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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttcaagctgatttcgtactatgtccgttctcaatatttcgtcagcacctttttctttaacaatatctgatgtttagctatttatctgtctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 6
------gatttcaagctgatttcgtactatgtccgttctcaatat--ttcgtcagcacctttttctttaacaatatctgatgtttagctatttatctgtctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
      || ||||||||  ||| |||  |||||  ||| ||| |    |  |   |  |  ||||||  |||||         | || |||||  ||      ||||| ||| || |||||||  | || || |||||||| ||||||||||||||||| |||| ||| ||||||||||||||||
gtcaatgaattcaagcttgttttgtatcatgtcatttcacaaaaaaactgattgccggcaatttcttctacaatta-------tcagttattt-cctactgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 6
------gatttcaagctgatttcgtactatgtccgttctcaata---tttcgtcagcacctttttctttaacaatatctgatgtttagctatttatctgtctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
      || |||| | |  ||| | |  ||| |  ||| ||| |   | |  |   || |  ||||||   ||||       | | || |||||   | | |  ||||| ||| || |||||||  | ||||| |||||||| ||||||||||||||||| |||| ||| ||||||||||||||||
gtcagtgaattcacgttt-ttttgcatcatgccatttcacaaaaaattctgattgccaacaatttcttctgcaat-------gatcagttatttccttctgta-accagGTCATTGATTGCAAATCTGTCAGCGGCAAACTGTTACAAATCTGAGCATCTAAAGAGACCAGAGAACTGGGCACTAG

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------gatttcaagctgatttcgtactatgtccgttctcaatatttcgtcagcacctttttctttaacaat-atctgatgtttagctatttatctgtctgtac---cagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
                                                                |||| | |||| |||  ||   | | | |  ||||  |  | | |  || |  ||     ||||| || ||| |  |  ||||||   ||  | ||     || || || ||||| ||||||||||| ||||| |||||||| ||||||||| ||| || |||||| || |||||| |||
gtcagacgatcaagctttccttgattgttttattctacttattatataactcaataataatgatattttatgctgtttttttatagtatacttcttcaacttaacat-aatacttgattgcaagacaattatttgaagcctt-ctatttgattgcatctaaatgtagGTCCCTTGTTGCCAACTTATCAGCTGCAAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 3
-----------------------------------------------gatttcaagctgatttcgtactatgtccgttctcaatatttcg-tcagcacctttttctttaacaatatct-gatgtttagctatttatc-tgtctgtac-cagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
                                               | ||| | |||| || |  |  | ||   | | |   |    | ||   || |  || |  |||||| | | || || |  |  || ||    ||   |  ||| || || || || |||||| |||| ||||| |||||||||||||| ||| |||||| ||| || || ||||||||||
gtaagatgatcaaatttttgcgtgtttttttgtctgcctgtgtgtctgtttttatgctgtttccaaatgaagtatatgccctccagcctgatctttacttgattgtaaaacaattttttgaagtcttacatttgattgcatccaaatgcagGTCTCTTGTGGCGAACTTAGCAGCTGCAAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAG

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------gatttcaagctgatttcgtactatgtccgttctcaatatttcgtcagcacctttttctttaacaat-atctgatgtttagctatttatctgtctgtac---cagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
                                                                |||| |  ||  |||   |   | | | |  |||   |  | | |  || |  ||    | |||| || ||| || |  ||||||   ||  | ||     || || || ||||| ||||||||||| ||||| ||||| || ||||||||| ||| || |||||| || |||||| |||
gtcagatgatcaaactttccttgactgttttattctacttattatatgactcaataataattatattttatacttctttttaatagtatacttcttcagcttaacat-aatacttgattgcaaagcaattatttgaagtctt-ctatttgattgcatctaaatatagGTCCCTTGTTGCCAACTTATCAGCTGCAAATTGCTATAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 6
gatttcaagctgatttc---gtactat-gtccgttctcaatatttcgtcagcacctttttctttaacaatatctgatgtttagctatttatctgtctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
| || |    | |||     |    ||  |   |||     ||||  |||| || | |  |   |||  | ||  ||||       | ||||  | | | | || |||||  |||| |||||||| || ||||| |||||||| ||||| ||| ||||||  || || |||||||||||||
gcttcccgtgtcattgtcaagggtcatcatattttcctgtgattttttcagaacatatgccagcaacc-tgtcc-atgtgctctcttctatc-atttatgc-agGTCACTCATTGCCAACTTATCGGCTGCAAATTGCTACAAGTCTGAACATTTGAAGAGGCCTGAAAACTGGGCACTAG

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|84117280|gb|CD151047.1|CD151047
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|27576661|gb|CA999355.1|CA999355
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|300215864|gb|HO088490.1|HO088490
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|163918496|gb|EG710298.1|EG710298
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|38470488|gb|CF954619.1|CF954619
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|88719065|gb|CI742575.1|CI742575
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|88694901|gb|CI738939.1|CI738939
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|55410432|gb|CV722808.1|CV722808
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTG
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTG
EST: gi|58657974|gb|CK046654.1|CK046654
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACCAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|2311475|gb|C27630.1|C27630
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
EST: gi|88729190|gb|CI752700.1|CI752700
EST:     GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG                         ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT
genomic: GAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCT

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), 73 (downstream exon)
Score: 154

GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatc ... tctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcacctttttctttaacaatatctgatgtttagctatttatctgtctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG
                                         tctgtct  CT-rich tract
      tttttctttaacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttcaagctgatttcgtactatgtccgttctcaatatttcgtcagcacctttttctttaacaatatctgatgtttagctatttatctgtctgtaccagATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt