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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA

Basic information

species Oryza sativa
transcript LOC_Os02g47850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147450_T01 (Zea mays), 3'ss of exon 2
gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgc--tacggatttgcgattaggcaattgtgctccacagttaagaagat--gatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
        ||||| |||||   ||| || |||  |    || |||| || | |||   || ||| |  |  |   || |  ||    |||| |   ||||||      ||| |   ||| || |  || |  | |   |   |||| |||||||||| | | |   ||||| | |||| || ||||||||||| |||||||| || || || || ||||||||||| |||| ||||||||||||||| || |||||||||||||| |||||
-----gtgggttgtctttt-attagttg-ttcagaca--tcaagttgtgtattcggcacgtggagtgtgcacctgggatcttgtagcacggttcatcgatta------tgtaccttacaatttaagagctctgttatttctggttttaccatttttgaaatgtctatgcagCGAAAAGGCCGTGGAAGCTCAGTGATGCTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGA

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 2
gtgagtcaggttgccttttcgctagctgattcga-atc--gctcta-gttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctcc--acagttaagaagatg-atgaatactg-tttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
        ||||| ||||   ||||||| |  || |||  | | |   ||  |||||||   || ||| || | |||  || || ||   |       |||||   ||||| ||  ||  ||| || |  || |  || | | ||| |||||| ||||||| | ||| | ||||| | |||| || ||||||||||| |||||||| || || || || ||||| ||||| |||| |||||||||||||||||||||||||||||||||||||||
-----gtgggttgtcttt--actagctgttcagatatcaagttttgtattcggcagtcggcacgtggagtatgcgcttgggattttgtagca------cgattcatcaattatgtaccttacaatttaagagctctattatttctggtttcactatttttgaaatctccatgcagCGGAAAGGCCGTGGAAGCTCAGTGATGCTCGTCTTGTCCTGGAAGATGGATCAGTGTGGACGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
                                  ||| |  || ||||  | |  ||   |                  | |   ||| |||   | ||||  |  |    |    ||||   |      |  ||| | |||     || ||| |   |  ||   |   ||||||| |||||      ||||||| | || |||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||| |||||      
--------------------------------agatcaccttatttttcaattttcactcc-----------------ctttctaacgcattattgtttagaaacataca-tatgtagtttgaa------ttgatagtcttt-----ttgttgaaccttagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT------

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ07419 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtg---cagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
                                                                             ||   |||   |   || |  || |  |||          | |            | |    | |   | || |||| |  || |||   ||||  |  | |||||||||   |  ||  |  |||| |||||| ||||||| ||||| ||||| | |||||||||||| ||||| ||||| ||||| || ||
-----------------------------------------------------------------------------gtgtcgctggcgcgctgtg--tatgtgatttcatcttcttgcttgctttggatccattgtaatctt--ctttcttggctcttttgtgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ19894 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
                                                                                                  || |  |||          | |            | ||   | |   |  |||||      | |  ||||  |  | |||||||||   |  ||  |  |||| |||||| ||||||| ||||| ||||| | |||||||||||| ||||| ||||| ||||| || ||
-------------------------------------------------------------------------------------------------gtatgtgatttcatcttcttgcttgctttggatccattataatcttggctcttttg------tgggacagTTGAGCGGCCATGGAAGACTAAAGACACAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGA

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|58656843|gb|CK045523.1|CK045523
EST:     GCTGTCAGTGGCGTGCAGAGTGGTACCGTGGTGGATGATGGAG                         TGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTT
genomic: GCTGTCAGTGGCGTGCAGAGTGGTACCGTGGTGGATGATGGAGgtgagtcagg ... cttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTT
EST: gi|88364901|gb|CI614519.1|CI614519
EST:     GGTGTCAGTGGCGTGCAGAGTGGTACCGTGGTGGATGATGGAG                         TGCAAAGACCATGGAAGCTCAGGGATGCTCGGCTCGTTCTTGAGGATGGTT
genomic: GCTGTCAGTGGCGTGCAGAGTGGTACCGTGGTGGATGATGGAGgtgagtcagg ... cttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTT
EST: gi|58690939|gb|CK079626.1|CK079626
EST:     TGCCAAGGCTGTCAGTGGCGTGCAGAGTGGTACCGTGGTGGATGATGGAG                         TGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTT
genomic: TGCCAAGGCTGTCAGTGGCGTGCAGAGTGGTACCGTGGTGGATGATGGAGgtgagtcagg ... cttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA
                                           ttcttcgt  CT-rich tract
                                  attttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcaggttgccttttcgctagctgattcgaatcgctctagttttgcagtcgcagcgcggaatacgtgctcagggttctgctacggatttgcgattaggcaattgtgctccacagttaagaagatgatgaatactgtttcaccatttttggattcttcgtgcagTGCAAAGACCATGGAAGCTCAGCGATGCTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG