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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgttttgttttgttttgtaacttacaaatgtcttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT

Basic information

species Oryza sativa
transcript LOC_Os08g02340.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S68_115V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgtttt-----gttttgttttgtaacttacaaatgtcttggttttcctcttatca------gGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACA---GATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT
                                                                  ||| ||  || | | |   ||||  |  |||  |  |    | |||  |||     | |   ||  ||   |  ||| |  |||   |||  | |    |      ||||||| ||||||||||||| || || || |||||||||||| ||||||| ||     ||   |   ||| | ||    || |  ||||||   |||  |   
gtacattcattgctagctgatttgaccataacagcccaaaaatcttactgaatcttcttcatgacaagcaattaattcgaatattttgtcgtggttgctagaatgagtttattcttttacatgctgaattcggtgtgtagcaactaacttttcttttttgtcgaaaaatgaagGAGGAGCCGAAGGAGGAGAGTGATGACGATATGGGTTTCAGCCTGTTCGATTAGATTTTCTTTATCGGATATGAGAAGCTCTGGTTATGCT--ACAATCCGG-

upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S134_153V6.1 (Physcomitrella patens), 3'ss of exon 3
--gtg-agctatacatacaatt-tgcttgttatttttgtcatgacacatgtatgttttgttttgttt-tgtaacttacaaatgtcttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAG--CAGTCCACAGATGTTAGCCAGT-CCGCCTATGCTTTGCAAGACTAT
  ||  || |    ||||||   ||  ||     || | |  | | ||  |  ||||| || |  ||  ||     |    ||  |    ||   |     ||||||||| | ||||| || ||||| || ||||||||||||||||||||||| ||     |      || | |     | | |   ||||||    |  |     
atgtatagtttcctatacaaaaatgggtgacgcattcggcg-gtcgcagattggttttattctaattacgtgctccatttctgcatgaacttgtttt---gcagGAGGAGCCAAAGGAAGAAAGCGATGAAGACATGGGTTTCAGCTTGTTCGATTAGAATTATCTTGTAGGTATAGAGGAATGCTATCTATGCCGATCTTGCG---

upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S28_131V6.1 (Physcomitrella patens), 3'ss of exon 3
-gtgagctatacatacaatttgcttgttatttttgtc-atgacacatgtatgttttgttttgttttgtaacttacaa-atgt-cttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATG-TTAGCCAGTCCGCCT--ATGCTTTGCAAGACTAT
  |  |  |    | | ||     ||     |  | |  || |  || | | |  |  |  |  | || |   | ||  ||| ||| ||     |  |  ||||||||| | ||||| |||||||| ||||||||||| || |||||||| || ||     ||    |    |||  ||   ||  |  ||  |||     |    
acttcgtcacgagttctatcca--tggcgcctccgcctgtgtcggatcttt-tcattctgggcatagttatcaataatgtgttctttgtggcgatgatcgcagGAGGAGCCAAAGGAAGAGAGCGATGATGACATGGGATTTAGCTTGTTTGATTAGATGATCATTTGTCAATTAAACACGACGGATGAATATTTTTTCTCAT---

upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S34_305V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgttttgtt-ttgttttgtaacttacaaatgtcttggttttcctcttatca-----gGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT
                                                             | |  | |  |  | ||||   | ||||   |||   |      | | ||    ||  |  ||   || ||   | |   ||| || | ||  | | |     |||||||   |||||||| ||||||||||||||||| || ||| ||||||| ||                                               
gtacggatagttttgttcattcagtaattatgtgtctaaactagtaaatgcacagcggttataatgttt-taccctatttaaattttatgcatgtttgggtttccgaaggtgagattactacttaccaaattctcactcatttgtttctgctggtgtaactgaagGAGGAGCTAAAGGAGGAAAGCGACGATGACATGGGATTTAGCCTGTTCGATTAG----------------------------------------------

upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ07677 (Selaginella moellendorffii), 3'ss of exon 3
gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgttttgttttgttttgtaacttacaaatgtcttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT
                                    |||| |  ||   || ||  | || | | |    |  || |   ||  |||  ||   | |||||||| ||||| || |||||||| ||||||||||| || ||||||||||| ||                                               
----------------------------------gtatga-atttgggggtgttactctggtctcttggctgaaattaggttt-tttggcttgaaacagGAGGAAGCGAAAGAAGAGAGCGATGATGACATGGGCTTTAGCTTGTTCGATTAG----------------------------------------------

upper sequence: LOC_Os08g02340.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ07730 (Selaginella moellendorffii), 3'ss of exon 3
gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgttttgttttgttttgtaacttacaaatgtcttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT
                                    |||| |  ||   |||||  | || | | |    |  || |   ||  |||  ||   | |||||||| ||||| || |||||||||||||||||||| || ||||||||||| ||                                               
----------------------------------gtatga-atttgggggttttcctctggtctctgggctgaaattaggttt-tttggcttgaaacagGAGGAAGCGAAAGAAGAGAGCGACGATGACATGGGCTTTAGCTTGTTCGATTAG----------------------------------------------

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|88535211|gb|CI463997.1|CI463997
EST:     GCTGCTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: GCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88661157|gb|CI451272.1|CI451272
EST:     CCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCNAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88482705|gb|CI419976.1|CI419976
EST:     CCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGANCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88288178|gb|CI515322.1|CI515322
EST:     CTGCTGCTGGCGGTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CTGCTGCTGGCGGTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88501929|gb|CI429435.1|CI429435
EST:     CTGGCGGTGGTNCTGCTNCTGCCCCAGCTGCCGAGGAGAANAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CTGGCGGTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88255129|gb|CI353953.1|CI353953
EST:     TGGCGGTGGTGCTGCTGCTGCCCCATCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAG
genomic: TGGCGGTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGA-
EST: gi|89170762|gb|CI040039.1|CI040039
EST:     GCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: GCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88488365|gb|CI425636.1|CI425636
EST:     GTGGTNCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: GTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88555580|gb|CI485847.1|CI485847
EST:     CTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88374049|gb|CI510867.1|CI510867
EST:     TGGCGGT-GTGATGCTGCTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: TGGCGGTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88517857|gb|CI444426.1|CI444426
EST:     CTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
EST: gi|88559417|gb|CI489989.1|CI489989
EST:     CTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAG                         GAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC
genomic: CTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGAC

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: 73 (upstream exon), 75 (downstream exon)
Score: 168

GTGGTGGTGCTGCTCCAGTTGCTGCTGCTGCTGCCCCTGCTGCTGGCGGTGGTGCTGCTGCTGCCCCAGCTGCCGAGGAGAAGAAGgtgagctata ... ctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgttttgttttgttttgtaacttacaaatgtcttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT
                      aacttac  putative branch site (score: 168)
                                  tcttggttttcctctt  putative PPT
      ttttgttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctatacatacaatttgcttgttatttttgtcatgacacatgtatgttttgttttgttttgtaacttacaaatgtcttggttttcctcttatcagGAGGAGGCGAAGGAGGAGAGCGACGATGACATGGGTTTCAGCTTGTTCGACTAAGCAGTCCACAGATGTTAGCCAGTCCGCCTATGCTTTGCAAGACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA