Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCTCTACCTCGTCTTCGAGTACATGGACACCGACCTCAAGAAGTTCATCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatccggctacgaccgcttcagatctggatcaggggttcttcttcttgtttttttttcccgtgcacgcggggtgtttgtgtgaatgcctcgtccgtgtttgtctggttcgatgggggtgattgatgggggatgcgcttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os08g40170.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40170.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G068193_T02 (Zea mays), 5'ss of exon 1
CATCCTCTACCTCGTCTTCGAGTACATGGACACCGACCTCAAGAAGTTCATCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatccggctacgaccgcttcagatctggatcaggggttcttcttcttgtttttttttcccgtgcacgcggggtgtttgtgtgaatgcctcgtccgtgtttgtctggttcgatgggggtgattgatgggggatgcgcttgtgcag
|||||||||||| ||||||||||||||||||||||||||||||||||||||||| |  ||||||   ||   | |||||||||||| | ||||||||||||||| |    || | |  | ||  |   |||          | |  | |||   |       | | |||| ||  |||||||||   ||||| ||  || |||||||   |  ||  |                               
CATCCTCTACCTGGTCTTCGAGTACATGGACACCGACCTCAAGAAGTTCATCCGGGGACACCGCAGCAACAACGAGAAGATCCCCGCGGCCACCGTCAAGgtatacgagtggtttc--ctgccccctctct----------tccaccgtctccatcccagcgcgc-tgcatgccaggtgtttgttcaaatgcgtcacccatgtttgt---gcccgcag-------------------------------

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G07640.1 (Glycine max), 5'ss of exon 2
CATCCTCTACCTCGTCTTCGAGTACATGGACACCGACCTCAAGAAGTTCATCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatccggctacgaccgcttcagatctggatcaggggttcttcttc-ttgtttttttttcccgtgcacgcggggtgtttgtgtgaatgcctcgtccgtgtttgtctggttcgatgggggtgattgatgggggatgcgcttgtgcag
  |  | ||| | || || ||||||||||||||||| |||||||| ||||||||| ||  |   ||       || || || ||       ||  |||| |||   ||     ||   |    |||  | ||       | |   | ||| ||   |||| |     ||    | |                                                                          
AGTGTTGTACTTGGTGTTTGAGTACATGGACACCGATCTCAAGAAATTCATCCGCTCCTTCGATCAACCGGGACAAAACATTCCACCCGAAACTATCAAAgtaat-at---attatatctctctcaattttgtgaatttgttcaatgttcattcaattttgtgaatttggttacag--------------------------------------------------------------------------
















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|58674313|gb|CK062999.1|CK062999
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|29663133|gb|CB659408.1|CB659408
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58604316|gb|CK014844.1|CK014844
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58684825|gb|CK073512.1|CK073512
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|29663132|gb|CB659407.1|CB659407
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58676453|gb|CK065140.1|CK065140
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58678707|gb|CK067394.1|CK067394
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTAGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58657532|gb|CK046212.1|CK046212
EST:     TCCGGGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCT
EST: gi|58600858|gb|CK011386.1|CK011386
EST:     CCGGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTC
genomic: CCG-CGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTC
EST: gi|58677365|gb|CK066052.1|CK066052
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58597617|gb|CK008145.1|CK008145
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCCCATGGCCGCG
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCC--ATGGCCGCG
EST: gi|3768776|gb|AU032803.1|AU032803
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|33801903|gb|CF326823.1|CF326823
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|58603691|gb|CK014219.1|CK014219
EST:     TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
EST: gi|38479047|gb|CF963180.1|CF963180
EST:     TCGGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAG                         ATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT
genomic: TCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGT

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: 68 (upstream exon), 72 (downstream exon)
Score: 14

CATCCTCTACCTCGTCTTCGAGTACATGGACACCGACCTCAAGAAGTTCATCCGCGCCCACCGCCAGAATCTCCAGAAGATCCCCGTGCCCACCGTCAAGgtatccatcc ... gcttgtgcagATCCTGATGTACCAGCTCTGCAAGGGCGTTGCTTTCTGCCATGGCCGCGGTGTGCTGCACCGTGACCTCAAGCCGCATAACCTGCTCATGGACCGCAAGA




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