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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtcctagaaatcattgtctttgaatttactgttctgaatgtatgccagttagaaaaagggtgcctttataaatttgtgatatatcttttaggtttg...

Basic information

species Oryza sativa
transcript LOC_Os05g01060.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G104377_T03 (Zea mays), 5'ss of exon 17
GGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatg-tcctagaaatcattgtctttgaatttact------gttctgaa---tgtatgccagttagaaaaagggtgcctttataaatttgtgatatatcttttaggtttg
|||||||||| | ||||||||||||||||||||||||||| ||||||||||||| ||||| ||||| ||| | |  || ||||| |||||||| |   | ||||| |     ||||||||||| |  || || ||      |||    |   | | | |    |  |  ||   || |||     ||||||    |   |||        
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttccaaaatcattgtcctcaaaatttctcagtttgtttaatactttatcttctttctttaggaaaaatgtcttg--ggatttgtagcctcctttt--------

upper sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
GGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtcctagaaatcattgtctttgaatttactgttctgaatgtatgccagttagaaaaagggtgcctttataaatttgtgatatatcttttaggtttg------
||||||||||   ||||| || |||||||||||||||||||| ||||||| ||| |   |||||| |||  |  | || || ||      ||||||   ||||||       | |   |   |||   | || ||||   || |    ||   ||   ||| ||||     |   | ||    |     | |||||  |       
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattacttatttgctcaatttttttctattgtttgaaaagctatccgcata---aaatggtggtcagaaggacttcctgtgg---tcttaggaataacagag
















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|88535922|gb|CI465638.1|CI465638
EST:     GAAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGA
genomic: GAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATAT-GGGCGTCCTACTGAATTTTCTATATTGGCTGCTGA
EST: gi|88270445|gb|CI385703.1|CI385703
EST:     TGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCACCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: TGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|86479064|gb|CI121697.1|CI121697
EST:     ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|218494468|gb|FG943637.1|FG943637
EST:     ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTTCTGAT
genomic: ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|88478697|gb|CI415968.1|CI415968
EST:     AAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: AAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|58660469|gb|CK049149.1|CK049149
EST:     ATTACAGAATAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTTCTGAT
genomic: ATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|87031000|gb|CI270148.1|CI270148
EST:     ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|88522470|gb|CI450233.1|CI450233
EST:     ACAGAAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: ACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|88518199|gb|CI445853.1|CI445853
EST:     ATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: ATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|87014168|gb|CI273358.1|CI273358
EST:     ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
EST: gi|86599676|gb|CI253661.1|CI253661
EST:     ATGGCCAGCGTGGTGTTGTTATTACAGGAAAATTCCAGCAAGCCACTGCT                         ATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT
genomic: ATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtccta ... aattttccagATCAATATCCCATATGGGCGTCCTACTGAATTTTCTATATTGGCTGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtcctagaaatcattgtctttgaatttactgttctgaatgtatgccagttagaaaaagggtgcctttataaatttgtgatatatcttttaggtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa