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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaggctgtattatttcttctttatcatgagaccttcaatgttctaaaattaccacttttcatgtagttcattcatcctctgctcgttatcattttccttcttgaaacatctgcatggttattgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGCTTGTGCCACCTTATGTGTGACCAACCTGATGCTGCACTCAGGGACGCAA

Basic information

species Oryza sativa
transcript LOC_Os10g39670.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G026767_T01 (Zea mays), 3'ss of exon 7
---------------------gtaggaggctgtat-----tatttcttctttatcatgagac----cttcaatgt-----tctaaaattaccacttttcatgtagttcattcatcc-tctgctcgttatcattttccttc--ttgaaacatctg-catggttattgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGCTTGTGCCACCTTATGTGTGACCAACCTGATGCTGCACTCAGGGACGCAA
                      |   | ||| | |     |  | |  |     |  || |     ||  |||||     |  | |         |||  | || || ||| | |   || |       || |    |     |||  | |||  |   ||  ||||| |||||||||| |||||||||| ||||||||| || |||||||  |||||||| ||||||||| ||||||||||||||||||||||||| || ||| | || ||||
gtgggcatgtgcttcttgttcatgaaaagctatttaaaagtgctcccccgccccccagatatatcactcaaatgtagctgtagagagcggggtaatttggtttattttatttacctacctacaatgggacactccaatgtagctgattcttctttccccgtgtttgttgcacagTTTGTCGATGTGGGGATAATGGTGTCACCGACTGTATTCGCCAGACGAAGCTTGTGCTACCTTATGTGTGACCAACCTGATGCGGCCCTCCGTGATGCAA
















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|58597367|gb|CK007895.1|CK007895
EST:     AATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: AATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
EST: gi|11025879|gb|AU162480.1|AU162480
EST:     TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
EST: gi|218489546|gb|FG966243.1|FG966243
EST:     TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
EST: gi|569871|gb|D40720.1|D40720
EST:     TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGGTGGG
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATG-TGGG
EST: gi|88313844|gb|CI597475.1|CI597475
EST:     TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
EST: gi|25803097|gb|CA759058.1|CA759058
EST:     TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
EST: gi|29663195|gb|CB659470.1|CB659470
EST:     TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC
EST: gi|66918229|gb|CX105077.1|CX105077
EST:     TTGCATTTCGAGACCAAAATTTCAAGCCAGCCATAGATTGTTACACTCAG                         TTTGTTGATGTGGGGACCATGGTGTCGCCAACTGTATATGCCAGACGGAGC
genomic: TTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGC

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), 71 (downstream exon)
Score: 8

ATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAGATTGTTACACTCAGgtaggaggct ... tgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGCTTGTGCCACCTTATGTGTGACCAACCTGATGCTGCACTCAGGGACGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgctcgttatcattttccttcttgaaacatctgcatggttattgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGCTTGTGCCACCTTATGTGTGACCAACCTGATGCTGCACTCAGGGACGCAA
                                            ttgtttc  CT-rich tract
         ttatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaggctgtattatttcttctttatcatgagaccttcaatgttctaaaattaccacttttcatgtagttcattcatcctctgctcgttatcattttccttcttgaaacatctgcatggttattgtttcacagTTTGTTGATGTGGGGACAATGGTGTCGCCAACTGTATATGCCAGACGGAGCTTGTGCCACCTTATGTGTGACCAACCTGATGCTGCACTCAGGGACGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC