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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaaattccttggtttcttttactgttaggtttgtcatattttatctttaagcctttgtgtgtacttcttatattgagtacatgttttccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAGCAATCAATGCTGTGATATGGGGAGTCGTCGGTACATTTTGGTGGAAGTT

Basic information

species Oryza sativa
transcript LOC_Os08g37600.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g37600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086258_T02 (Zea mays), 3'ss of exon 3
taaaaaattccttggtttcttttactgttaggtttgtcata-----ttttatctttaagcctttgtgtgtacttcttatattgagtac----atgttttccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAGCAATCAATGCTGTGATATGGGGAGTCGTCGGTACATTTTGGTGGAAGTT
        |  || | || ||||| |   |   |  | |||     ||| ||   |||  ||||   | |   |  | |  ||||||     ||||||| || ||||||||||||||||||| ||||| ||||||||||| |||||||||| |||||| |||||||||||||| || |||||||| |  ||| |||| |||||||| ||
--------ttttttgcttgttttagttagatcatccttataggcgctttaataaataaagcttta-atatttgttctgtgctgagtaacctgatgtttttctcgtgcagCGGGGTATGTTGACCTTCCGGATGTATTCAAGCTGGGTTTTATAACAGCCGCAATCAATGCTGTAATTTGGGGAGTTGCTGGTGCATTATGGTGGAAATT

upper sequence: LOC_Os08g37600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G64290.1 (Arabidopsis thaliana), 3'ss of exon 3
taaaaaattccttggtttcttttactgttaggtttgtcata-ttttatctttaagcctttgtgtgtacttcttatattgagtacatgt-tttccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAGCAATCAATGCTGTGATATGGGGAGTCGTCGGTACATTTTGGTGGAAGTT
            |  |  | || | || |     ||  | |  | | ||||||   ||  || | |    ||| |   |  | | ||| |||| || ||||||||| ||||||||||| ||||||||||||||  | || ||    |  ||  | || |||||  | || |||||||| || || || || |||||||| ||
-----------gtattcccattgattgatgaacatgatagagctctctctttatagctaagtctctttaacttttgc-gtttgcttgtgtttctttttgcagCGGGTTATGTTGATCTGCCTGATGTATTCAAGATTGGATTCGTGATGGCGACGATTAATGCGATAATCTGGGGAGTAGTTGGGACTTTCTGGTGGAAATT
















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|27548122|gb|CA767479.2|CA767479
EST:     TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
genomic: TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
EST: gi|88320161|gb|CI671602.1|CI671602
EST:     TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGT
genomic: TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGT
EST: gi|88510472|gb|CI437978.1|CI437978
EST:     CAGTCTCCAGTATACTATGGAG                         CGGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACACCA
genomic: CAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagC-GGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCA
EST: gi|88416753|gb|CI546032.1|CI546032
EST:     TCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
genomic: TCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
EST: gi|29683199|gb|CB679474.1|CB679474
EST:     TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCA
genomic: TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCA
EST: gi|88516762|gb|CI442418.1|CI442418
EST:     CAGTCTGCAGTATACTATGGAGG                         CGGGGTATGTTGATCTTCCTAATGTATTC-AACTGNGGTTTTACAACAGC
genomic: CAGTCTGCAGTATACTATGGA-Ggtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTG-GGTTTTACAACAGC
EST: gi|86838702|gb|CI329185.1|CI329185
EST:     TGGTGCACTGACACATTATAGTAGTGGCCAGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
genomic: TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
EST: gi|29635537|gb|CB640546.1|CB640546
EST:     ATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAAACTGGGTTTTACAACAGCA
genomic: ATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTC-AAACTGGGTTTTACAACAGCA
EST: gi|88847909|gb|CI006095.1|CI006095
EST:     TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
genomic: TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
EST: gi|88450843|gb|CI549929.1|CI549929
EST:     AGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
genomic: AGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
EST: gi|88661034|gb|CI449313.1|CI449313
EST:     TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAG                         CGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG
genomic: TGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAG

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: 75 (upstream exon), 68 (downstream exon)
Score: 25

GTTCCAGCTATACTGTCGGCACTTGCTTTGACATACAATTCAAATCTCTTTGGTGCACTGACACATTATAGTAGTGGGCAGTCTGCAGTATACTATGGAGgtaagttttt ... ccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAGCAATCAATGCTGTGATATGGGGAGTCGTCGGTACATTTTGGTGGAAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttaagcctttgtgtgtacttcttatattgagtacatgttttccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAGCAATCAATGCTGTGATATGGGGAGTCGTCGGTACATTTTGGTGGAAGTT
                                       tgttttcctt  CT-rich tract
                      ttcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaaaattccttggtttcttttactgttaggtttgtcatattttatctttaagcctttgtgtgtacttcttatattgagtacatgttttccttgtgcagCGGGGTATGTTGATCTTCCTGATGTATTCAAACTGGGTTTTACAACAGCAGCAATCAATGCTGTGATATGGGGAGTCGTCGGTACATTTTGGTGGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-aaaaaat
- - - - - - - - - - - tactgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatg