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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGAGAACCACTCTATGTTAGAATCCGTGAGCACCGGGGTTCTACTGACATCG

Basic information

species Oryza sativa
transcript LOC_Os11g36070.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G135314_T01 (Zea mays), 3'ss of exon 2
gtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttg----ctattgacttatctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGAGAACCACTCTATGTTAGAATCCGTGAGCACCGGGGTTCTACTGACATCG
|| ||||||     |  |    || |||  | |   |||    |||||    |    ||| | |||| |  || ||||       || ||   |   | | | ||  | | |   ||  |||      || |||  |  ||  || |||||       ||| |||   || | |||||||||||||||||||||| | |  |||||  || |||| |||||||||||||| | ||||||| |  || ||||||||  ||| || ||||  | |||  |
gttagtggctggtaatgttttcacatttcagctatattgtctacaata---gttttccttgtaccatagt-gtgtggtggggtggtaaatcagggcat-cagataaatcgtgcatgctgattaatgagcatgag--cttctaattgaacaccaataacctactgaagcatttctgcagGCAGTCAGTACTGTGGCCAGTCATGATGGTGACTACAGGAAAGCTTTGAGAGGATCACTCTACGCCAGGATCCGTGAATACCAGGATTCTGATAACAAGG

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G104449_T03 (Zea mays), 3'ss of exon 9
gtcagtggc--atactacctcg-atacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatag-atttcgtggtact-gctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGAGAACCACTCTATGTTAGAATCCGTGAGCACCGGGGTTCTACTGACATCG
|| ||||||   ||  |  | | | | ||  ||   | | || | || | |   ||||   ||||   |    ||| ||   |  |  | | |  ||  || |   | ||  |   |   |  ||||      || ||||| |        | || || ||||||   | || | |||||||||||| || ||||| | |  |||||| || |||| |||||||||||||| ||| ||||| || || ||||||||| ||| || ||||  |||||  |
gttagtggctggtaacattttgcacatttcagttcagctgtgttctctaca---atagttttttttggaccatagtgtgtggtggaggtggtaaatcagggcatcagataaatactgcatgataattgatgagcatgagattc--------agcattt-ctattggaatgtcat-gcagGCAGTCAGCACCGTGGCCAGTCATGATGATGACTACAGGAAAGCTTTGAGAGGACCGCTCTACGTCAGGATCCGTGAGTACCAGGATTCTGATGACAAGG
















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|58606537|gb|CK034570.1|CK034570
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|88273561|gb|CI393967.1|CI393967
EST:     ACTTCATATCAAGGCAACTAATTTGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|29688057|gb|CB684332.1|CB684332
EST:     ATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|27576960|gb|CA999654.1|CA999654
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|88581594|gb|CI698792.1|CI698792
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|27578183|gb|CB000878.1|CB000878
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|25778077|gb|CA752829.1|CA752829
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTAC
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGAGAACCACTCTATGTTAGAATCCGTGAGCACCGGGGTTCTACTGACATCG
                                    tattgac  putative branch site (score: 2)
                                          cttatcttt  CT-rich tract
                     tgtttaaa  TA-rich tract