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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacattttgccctgccagaacaatttatttctggagccttcatgttttggcatatggttgcagcttgtagcatcttgtgccagatccttgttaaaatgcattaacttctgctcattgcttctttagctgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA

Basic information

species Oryza sativa
transcript LOC_Os08g31470.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G150212_T03 (Zea mays), 3'ss of exon 6
gtaacattttgccctgccagaacaatttatttctggagccttcatgtttt--ggcatatggttgcagcttgtagcatcttgtgcca-gatccttgttaaaatgcattaacttctgctcattgcttctttagctgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA
||||     |    |||||  |  |  | |          ||||   |||  ||||| |     | |||  | |||   | | |   ||   || ||   |   ||  | || |  |||  |    | |   ||  |||    |  ||||  ||| |  |||          | || |   ||||||| || |||||| |||||||||||||||||||||||||||||||||| | ||| ||  ||||||| |  ||||| || ||||||||||||||||| ||| |
gtaa----gtaagatgccaataataactgtggtcaagtttttcacactttatggcat-tccccactgctcattgcagtgtttactttgacttttattgtgagatat--atttttcttcaggg----tattattgatatccttatcctcatgtcatctacgtt---------gtaatgtgg-ctgcagAAACTTTTGTCCGAGCTGATGGTGCATTTATACCGTTTGCTGATGACTTTGAAATTGCTAGTGTCAGCACCTCCGTTAAAGGAGTTGGAGTCATTGGTAA

upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G078541_T01 (Zea mays), 3'ss of exon 5
gtaacattttgccctgccagaacaatttatttctggagccttcatgttttggcatatggttgcagcttgtagcatcttgtgcca-gatccttgttaaaatgcattaacttctgctcattgcttctttagctgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA
|||| || |       | | || || ||   ||  |    | ||  || |||||| |     |  ||  |  |    |   |   ||   || ||   ||  ||  |  | |  |||  |  |  ||   | |  | ||  |  ||||  | | | |||| | |               ||||||| || |||||| |||||||||||||||||||||||||||||||||| | |||||| || ||||| |  || || || ||||||||||||||||| |||||
gtaagatgt-------caataataactttggtcaagtttttgcactttatggcat-tccccactcctcatttcggtgttcactttgacttttattgtgatatat--atgtttattcagggtattattga-tattcttta--tcctcatgtcctctatgttgtatgt-----------ggctgcagAAACTTTTGTCCGAGCTGATGGTGCATTTATACCGTTTGCTGATGACTTTGACATTACAAGTGTCAGCACATCGGTTAAAGGAGTTGGAGTCATTGGTGA

upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G18300.1 (Glycine max), 3'ss of exon 4
gtaacattttgccctgccagaacaatttatttctggagccttcatgttttggcatatggttgcagcttgtagcatcttgtgccagatccttgttaaaatgcattaacttct-gctcattgcttctttagctgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA
                                                                    ||| |||    |    ||  ||  || |  | | |    | || ||   ||| | |    ||   |  || | |  ||       ||  ||  ||     |    |||  | ||||||||| ||||| ||||||||||||||||| || || ||||||||||| | ||||||  | | ||||| ||| ||||| |  || |||||||  || |||||
--------------------------------------------------------------------gtaacataa-atttaggagtctaattgatttacttgggttacttgcattttgttccccacgcatgctccttagtcctcgctcgtcatgagtcatg-----atgtgtttcttgtgcagAGACTTTTGTGAGAGCTGATGGTGCATTCATTCCTTTTGCTGATGACTTTGACATGTCCACTGTTACTACTTCAGTGAGGGGTGTTGGAGATATTGGTGA

upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G40700.1 (Glycine max), 3'ss of exon 4
gtaacattttgccctgccagaacaatttatttctggagccttcatgttttggcatatggttgcagcttgtagcatcttgtgccagatccttgttaaaatgcattaacttctgctcattgcttctttagctgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA
                                                                                   |  ||     |   ||   ||  |   | | ||   |||   |  || | | | ||   | |      |  |   | ||| |  |     ||  | ||||||||| ||||| ||||||||||||||||| || || ||||||||||| | ||||||  | | ||||| ||| ||||| |  || |||||||  || |||||
-----------------------------------------------------------------------------------aattcaaacatttcatctcttttcactttcacacccctttcattcctttaaaccaaacatacccttagtcctcact-tgtcatgatatgattcttgtgcagAGACTTTTGTGAGAGCTGATGGTGCATTCATTCCTTTTGCTGATGACTTTGACATGTCCACTGTTACTACTTCAGTGAGGGGTGTTGGAGATATTGGTGA

upper sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 3
gtaacattttgccctgccagaacaatttatttctggagccttcatgttttggcatatggttgcagcttgtagcatcttgtgccagatccttgttaaaatgcattaacttctgctcattgcttctttagctgtcatctaatttt-tcataacatatttgttctgtaacaaatca---ttta----atctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA
                                                                                           | ||||||  | ||  ||   |  |||| ||    ||   |    |||| || ||||  | |        |   |||||| |   |||     || ||||||||||||||| ||||| ||||| ||||| ||||| ||||||||||||| |||||| |  |   | |  || |  || ||||| || ||||  ||||| ||
-------------------------------------------------------------------------------------------gataaaattgacta-ttttgacaaattggtttcccagtaatttgataatcttgtcatctcctgaaccccatagtacaaattacggtttgctgcatttgcagAGACATTTGTGAGAGCGGATGGGGCATTCATACCATTTGCTGATGATTTTGACATGAGCACAATAACAACATTGGTAAAAGGTGTAGGAGAGATAGGAGA

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|58667597|gb|CK056283.1|CK056283
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|58609731|gb|CK037764.1|CK037764
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|58657265|gb|CK045945.1|CK045945
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|58659505|gb|CK048185.1|CK048185
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|29616112|gb|CB621124.1|CB621124
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|58694123|gb|CK082810.1|CK082810
EST:     ATTTATCACAGATGATG-TTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|58678913|gb|CK067600.1|CK067600
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
EST: gi|58602503|gb|CK013031.1|CK013031
EST:     ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAG                         AGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG
genomic: ATTTATCACAGATGATGTTTGGTATGGTATCTATGCGGGAACAAATCCAGgtaacatttt ... taatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA
       taatttttcataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacattttgccctgccagaacaatttatttctggagccttcatgttttggcatatggttgcagcttgtagcatcttgtgccagatccttgttaaaatgcattaacttctgctcattgcttctttagctgtcatctaatttttcataacatatttgttctgtaacaaatcatttaatctgcagAGACATTTGTCAGAGCTGATGGTGCATTTATACCGTTTGCTGATGATTATGACATAACTAGTGTTAATACCTCAGTCAAAGGAGTTGGAGTCATAGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG