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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattgcttttatgcaagaaagcaaacaatgagcctgctccatcaacatatcatttatctttccatttggtaaaagaaatgcatcttgttttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG

Basic information

species Oryza sativa
transcript LOC_Os02g05630.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G829894_T03 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------tcattgcttttatgcaagaaagcaaa--caatgagcctgctccatcaacatatcatttatctttccatttggtaaaagaaa-tgcatcttgtt-ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG
                                                                                         |  |      |    || || |   |  | || |    ||    |||  | ||||   |     ||  | |  |   ||||  |  | ||| | |||    ||||||||| | ||||| ||||||||||| ||||||||||||||||| |||||||| ||||||||||| | |||  ||
gtttgtcatgcacttatgttttattacggattgtcgggatagtttttcagacctatcatggtttgagggaatatggtggggttgtaaacttgtaataagtgcctaaaaatggggattccatcatttagcaatgtca-tacatcacccacaccccctgtagccatctgaaaacgatttttgctgttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G166035_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------tcattgcttttatgcaagaaagcaaacaatgagcctgct-ccatcaaca-tatcatttatctttcca-----tttggtaaa-----agaaatgcatcttgtt-ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG
                                                                              ||| ||| |   | |   | || || | |  | |   ||| | || | ||||  |||  |||          |||         ||| |  | ||| | |||    ||||||||| | ||||| ||||||||||| |||||||||||||||||||| ||||| ||||||||||| | |||  ||
gtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------tcattgcttttatgcaagaaagcaaacaatgagcctgct-ccatcaaca-tatcatttatctttcca-----tttggtaaa-----agaaatgcatcttgtt-ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG-------------------------
                                                                              ||| ||| |   | |   | || || | |  | |   ||| | || | ||||  |||  |||          |||         ||| |  | ||| | |||    ||||||||| | ||||| ||||||||||| |||||||||||||||||||| ||||| ||||||||||| | |||  ||                         
gtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGGTACCTACAGATGTTACTAAATATC

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 7
-tcattgcttttatgcaagaaagcaaacaatgagcctgctccatcaacatatcatttatctttccatttggtaaaagaaatgcatcttgttttat-ttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG
  | ||   ||||||  |            |    |   ||||  ||  | ||       |   || |   |||   |   |||| ||  |  |  || |||||||| |   | || |||||||| ||||| || |||||||| || |||||||| ||||||||||| |  ||  ||
tgctttagatttatgtcattctttgccttctccctccattcca--aaactttctgcagaatcagcactaattaatttactggcatttttctgaaaattgcagGAGGAAAAGATTGACAGCTCCCTCGAGTTTCTTATCCTTGCCAGTGATGGACTGTGGGATGTTGTCACAAATGAG

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|66916002|gb|CX102850.1|CX102850
EST:     ATGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAT                         GATGAGATTGTCGATAGCTCCCTCGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|29677669|gb|CB673944.1|CB673944
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|163926798|gb|EG715086.1|EG715086
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|5003494|gb|AU068643.1|AU068643
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|29662048|gb|CB658323.1|CB658323
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|29615476|gb|CB620488.1|CB620488
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|29666985|gb|CB663260.1|CB663260
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|163920197|gb|EG714431.1|EG714431
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|29666852|gb|CB663127.1|CB663127
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|33681625|gb|CF309864.1|CF309864
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|568785|gb|D39634.1|D39634
EST:     TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCNTTGAGTTCCTCATCCTTGCTAGCGATGGA
genomic: TTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGA
EST: gi|87019102|gb|CI297303.1|CI297303
EST:     TTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG                         GAGGAGATTGTCGATAGCTCCCTTGACGTTCCTCATCCTTGCTAGCGATGG
genomic: TTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGA-GTTCCTCATCCTTGCTAGCGATGG

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), 67 (downstream exon)
Score: 76

GGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgactta ... ttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatcatttatctttccatttggtaaaagaaatgcatcttgttttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG
                                      tcttgtttt  CT-rich tract
                                     atcttgttttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattgcttttatgcaagaaagcaaacaatgagcctgctccatcaacatatcatttatctttccatttggtaaaagaaatgcatcttgttttatttacagGAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - -ttatgca
- - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - ctgctcc
- - - - - - - - - - - - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatc