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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcagttttgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os08g41460.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G885392_T01 (Zea mays), 3'ss of exon 5
gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcag--ttttgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtcttc---acagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG
||||| || |||| |||||        |   |||        |  |    |   || ||||  | |  |    | |   |||  ||| | |||   ||   |     |       ||||||||| ||  |  |  | |||   |  | |||  ||| |    || ||||||  |  |||  |  ||   |||||||||||||  |||||||||| || || ||||| ||||||||||||||||||
gtgagtattatattacatggaactctgg---catgaaaagaatagaaagaggattgcttaaattctcctgatgtcaaatgatc-atgttaatt--acagcacagcccaatgcagctattgttttaggaggaatactattttaattcattaacaactctaag-atgtctaatgcacgttttcttctcttgacagATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG

upper sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 6
gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcagttttgtttatgtgtactaaatactgtgtttatatctaatc--tagatttcgtcttcac-agATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG
                                                                                        |  ||||   | |  | ||   ||     ||| |  | ||| | |  | |   |  |||   |  ||  |||   | ||||   ||    ||   ||||  || ||||||||||| |||||| |||| || ||||||||||||||||| || |||
----------------------------------------------------------------------------------------tttttttcatcctaaaagatagattgaagttgctgcttgca-tatgatatgccttgactt--ttttgcctttgattttaattattatccctctcattcattagGTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAG

upper sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 6
gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcagttttgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtc--ttcac-agATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG
                                                                                       ||  ||||   | |  | ||   ||     ||  | || ||| | |  ||| | |  |||   |  ||  ||||  | ||||     |   |    ||||  || ||||||||||| |||||| |||| || ||||||||||||||||| || |||
---------------------------------------------------------------------------------------gtt-ttttcatcctaaacgatagattgaagttactgtttgca-tatgatttgtcttgactt--ttttgcctttaattttaattcttttcctgctcattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGAG

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|29625905|gb|CB630916.1|CB630916
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTGTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|29662553|gb|CB658828.1|CB658828
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|58595312|gb|CF993620.1|CF993620
EST:     TCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTGGTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTT-TAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|87029164|gb|CI276432.1|CI276432
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|58681495|gb|CK070182.1|CK070182
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTGTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|29683116|gb|CB679391.1|CB679391
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|29684941|gb|CB681216.1|CB681216
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGCTTTGAGATCACATATC
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATC
EST: gi|29663222|gb|CB659497.1|CB659497
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|86505080|gb|CI147713.1|CI147713
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|29615644|gb|CB620656.1|CB620656
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTGTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|33800060|gb|CF325896.1|CF325896
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|29683115|gb|CB679390.1|CB679390
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|25806680|gb|CA762641.1|CA762641
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTGTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|88966192|gb|CI013068.1|CI013068
EST:     TTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|29684942|gb|CB681217.1|CB681217
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|163920678|gb|EG710011.1|EG710011
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
EST: gi|33801003|gb|CF326375.1|CF326375
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGGTTTTGAGATCACATATCTTCTTG
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGG-TTTTGAGATCACATATCTTCTTG
EST: gi|38473511|gb|CF957643.1|CF957643
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTGTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTT
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTT
EST: gi|29662552|gb|CB658827.1|CB658827
EST:     TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACT                         ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA
genomic: TTCAAGATGTTCCTGCTAAATGTTCCAGCAGCAGTTTTAGCTCTGACACTgtgagaatca ... gtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG
                                         tttcgtcttc  CT-rich tract
                        tttatatctaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcagttttgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtcttcacagATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA