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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtttttccatcatagatgtatgttttcacattaaaggcgttagtagtagtggagtactaatattgtggttatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCACTCATGCCCTGAGTTGTGATTGTACCTCCTTCCGTTGCATATATCTTCT

Basic information

species Oryza sativa
transcript LOC_Os07g37750.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 31
gtatatgtttttcca--------tcataga--tgtatgttttcacattaaaggcgt-tagtagtagtggagtactaatattgtggttatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCACTCATGCCCTGAGTTGTGATTGTACCTCCTTCCGTTGCATATATCTTCT-
||| ||  |||  ||        |  ||||  | || ||     ||   ||  | | |  ||      |||   |||| |||||||||  |  ||||||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||| |||||  | ||   |||  |||| |||||||||||||||| | 
gtacatactttctcaggtttagtttctagaattctaggtaccatcaacgaaaacatgtgataacgccagagctttaat-ttgtggttacacttcagATGGATGTTCGTGGAGCCCTTGGTGATCTCTTTAGCAAACAGCTTACTCCACTCATGTCCTGAAGTATGGCAGTATTTCCT-CCGTTGCATATATCTTGTT
















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|88845231|gb|CI084156.1|CI084156
EST:     ACATCAGAGAGTTCTATCCATGAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
genomic: ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
EST: gi|86418489|gb|CI032698.1|CI032698
EST:     ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTTACCCC
genomic: ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAAC-TTACCCC
EST: gi|33688752|gb|CF316991.1|CF316991
EST:     ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
genomic: ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
EST: gi|87018208|gb|CI297421.1|CI297421
EST:     ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCC
genomic: ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCC
EST: gi|29680773|gb|CB677048.1|CB677048
EST:     ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
genomic: ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
EST: gi|88840490|gb|CI079944.1|CI079944
EST:     ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
genomic: ACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
EST: gi|88218219|gb|CI218068.1|CI218068
EST:     TTCTATCCATGAATTACAAAACTTATCTGCTGTGATCAG                         ATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA
genomic: TTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCA

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: 9 (upstream exon), 70 (downstream exon)
Score: 2

GTTTTGAATGGAATGTGTATCATGGACGCTCAGATATTCAAGAAGCACATCAGAGAGTTCTATCCATTAATTACAAAACTTATCTGCTGTGATCAGgtatatgttt ... tatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCACTCATGCCCTGAGTTGTGATTGTACCTCCTTCCGTTGCATATATCTTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacattaaaggcgttagtagtagtggagtactaatattgtggttatgccgcagATGGATGTTCGTGGTGCCCTTGGTGACCTTTTCAGCAAACAACTTACCCCACTCATGCCCTGAGTTGTGATTGTACCTCCTTCCGTTGCATATATCTTCT
                              tactaat  putative branch site (score: 2)
                              tactaatatt  TA-rich tract