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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g08400.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G017845_T01 (Zea mays), 3'ss of exon 10
---tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
   | | |||  ||  || |||  | || |   |  | |||       |||  |    |   || |   ||||    | ||| |||   | |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||
ttctcctatac-catgttgttttgtttggttctacattgttgaat--cattaaggatgctcaaatttgtttgtatagacttttatggtgttttgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCATGGTTGCGGCTTAAAG

upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 10
tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagt-acattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
   || |      ||  |            ||||  |||      | |  | | |||| |  | |  || |   ||  | | | | || || || |  ||| ||  | || || |||||  |||||||||||||||||||||| ||| |||| |||||||
-gaaagaaaatccttcctccccaccaccctatttctttcacaacaactttgtcttcatcagttgattttatttatacatgatttttttcttcttttcacagGTTACTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG

upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G38640.2 (Glycine max), 3'ss of exon 7
tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
     ||| |   ||||    | |  | ||||     ||| | ||  | |   |  ||||  | |    |   || || ||| | || || |   |  || ||||| ||||| |||||  |||||||||||||||||||||| ||| |  | |||||||
----gtatccttcttatacaatctactttcat---aatctacagtgcttg---catatgacattccccatatataattcaatttctt-ttatgtatatagGTTGTTAACAGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTTAGGCTTAAAG

upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G38640.3 (Glycine max), 3'ss of exon 7
tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG-----------------------------------------
     ||| |   ||||    | |  | ||||     ||| | ||  | |   |  ||||  | |    |   || || ||| | || || |   |  || ||||| ||||| |||||  |||||||||||||||||||||| ||| |  | |||||||                                         
----gtatccttcttatacaatctactttcat---aatctacagtgcttg---catatgacattccccatatataattcaatttctt-ttatgtatatagGTTGTTAACAGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTTAGGCTTAAAGGTATTCAGCCATTAACATGATGCAGAAAGTTTATATTTTTG

upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 6
tacaatatgcaaattatttgttgtgttatc-atttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
              |  || ||||   ||| | ||   |  |||  | ||    |  ||||  | | |  |   || || ||| | || || |  ||  || ||||| ||||| |||||  |||||||||||||||||||||| ||| |  | |||||||
-----------gtatccttcttgtacaatctactttcataatctacagtgcttgcatatgacattcctcatatataattcaatttttttttatgtttatagGTTGTTAACAGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTTAGGCTTAAAG

upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 9
tacaatatgcaaattatttgttgtgttatcatttggttcttctgta-ttgggacctcatgaagt-acattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
   |||   |          |        |  ||  ||   |   |  |  |   ||||    | |  |  |       | ||||| || || || |  ||| ||| | || || |||||  |||||||||||||||||||||| ||| |||| |||||||
--gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttttcatatgttgatttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG

upper sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
       |  |||  | |  || || |  ||||   ||  |||    |   |  ||| |     |||||  |||  |||  ||  || ||||||    || ||  | || ||||| ||| |||||||||||||||||||||||||| || | || ||||
------gtaaaaaagactctttttgcttccattgaattgatcttatgtcacagttcaag-----cattgatggt--tttgctgaatt-ttgttc----agGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG

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|87024665|gb|CI259380.1|CI259380
EST:     TTCTCATTCTTTATGGTCTCCCAAG                         ATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
genomic: TTCTCATTCTTTATGGTCTCCCAAGgtgaaccact ... gttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
EST: gi|3766689|gb|AU030799.1|AU030799
EST:     TGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAG                         ATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
genomic: TGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAGgtgaaccact ... gttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
EST: gi|86481569|gb|CI124202.1|CI124202
EST:     ACTCGTCGATGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAG                         ATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
genomic: ACTCGTCGATGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAGgtgaaccact ... gttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
EST: gi|86478774|gb|CI121407.1|CI121407
EST:     ACTCGTCGATGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAG                         ATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
genomic: ACTCGTCGATGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAGgtgaaccact ... gttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
EST: gi|29681610|gb|CB677885.1|CB677885
EST:     ACTCGTCGATGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAG                         ATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG
genomic: ACTCGTCGATGTGAAGTGACTGCAATTCTCATTCTTTATGGTCTCCCAAGgtgaaccact ... gttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG
                              ttttaat  putative branch site (score: 3)
                                           ttgttctt  putative PPT
                            tattttaatgtgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaatatgcaaattatttgttgtgttatcatttggttcttctgtattgggacctcatgaagtacattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG