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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcaactgtcttgtaactcatcatttgcagagggggttttacagttctaatgctatcttggtatggttgcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGGCGTACTCGGCAGTATGATTACTACCAGAGAGTATTGAATGGGATTTTAT

Basic information

species Oryza sativa
transcript LOC_Os11g10420.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g10420.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G176698_T01 (Zea mays), 3'ss of exon 15
gttagtcaactgtcttgtaactcatcatttgcagagggggttttacagttctaa-tgctatcttggtatggttgcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGGCGTACTCGGCAGTATGATTACTACCAGAGAGTATTGAATGGGATTTTAT
||| |   |||    |   | |||||||        |    |||    |||||| |  || |||  |||  ||||||||||| || || |||||||| ||||| |||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||| |||||||
gttggcttactaatcttcgagtcatcatcatttctagaaccttt----ttctaactattaccttattattcttgcagCAATGTGTATCCCTGGTGCTCTCACTGATCAGTAGCAGCATGGATGCTTGGCGCACTCGGCAATATGATTACTACCAGAGAGTATTGAATGGAATTTTAT

upper sequence: LOC_Os11g10420.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv04s0044g01210.t01 (Vitis vinifera), 3'ss of exon 14
------------gttagtcaactgtcttgta---actcatcatttgcagagggggttttacagttctaatgctatcttggtatggttgcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGGCGTACTCGGCAGTATGATTACTACCAGAGAGTATTGAATGGGATTTTAT
             ||  ||| |  | | |||    || ||   ||   |||  | |  | || |   | |  | ||||| | |  | ||||||||| || ||| ||||||| || || ||||| |||||| | ||||||||||| || |||||||||||||| || ||||| || || |||||||| || |
gtttgattttaattttatcatcattttagtattagctaatatatttttgagatgatggt-cattgacagtatt-tcttgatttc-tagcagCAATGTGTATCTTTGGTGCTCTCCCTGATCAGCAGCAGCTTAGATGCATGGCGGACACGGCAGTATGATTATTATCAGAGGGTTTTAAATGGGATCTTGT

upper sequence: LOC_Os11g10420.2 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ26597 (Selaginella moellendorffii), 3'ss of exon 15
gttagtcaactgtcttgtaactcatcatttgcagagggggttttacagttctaatg--ctatcttggtatggtt---gcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGGCGTACTCGGCAGTATGATTACTACCAGAGAGTATTGAATGGGATTTTAT
    || |  | || |  ||||      ||||| |    ||||     |||| |||  || |||| || || |    ||||||||| || ||  ||||  | || || ||||| || ||| | ||||| |||||||||||||||||||||||||| ||  | || |||||||| ||   ||
----gtgagttatcctagaact------ttgcaaactttgtttcgttcttctcatggtctttctttgtttgttcttggcagCAATGTGTCTCCTTGGTCTTGTCGCTCATCAGCAGTAGCTTAGATGCTTGGCGTACTCGGCAGTATGATTACTATCAACGTGTTTTGAATGGAATCCAAT

upper sequence: LOC_Os11g10420.2 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ06373 (Selaginella moellendorffii), 3'ss of exon 17
gttagtcaactgtcttgtaactcatcatttgcagagggggttttacagttctaatg--ctatcttggtatggtt---gcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGGCGTACTCGGCAGTATGATTACTACCAGAGAGTATTGAATGGGATTTTAT
    || |  | || |  ||||      ||||| |    || |     |||| |||   | |||| || || |    |||||||||||| ||  ||||  | || || ||||| || ||| | ||||| |||||||||||||||||||||||||| ||  | || |||||||| ||   ||
----gtgagttatcctagaact------ttgcaaactttgtctcgttcttctcatggtttttctttgtttgttcttggcagCAATGCGTCTCCTTGGTCTTGTCGCTCATCAGCAGTAGCTTAGATGCTTGGCGTACTCGGCAGTATGATTACTATCAACGTGTTTTGAATGGAATCCAAT

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|29682738|gb|CB679013.1|CB679013
EST:     GCACTATTCAGAACTTGAGGAAGAGGTTTCACTTGAGTCTTACTGAAGAG                         CAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGG
genomic: GCACTATTCAGAACTTGAGGAAGAGGTTTCACTTGAGTCTTACTGAAGAGgttagtcaac ... atggttgcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGG
EST: gi|27920964|gb|CB096772.1|CB096772
EST:     GAAGAGGTTT-ACTTGAGTCTTACTGAAGAG                         CAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGG
genomic: GAAGAGGTTTCACTTGAGTCTTACTGAAGAGgttagtcaac ... atggttgcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcatttgcagagggggttttacagttctaatgctatcttggtatggttgcagCAATGCGTGTCTCTGGTGCTTTCACTTATCAGTAGCAGCATGGATGCATGGCGTACTCGGCAGTATGATTACTACCAGAGAGTATTGAATGGGATTTTAT
                           ttctaat  putative branch site (score: 2)
                   ttttaca  TA-rich tract