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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 15
gtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
||   ||||  |   ||  | || |     | | | | | || ||    |||||  ||   || | ||||| ||| | |||||| ||||||||||| ||||||||||||| ||||| ||||||||||||
gttccctacc-tacactcatgctataccactaggtgttcattctgtcattgttttgttttaatat-atgcacttgttgcagGTCACTCAGGCAGATCTGAAATTGTTCTTTGAGTCTATATGTGGAGAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 5
gtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
||   ||||  |   ||  | || |     | | | | | || || ||||  |||| |   | |  ||||| ||| | |||||| ||||||||||| ||||||||||||| ||||| ||||||||||||
gttccctacc-tacactcatgctataccactaggtgttcattctg-tcattgttctgttttaatatatgcacttgctgcagGTCACTCAGGCAGATCTGAAATTGTTCTTTGAGTCTATATGTGGAGAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 5
gtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
||   ||||  |   ||  | || |     | | | | | || || ||||  |||| |   | |  ||||| ||| |||||||| ||||||||||| | ||||||||||| ||||| ||||||||||||
gttccctacc-tacactcatgctataccactaggtgttcattctg-tcattgttctgttttaatatatgcacttgctacagGTCACTCAGGCAGATCTAAAATTGTTCTTTGAGTCTATATGTGGAGAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 4
gtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
||   ||||  |   ||  | || |     | | | | | || || ||||  |||| |   | |  ||||| ||| | |||||| ||||||||||| | ||||||||||| ||||| ||||||||||||
gttccctacc-tacactcatgctataccactagctgttcattctg-tcattgttctgttttaatatatgcacttgctgcagGTCACTCAGGCAGATCTAAAATTGTTCTTTGAGTCTATATGTGGAGAG

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|86899176|gb|CI298078.1|CI298078
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|87029144|gb|CI276412.1|CI276412
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86495223|gb|CI137856.1|CI137856
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86849377|gb|CI297825.1|CI297825
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|29646834|gb|CB651841.1|CB651841
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|29643786|gb|CB648793.1|CB648793
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|29646833|gb|CB651840.1|CB651840
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86859325|gb|CI278774.1|CI278774
EST:     AGCGT-AGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|218493611|gb|FG968673.1|FG968673
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86495871|gb|CI138504.1|CI138504
EST:     AGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG

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), 72 (downstream exon)
Score: 82

TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
                                            atttgat  putative branch site (score: 82)
                                            atttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA