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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

Basic information

species Oryza sativa
transcript LOC_Os06g07630.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 7
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgt---ggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
|| ||| || | ||| |   |||   ||   ||| | |||| | ||     || | |  |||  |||    |||    | |  |  | |||   ||| |||||||||| || ||||| |||||||||||||| || ||||| || ||||||||  ||||||||||||| ||||||||||| ||||| || || || || |||||||
gtcggtctcaacaactt---atgctcaaattgctgaagtttgt-cagtggctttcctcagtaggccatttatcacaactaacgtgttctgtattggtcctctgtagATCCATTCAAGGAAAATGAATGTAAATCCTGATGTCAACTTTGAAGAATTGGCTCGCTCAACTGATGACTTCAACGGAGCACAGCTAAAGGCAGTTTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatt-tgcttttgt---aatccacaagtcatgctttaactaatat-------gtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
|| ||| |||| ||| |   ||||  |||  ||| | |||| |  ||  ||  || |||||    | ||   | |||||     |||| || |        ||   | |||||||| || |||||||||||||| ||||| || ||||| || || |||||  ||||||||||||||||||||||||| ||||| || ||||| || || ||||
gtcggtctccacaactt---atgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 8
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                | || |||||       |||  || ||      | ||| ||||  ||   |  | | |     |  ||   |  | | | | |  |||| || || || || ||||||||  |||||||||| || |||||||| || ||||| || |||||||| ||||||||||| |||||||| ||||||||||
---------------gtttggtgtct------ttaaacttcatctgctgacttgtttttcaaacagaacatttactgactg-ctctcactttgatattt-cagATCCATTCGAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCTCGGTCCACAGATGATTTCAATGGAGCTCAACTGAAGGCTGTTTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctt-taactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                | || | |||  |||  |  | |||  | |  |||||  || | | |  || || |  ||||| |   |   |  |   | ||  ||||| || ||  | |||||||||||  |||| ||||| || ||||||||  | ||||| || |||||||| ||||||| ||| ||||| |||||||| ||||
---------------gtttggtatct--tcaaattttatttgctga--cattt-tttctctga--cagaacttttgcttatgtttttcacattaatatc-atagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
||  || ||    |  | | |    | | |   |  || | | | |       ||| |  |||  ||||| | |      |||| |    ||  ||     ||||||||||||| || ||||||||  ||||||| || || ||||| ||||| || || ||||||||||| ||||||||||| || |||||||| || ||||
gtttgtctctcccatttttcaaacatgaccc-ttggtgataagtaa----aaggctctcataa--cacaactaac---ccaactga---atgaatcc----agATTCACTCAAGGAAGATGAATGTCCACCCAGACGTCAACTTTGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------------------gtaggtttccagaacctgtg-atgtctaatc---agctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatat--gtggttct-ctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                                                                      |   | |||  | || |    | ||||       |  |  | | |||||  |   |  ||| | |     ||   |     |||   |||| |  | | |     |  |||| || ||||| ||||||||||| ||  |||| || |||||||||||||| ||||| ||||| ||||| ||||||||||| ||||| ||||| || ||||
gttctgtatcctttactgcatcttttcttttttctttctttatttctatgtcgttttaaagctaaaattagagagcttcatgcacttagacaagtcttgctgtgattttctatgtattccgcggataacttatcttgggtactgttttgtttttgcataatgttggcgatggggttacagATACATTCAAGGAAAATGAATGTGAATGCAGACGTCAATTTTGAAGAGCTTGCTCGGTCAACGGATGATTTCAATGGAGCTCAACTCAAAGCAGTGTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 8
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
||| || | ||     | |  | |   |       ||  |||  |||  ||     |||| |      |  || |  |    ||   |  | ||  | ||||||| ||||| ||||| |||| |||  | || ||||| ||||||||||| |||||||| || |||||||| |||||||| || |||||||||||||||||||
gtatgtcttcaatgaatattttcttcta------gatcattacacattgatcactctttgcag-----agctcttattgactctttcacattgtatt-tgtagATCCACTCGAGAAAGATGACTGTTCATCCGGATGTCAATTTTGAAGAACTGGCTCGATCCACAGATGATTTCAATGGGGCACAACTGAAAGCTGTTTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 9
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
||  |  |  |    | ||  |   |  ||||  | | |||     |  |||| |   | |  |    || || |  |||     || | |   | | || |||| || ||||| |||||||||||| ||||||| || |||||||| || || ||||| ||||| ||||| ||||||||||| || |||||||| |||||||
gtgagactgtactggcagtagtcctttgtcagaaattttttgcatttatatttaccactcttgt----aaatctt--tttg---gatgttttcctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------gtaggtttc-cagaacctgtgatgtctaatcagctaat-gtttattcatccatttgcttttgtaatccacaagtca-----tgctttaactaatatgt---ggttctct---gtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                                         |    |    | | ||| |  | |  ||| |  |  | ||| | ||||    ||    | |      || | | |        ||| | |||| |     |  | |||   | ||||||| || || ||||||||| |||  || ||||| || ||||| ||| |||||||||||||||||||||| || ||||| ||| |||| ||||| ||| 
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 8
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctct-gtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                                                  || | | ||      |  |     |  ||| |   | |     ||| || | |||||||||| || ||||||| ||| | | | |||||||| ||||| |||||||| ||||| || || ||||||||||| || ||||| || || || || |
-------------------------------------------------gttcgttcttcctcgtc-tagactgtattttgatcgaaagtcttttcgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaata-tgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                                                  || | | ||      |  |     |  ||| |   | | | |  ||   || |||||||||| || ||||||| ||| | | | |||||||| ||||| |||||||| ||||| || || ||||||||||| || ||||| || || || || |
-------------------------------------------------gttcgttcttcctcgtc-tagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG

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|88326087|gb|CI651141.1|CI651141
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|16579058|gb|BI813153.1|BI813153
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88376475|gb|CI535579.1|CI535579
EST:     CATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: CATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|2427528|gb|C71991.1|C71991
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|86435620|gb|CI106853.1|CI106853
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88503132|gb|CI430638.1|CI430638
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|86425443|gb|CI070540.1|CI070540
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88289586|gb|CI522719.1|CI522719
EST:     CTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: CTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88455818|gb|CI524237.1|CI524237
EST:     TGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: TGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88829402|gb|CI074272.1|CI074272
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|86845235|gb|CI340348.1|CI340348
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88510541|gb|CI438047.1|CI438047
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|89168249|gb|CI109453.1|CI109453
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCTAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|163929518|gb|EG709297.1|EG709297
EST:     CATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTT-AAGAGCTG
genomic: CATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|163918277|gb|EG713191.1|EG713191
EST:     AGATTGAGTTTCCTCATCCATCTAAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88967226|gb|CI392181.1|CI392181
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88408828|gb|CI554150.1|CI554150
EST:     TCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: TCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|86873519|gb|CI329897.1|CI329897
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88487321|gb|CI424592.1|CI424592
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88460271|gb|CI529346.1|CI529346
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG
EST: gi|88469152|gb|CI406423.1|CI406423
EST:     AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAA                         ATTCACTCAAGAAAAATGAATNTAAACCCAGATGTGAATTTTGAAGAGCTG
genomic: AGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTG

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: 72 (upstream exon), 75 (downstream exon)
Score: 50

TGCTGACATTCTTGATCCTGCTTTGATGCGATCTGGTCGTTTGGACCGAAAGATTGAGTTTCCTCATCCATCTGAAGAAGCAAGAGCTAGAATCTTGCAAgtaggtttcc ... ttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG
                                aactaat  putative branch site (score: 50)
                                             ttctctgt  putative PPT
                             tttaactaatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT