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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGCTGCCCTCTCTTCAGTTGCAAGGACATCCATGGTAACCATGCAGGACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagctgcatccaatcaccttgtataattcacatatactgctaaagcagtaattctaaaaacatcatttttttttacatccacag

Basic information

species Oryza sativa
transcript LOC_Os07g43390.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43390.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G013811_T01 (Zea mays), 5'ss of exon 15
CACTGCTGCCCTCTCTTCAGTTGCAAGGACATCCATGGTAACCATGCAGGACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagctgcatc--------caatcaccttgtataattcacatatactgctaaagcagtaat-tctaaaaacatcatttttttttacatccacag---
 || |||||||||||||| || || ||||| ||| |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||  | |||  | |        || ||  ||||||||   ||| |||  |  | || ||  | | ||   |||  | ||| |||| ||| | | |     
TACGGCTGCCCTCTCTTCCGTCGCGAGGACTTCCGTGGTAACCATGCAGGACATTCTTGGCCTTGACAGTTCTGCTAGAATGAATACTCCAGCTACCCAGgttgtccgctcgaccgtttctgacattctacttgtatataccacgtat-ttcatgaaacatcagtgtcgtgaaatcttattattttctactttccctacag
















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|86251678|gb|CI016967.1|CI016967
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|88538510|gb|CI467546.1|CI467546
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|89176204|gb|CI043225.1|CI043225
EST:     CATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: CATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|88225194|gb|CI225110.1|CI225110
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|86837121|gb|CI347629.1|CI347629
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|88832166|gb|CI017400.1|CI017400
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|89186521|gb|CI048193.1|CI048193
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAAACTGGAGATGGAG-A-GC-G-GCTCTGTCAGCTTCGACAGCCT
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAA-CTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCT
EST: gi|89163744|gb|CI100634.1|CI100634
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|88223687|gb|CI223536.1|CI223536
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
EST: gi|86504785|gb|CI147418.1|CI147418
EST:     ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAG                         AAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC
genomic: ACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTC

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), 73 (downstream exon)
Score: 45

CACTGCTGCCCTCTCTTCAGTTGCAAGGACATCCATGGTAACCATGCAGGACATTCTTGGCCTCGACAGTTCTGCTAGAATGAATACTCCAGCTACACAGgttaacagct ... acatccacagAAAGGGAACTGGAGATGGAGGATGCCGAGCTCTGTCAGCTTCGACAGCCTCAGCCCTGAAGCGGCGAAGCTGAAGGAATTGCTTGGACTGTACAACCGGC




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