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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttctcataatttcaaatagccaactgtatcatcattgatttgtgttgatgttcttacttataccctgaatgagttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCTGCCAAAACTGAGGAAAATGGCTGGTTTTTCACAGGATGAGGAAATTGAA

Basic information

species Oryza sativa
transcript LOC_Os07g06950.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 21
gtacttctcataatttcaaatagccaactgt-----atcatcattgatttgtgttgatgttcttacttatacc-ctgaatgagttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCTGCCAAAACTGAGGAAAATGGCTGGTTTTTCACAGGATGAGGAAATTGAA
|||||| |||||  ||| ||    | |||||     | | ||  |  ||| | ||    | | || |||  |  ||| |||  || |||||||||||||||||||| ||||| |||||||| |||| ||| |||||||||||||  ||  | ||||   |||| ||||||||||||||||| || ||||||
gtacttttcatagattccaactaactactgtttgacaccctcgatactttattttttgttgcatatttactctactggatggatttttcagGTATGTTGGTAGGCTTTTTGTAAAGGCTTCAGGAAGACCACAGGACATTCTGCTGAAGTTAAGGATGTTGGCAGGTTTTTCACAGGATGATGATATTGAA

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 15
gtacttctcata-atttcaaatagcca------actgtatcatca----ttgatttgtgttgatgttcttacttataccctgaatgagttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCTGCCAAAACTGAGGAAAATGGCTGGTTTTTCACAGGATGAGGAAATTGAA
|||||| ||||| ||| ||| |  |||          ||   |||    ||||||| |  |    |  |||||  |   ||| |||  || |||||||||||||||||||||||||| |||||||| |||| ||| |||||||||||||| || || | ||   |||| ||||||||||| ||||| || ||||||
gtacttttcatacattccaactcaccactatttgtcatacactcaatacttgattttttgttggatatttactcctctactggatggatttttcagGTATGTTGGTAGGCTCTTTGTAAAGGCTTCAGGAAGACCACAGGACATTCTGCCGAAGCTAAAGATGTTGGCAGGTTTTTCACAAGATGATGATATTGAA
















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|27577375|gb|CB000070.1|CB000070
EST:     GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCG                         GTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
genomic: GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCGgtacttctca ... agttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
EST: gi|58667338|gb|CK056024.1|CK056024
EST:     GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCG                         GTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
genomic: GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCGgtacttctca ... agttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
EST: gi|58656552|gb|CK045232.1|CK045232
EST:     CTCTATGATCCTGAAAAGGAACAACTGCG                         GTATG-TGGTAGGCTC-TTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
genomic: CTCTATGATCCTGAAAAGGAACAACTGCGgtacttctca ... agttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
EST: gi|33796382|gb|CF324058.1|CF324058
EST:     GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCG                         GTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
genomic: GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCGgtacttctca ... agttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
EST: gi|58693799|gb|CK082486.1|CK082486
EST:     GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCG                         GTATGTAGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT
genomic: GATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCGgtacttctca ... agttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCT

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: 67 (upstream exon), 73 (downstream exon)
Score: 25

GACCTTAAACCTCTTCCTCTGCCTGACAAGACCAGAGAAGATATATTGCTTTTCTTCAAACTCTATGATCCTGAAAAGGAACAACTGCGgtacttctca ... agttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCTGCCAAAACTGAGGAAAATGGCTGGTTTTTCACAGGATGAGGAAATTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatcattgatttgtgttgatgttcttacttataccctgaatgagttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCTGCCAAAACTGAGGAAAATGGCTGGTTTTTCACAGGATGAGGAAATTGAA
                        ttcttac  putative branch site (score: 25)
                                               ttcttc  putative PPT
                           ttacttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttctcataatttcaaatagccaactgtatcatcattgatttgtgttgatgttcttacttataccctgaatgagttcttcagGTATGTTGGTAGGCTCTTTGTTAAGGCTTCGGGAAAACCTCAGGACATTCTGCCAAAACTGAGGAAAATGGCTGGTTTTTCACAGGATGAGGAAATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG