Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaagctaacttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgctctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT

Basic information

species Oryza sativa
transcript LOC_Os03g13970.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G078663_T01 (Zea mays), 3'ss of exon 1
-----acaagctaacttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgctctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT--
     | |  ||   |  |   |      | |    ||  ||  |     |  ||   ||   ||  |    |  |  |  | |  || |    ||| |  | |||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| ||   
gggtgagagactggttcttccgggtccattgaa---gcgcagccatgggatcggaggattatgtgaaccactgctttctagtga--cactgatgtttatatgtagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGGT

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G007884_T01 (Zea mays), 3'ss of exon 3
----------------------acaagcta-acttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgc---tctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT--
                      |    ||| | || ||  | | |        ||| |  ||  | |||  |  | |  ||       |  || | |   ||   ||  || || ||| |  |||||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| ||   
gtgtgttttctcttatgtttgcagcttctacagttctagcgcatataatttgttgctatcaatta-attctggtagtgacaaatgaaccactgctttctagtgacactgatatg-tttatatgcagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGGT

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G078663_T02 (Zea mays), 3'ss of exon 1
-----acaagctaacttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgctctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT
     | |  ||   |  |   |      | |    ||  ||  |     |  ||   ||   ||  |    |  |  |  | |  || |    ||| |  | |||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| || 
gggtgagagactggttcttccgggtccattgaa---gcgcagccatgggatcggaggattatgtgaaccactgctttctagtga--cactgatgtttatatgtagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G700055_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------acaagcta-acttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgc---tctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT--
                                                 |    ||| | || ||  | | |        ||| |  ||  | |||  |  | |  ||       |  || | |   ||   ||  || || ||| |  |||||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| ||   
gtgcagttgaccctgacttagtgttgggtgtgttttctcttatgtttgcagcttctacagttctagcgcatataatttgttgctatcaatta-attctggtagtgacaaatgaaccactgctttctagtgacactgatatg-tttatatgcagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGGT

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G147671_T01 (Zea mays), 3'ss of exon 7
--acaagctaacttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgctctttggtctgatgtttaaccaatttgatt---tctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT
  ||  | |  ||| |  |  ||  |  |   |   |   |   |||||   | |||     |    |  ||| |  ||     | | |||||   | |  |||||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| || 
tcacttgttttcttttgtattaatacctatactattac--agttcattt---cttttatcaacatcattatctaacattcccatactctgattatttatatgcagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G180820_T01 (Zea mays), 3'ss of exon 1
----------------------acaagcta-acttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgc---tctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT--
                      |    ||| | || ||  | | |        ||| |  ||  | |||  |  | |  ||       |  || | |   ||   ||  || || ||| |  |||||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| ||   
gtgtgttttctcttatgtttgcagcttctacagttctagcgcatataatttgttgctatcaatta-attctggtagtgacaaatgaaccactgctttctagtgacactgatatg-tttatatgcagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCAGT

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 7
acaagctaacttgtaaagaaa-agctcagcatgcaaagaaacacatttagacat-ttccatgctctttggtct--gatgtttaaccaatttgatt---tctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT
       ||     |||  || ||   | ||        |  |||||   |  | ||  |||  | |   |||   || ||     | | |||||   | |  |||||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||||| | |||||  |||| |||||||| || 
-------aatacacaaaacaatagtctaacaatattgctattacattcccatttcttttatgaacctcattctctaatattcccatactctgattgtttatatgcagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG

upper sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G070550_T01 (Zea mays), 3'ss of exon 1
acaagctaacttgtaaagaaaagc-tcagcatgcaaagaaacacatttagacatttccat--gctctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT
      | ||||||        |  |    |   | |  |   || ||      ||  ||   |    |  ||| |  ||   |  | |  |||| |  |||||||||||||||||||||||||| |||  |  ||| ||| |  |||||||||| |||||||||||||||| | | |||||  |||| |||||||| || 
--cgcttcacttgttttcttttgtattgatacctatactatttcaattcatttcttttatcaacctcattatctaacattcc-catactctatttatatgcagCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACATAACGTTTGTGTCATCTATCCTTAATTCA

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|218485696|gb|FG969920.1|FG969920
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|5055982|gb|AU075361.1|AU075361
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|218483651|gb|FG955547.1|FG955547
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|33657882|gb|CF280496.1|CF280496
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86834663|gb|CI340780.1|CI340780
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|33801681|gb|CF326712.1|CF326712
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88247152|gb|CI247001.1|CI247001
EST:     TGATGCTGCTATGCCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88840672|gb|CI080126.1|CI080126
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCCTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88217668|gb|CI217517.1|CI217517
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88971753|gb|CI388991.1|CI388991
EST:     AGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: AGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|44670518|gb|CR283952.1|CR283952
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|58675750|gb|CK064437.1|CK064437
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|29678148|gb|CB674423.1|CB674423
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88840095|gb|CI079549.1|CI079549
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88841708|gb|CI080964.1|CI080964
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86537394|gb|CI177600.1|CI177600
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88262482|gb|CI366256.1|CI366256
EST:     TGGCAGAGGCTGCTGTAGATGACCAGGAC-TGGCACTAG                         CTCTTCAAATGTCTGTCCA-GACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88830946|gb|CI079380.1|CI079380
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86413292|gb|CI067697.1|CI067697
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86428134|gb|CI073231.1|CI073231
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAAAGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86486706|gb|CI129339.1|CI129339
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86419054|gb|CI053855.1|CI053855
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88245959|gb|CI245808.1|CI245808
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|6449564|gb|AU081506.1|AU081506
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88262261|gb|CI365837.1|CI365837
EST:     GCAGAGGCTTCTGTAGATGACCAGTACTGGGCACTAG                         CTCTTCAAATGTCTTTGCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: GCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA

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: 71 (upstream exon), 74 (downstream exon)
Score: 83

CAGGCTCTTGCAATGTCAATGGAGGAGGGTTCTTCAGGGGCTGCAGCGGCTGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagacatttccatgctctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT
                                            tttctgc  CT-rich tract
                                     aatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaagctaacttgtaaagaaaagctcagcatgcaaagaaacacatttagacatttccatgctctttggtctgatgtttaaccaatttgatttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGAGCAAGGTGTTTGAAGACAGATCATTTGTTACATCCATCCTTAACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - aaagaaa
- - - - - - - -aagaaaa
- - - - - - - - - - - - - agcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaccaa