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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttcacacttttgtacagttgaaccatgttttttgtcctttgatgtaggaccatttttgtatcctgtcaaactaataatacaatttggtttaatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG

Basic information

species Oryza sativa
transcript LOC_Os03g01890.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 9
gtatttttcacacttttgtacagttgaaccatgttttttgtcctttgatgtaggaccatt--tttgtatcctgtcaaactaataatacaatttggtttaatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG
            ||  | | || ||   |  |  ||||   | |||||||     |||||  | |||||  |||| |  |||| ||   ||| ||||| |||||||||||||||||||||||||| |||||||| ||||| ||||| ||||| || ||||| ||||||||||||||||||| |
----------gtctggtttccattttgtcttttgttttaaccttttgatg-----ccattagtatgtatgttgtcca-ttaatgattgtattgggtttcatctttcagGCATGGAGTGTTCCTGAAGTGCTTCGACCACTATATGAGTCTTCTAGAGTAGTTGCTCAGAAAATGACTACTGTG

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 9
gtatttttcacacttttgtacagttgaaccatgttttttgtcctttgatgtaggaccatttttgtatcctgtcaaactaataatacaatttggtttaatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG
|| |  ||| |||||||    | || ||      ||||  |  |||||||  |       | |||||  |||| |  |||| ||   ||| ||||| |||||||||||||||||||||||||| |||||||| ||||| ||||| ||||| || || || ||||||||||||||||||| |
gtctggttctcactttt---tattttaa------ttttaatgttttgatgctg---ttagtctgtatgttgtcca-ttaatgatcgtattgggtttcatctttcagGCATGGAGTGTTCCTGAAGTGCTTCGACCACTGTATGAGTCTTCTAGAGTTGTTGCTCAGAAAATGACTACTGTG

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 8
gtatttttcacacttttgtacagttgaaccatgttttttgtcctttgatgtaggaccatttttgtatcctgtcaaactaataatacaatttggtttaatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG
                               |||||  |  |  |      | |   |||||| | |  | | | |   || |      ||  | |  ||||| ||||||||||||| || || ||| | |||||||| |||||||| || | ||| || |||||||||||||| | ||| 
---------------------------gttttgtttcgtaacactgagctaatgtatatttttttcttttcttatatacattaatttgcttattgttttcttttagGCATGGAGTGTGCCAGAAGTGTTGCGGCCACTTTATGAATCATCCAAGGTGGTTGCTCAGAAAATGACAATTGCA

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 8
gtatttttcacacttttgtacagttgaaccatgttttttgtcctttgatgtaggaccatttttgtatcctgtcaaactaataatacaatttggtttaatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG
                               ||||| ||  |  |      | |   ||||||   | |  |      | ||||     ||  | |  ||||| ||||||||||||| || || ||| | |||||||| |||||||| || | ||| || |||||||||||||| | ||| 
---------------------------gttttgtttcttaacactgagctaatgcatatttttcctttccttatttacattaatttg-cttattgttttcttttagGCATGGAGTGTGCCAGAAGTGTTGCGGCCACTTTATGAATCATCCAAGGTGGTTGCTCAGAAAATGACAATTGCA

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 8
gtatttttcacacttttgtacagttgaaccatgttttttgtcctttgatgtaggaccatttttgtatcctgtcaaactaataata--caatttggtttaatcttt-cagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG
                                    ||||   ||||      | |  || ||  ||  |       |   |||     ||||  ||  |||||| |||||||||||||| || |||||||| || ||||| |||||||||||||| || || |||||||||||||||| ||| 
-----------------------------------gtttgatttttggcagttggc--ttcttagatttttcttgcttggcaatggcttatttccttacatctttgcagGCATGGAGTGTGCCAGAGGTGCTGCGACCACTTTATGAATCTTCAAGAGTTGTAGCTCAGAAAATGACTATTGCA

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|58595991|gb|CK006519.1|CK006519
EST:     GTGAACGTGGGGGATCAATTGTGCACATAGTGGACCATCTGGATCTTGAG                         GCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTA
genomic: GTGAAGGTGGGGGATCAATTGTGCACATAGTGGACCATCTGGATCTTGAGgtatttttca ... aatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTA
EST: gi|58669023|gb|CK057709.1|CK057709
EST:     GTGAAGGTGGGGGATCAATTGTGCACATAGTGGACCATCTGGATCTTGAG                         GCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCCAGGGTA
genomic: GTGAAGGTGGGGGATCAATTGTGCACATAGTGGACCATCTGGATCTTGAGgtatttttca ... aatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaccatttttgtatcctgtcaaactaataatacaatttggtttaatctttcagGCATGGAGTGTTCCTGAGGTGCTTCGGCCACTCTATGAATCTTCAAGGGTAGTCGCTCAGAAAATGACTACTGCG
                                               tctttc  CT-rich tract
                          taataatacaatttgg  TA-rich tract