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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG

Basic information

species Oryza sativa
transcript LOC_Os02g40830.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 7
gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttat----gact---------aatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG
|||  || | | ||| |||      ||||            |||  | | |  |  ||||    || |         ||||||||    | |||||||||||| |||||||| || |||||||||||||||||||| || |||||||||||||| |||||||||||||| |||||||| ||||| |||||||| |||||||
gtatgcagtgagaaaaggtcctcattttgatgctttttatcttattattacgttttttatctgtgaatttgtactgtaatttggatgcttaatgtgggtagATAAATCCTCTGGCGGAGACAGCTGACAACAAGCTTGTTGCTGCTGATGCAAAATTGAACTTTGATGATAATGCTGCATTTAGACAGAAAGAAATATTTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 7
gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG
        |||  | | | |  ||||        ||    ||||  | ||      | ||||  || |||   || ||    |   |||| |||||  | || ||||||||||| ||| |  |||| ||||||||||| |||||||| |||||||| |||||||| | | | ||||||||||||||| 
-------gtaagcatttgcacttcatacaa----gcttaatttatgaatg--tctataatga--aaattgattatttt----gaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 7
gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacat--gttatgt-gggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG
|||| || |  |||||  ||  |||| || | |      |      | |  |      ||| |||   || | ||  ||||| | |   |||| |||||  |||| ||||||||||| ||| |  |||| ||||||||||| |||||||| ||||| || |||||||| | | | ||||||||||||||||
gtaagcatttgcaaattttaa-tcatgtgcactt-tatacaagcttaatttatgaagaatgtctatgatgaaaattggttattttgaacagATCAATCCCATTGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGACGATAATGCTGCATATCGCCAGAAAGAGATATTTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG
                           || || | || ||     |  ||||  |      | ||      |  |  |       || |||     || || | ||   |||| |||||  | || |||||  | || ||| |  | || |||||||||||||||||||||||||| || |||||||| ||| | |||||| | |||||||
gtgagcataaactccctattttcaagctccatgaaaattgaccatttgtttgataattttagattc----ttttatcgaaagaatcttattc---tattttgtttgaacagATCAATCCCATCGCAGAGACTTCAGATAACCAATTAGTAGCTGCTGATGCAAAGTTGAACTTTGACGATAATGCTGCTTTTCGTCAGAAACATATATTTG

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|163921201|gb|EG714126.1|EG714126
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAATCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|163929534|gb|EG713477.1|EG713477
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAATCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|13420568|gb|AU174658.1|AU174658
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG
                           gactaat  putative branch site (score: 2)
                            actaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA