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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccgtccttgtttctcgcagtgactgtaccatcaatttcacagttcgcacgcgtcacaggaaagatgacactgttatcctcgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTATCTGGTCTGGGCGCGGGCTTCTTCGCTGTCTGTGTTGGTTCTCCAGTGG

Basic information

species Oryza sativa
transcript LOC_Os11g48040.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G000510_T02 (Zea mays), 3'ss of exon 5
gttccgtccttgtttctcgcagtgactgtaccatcaatttca-cagttcgcacgcgtcacaggaaagatgacactgttatcctcgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTATCTGGTCTGGGCGCGGGCTTCTTCGCTGTCTGTGTTGGTTCTCCAGTGG
||   ||   || ||||   |    ||   | |  || | || | | ||     | ||||  |       | ||||   |||| ||  ||||| | |||||||| || |||||||||||||||||||||||||| ||||| ||  ||||||| || || |||||||| ||||| ||||||||||| ||||| |
gtgttgt--gtgcttcttttaaattctcctcgaataactccatcggctc---ttcctcacttgcctatacatactg---tccttgc--tgcagTCAATTTTGAAACTCCCTGGGTTCAAAGATGATGTGGTCACCCACCTTTTTGCTGGTCTTGGTGCTGGCTTCTTTGCTGTTTGTGTTGGTTCCCCAGTTG
















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|29642995|gb|CB648002.1|CB648002
EST:     ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG                         ACTATTTTGAAGCTTCCTGGGCTCAAAGATGATGTGGTCACTCACCTCTTA
genomic: ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
EST: gi|117251481|gb|CT844185.1|CT844185
EST:     ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG                         ACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
genomic: ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
EST: gi|29643037|gb|CB648044.1|CB648044
EST:     ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG                         ACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
genomic: ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
EST: gi|86412895|gb|CI067300.1|CI067300
EST:     ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG                         ACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTAA
genomic: ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
EST: gi|88975591|gb|CI021673.1|CI021673
EST:     ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG                         ACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
genomic: ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
EST: gi|88975293|gb|CI023544.1|CI023544
EST:     ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG                         ACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA
genomic: ATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTA

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: 72 (upstream exon), 75 (downstream exon)
Score: 40

GAAGGGTTTGCTGCTTTGTGGACTGGCATTGGACCCAATGTTGCGCGCAATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAGgttccgtcct ... cgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTATCTGGTCTGGGCGCGGGCTTCTTCGCTGTCTGTGTTGGTTCTCCAGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacagttcgcacgcgtcacaggaaagatgacactgttatcctcgccttgcagACTATTTTGAAGCTTCCTGGGTTCAAAGATGATGTGGTCACTCACCTCTTATCTGGTCTGGGCGCGGGCTTCTTCGCTGTCTGTGTTGGTTCTCCAGTGG
                                         tcctcgcctt  CT-rich tract