATCC--CGAGCAAGCAAGCCGCCGCCGCCGACGACCTAGCTCCCCGATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagcccccatactcgatccccgcccgccgcc--gtggtttcctccggctctcgctgacgacggccgcgggttgttgttggtgtgtgtgtgcctgcag
  |||  |||   ||     | | | ||  ||   |  |     || | |||| |   ||||||||||||||||||||||||||||||||||||||||||||||| || |||   |||  |||   | |||   |  || || ||||  |  || | || |||| || |   | ||||| |||  |               
--CCGACTCCGGTGACTCCACCACCAGCAACCCGTGCAGCGAGCGCACTCCGACCATCGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaggctccctgcctccttccaacctcgcttgctggtcgtatcctatgtgtc-ctctaacgagggtct--gtttgttcttgcag---------------

upper sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G074386_T02 (Zea mays), 5'ss of exon 1
-CGCCGCATCCCGAGCAAGCAAGCCGCCGCCGCCGACG-ACCTAGCTC--CCCGATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagcccccatactcgatccccgcccgcc-gccgtggtttcctccggctctcgctgacgacggccgcgggttgttgttggtgtgtgtgtgcctgcag
    |  |  |||      | | |    ||  ||   | | | ||| |  ||||| | | |||||||||||||||||||||||||||||||||||||||||||||||  | |||     |  ||||  | |||| || |    |  |    |   || || |||| || |   | ||| |  ||  |               
GTTTCTAACTCCGGTGGCTCCACCACTAGCAACCCGTGCAGCGAGCCCACCCCGACCACTGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGgcgggtagcctccctgcggccttcccacctcgcctgctggccgtatcctatgtgttctctaacgagggtct--gtttggtcctgcag---------------

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|33804936|gb|CF328345.1|CF328345
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|58599894|gb|CK010422.1|CK010422
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33818104|gb|CF334878.1|CF334878
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|38472549|gb|CF956681.1|CF956681
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33678412|gb|CF306651.1|CF306651
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33660627|gb|CF291594.1|CF291594
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33683337|gb|CF311576.1|CF311576
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|38477362|gb|CF961495.1|CF961495
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|58694905|gb|CK083592.1|CK083592
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|55439808|gb|CV733214.1|CV733214
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33681495|gb|CF309734.1|CF309734
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33683521|gb|CF311760.1|CF311760
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|66915431|gb|CX102279.1|CX102279
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|58593878|gb|CF992186.1|CF992186
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|58678279|gb|CK066966.1|CK066966
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|55413999|gb|CV726375.1|CV726375
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|218497460|gb|FG955186.1|FG955186
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|87023706|gb|CI286457.1|CI286457
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33823301|gb|CF337451.1|CF337451
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33803800|gb|CF327774.1|CF327774
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|56158103|gb|C73010.2|C73010
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|58667664|gb|CK056350.1|CK056350
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|27577357|gb|CB000052.1|CB000052
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|55412184|gb|CV724560.1|CV724560
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|58674446|gb|CK063132.1|CK063132
EST:     ATCGTGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATAGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
EST: gi|33818151|gb|CF334904.1|CF334904
EST:     ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGG                         GACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC
genomic: ATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATAC

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: 56 (upstream exon), 73 (downstream exon)
Score: 10

CGCCGCATCCCGAGCAAGCAAGCCGCCGCCGCCGACGACCTAGCTCCCCGATCGCGGCCATGTCGAGGCGCGGCGACTGGGTCTACGAGAACAACGGCGGgtaagccccc ... gtgcctgcagGACGTGCGTGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATACCCGCCTTTCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATC




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