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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggggaattttatctgtttatgatgcctcttgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAACTGGAGAGAAGGATAACAAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g52390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G055276_T03 (Zea mays), 3'ss of exon 2
gtaggggaattt-tat-ctgttt-----atgatgcctct-tgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAAC------TGGAGAGAAGGATAACAAGGAG--
||| ||  | |  |||  |||||     ||  |   ||| || ||  |    || | |     ||    | || ||     ||  ||   ||||||  | |||||  |   |||| | ||||||  ||||||| ||||||||||||| ||||||||| ||||||| ||| |      ||   | || |||||||||||   
gtaaggagactagtatattgtttttagcatagtatttctgtgactatgcctctggaaggtttaattgtac-taatgaagccctctgtgactagggatgcagAGGACTCTCCGAAGATGGAGGAGGCTGCTCCTGTTGCTGAGAAACAAGGTGAGCAGAATGATGCCCCAGCAGCAGATGAGAACAAAGATAACAAGGATGC

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G055276_T02 (Zea mays), 3'ss of exon 2
gtaggggaattt-tat-ctgttt-----atgatgcctct-tgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAACTGGAGAGAAGGATAACAAGGAG
||| ||  | |  |||  |||||     ||  |   ||| || ||  |    || | |     ||    | || ||     ||  ||   ||||||  | |||||  |   |||| | ||||||  ||||||| ||||||||||||| ||||||||| ||||||| ||| | | |||  || | ||  |  | 
gtaaggagactagtatattgtttttagcatagtatttctgtgactatgcctctggaaggtttaattgtac-taatgaagccctctgtgactagGGATGCAGAGGACTCTCCGAAGATGGAGGAGGCTGCTCCTGTTGCTGAGAAACAAGGTGAGCAGAATGATGCCCCAGCAGCAGATGAGAACAAAGATAAC
















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|218486753|gb|FG965219.1|FG965219
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|157652089|gb|EX451723.1|EX451723
EST:     GGTGCAGGNCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGNAAGGTTGAGGAGAGTGCTCCTATTGCTGAGA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTG-AAGGTTGAGGAGAGTGCTCCTATTGCTGAGA
EST: gi|427517|gb|D23584.1|D23584
EST:     GGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|427486|gb|D23553.1|D23553
EST:     GGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTNCTCCTATTGCTGAGAA
genomic: GGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|55409956|gb|CV722332.1|CV722332
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|29686653|gb|CB682928.1|CB682928
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|218490755|gb|FG964437.1|FG964437
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|29614482|gb|CB619495.1|CB619495
EST:     ACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: ACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|300216202|gb|HO087987.1|HO087987
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 57 (upstream exon), 72 (downstream exon)
Score: 90

ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAACTGGAGAGAAGGATAACAAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAACTGGAGAGAAGGATAACAAGGAG
                       agataac  putative branch site (score: 90)
                                      ttattctt  putative PPT
                                      ttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggggaattttatctgtttatgatgcctcttgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAACTGGAGAGAAGGATAACAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG