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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaacggaggaagtcttgttctttattgctatgacattccaatatgctcgttatcaataatacaaaattaagacattttttctttttttcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG

Basic information

species Oryza sativa
transcript LOC_Os09g32800.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32800.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G817037_T02 (Zea mays), 3'ss of exon 2
aaaaaacggaggaagtcttgttctttat-tgctatgacattccaat----atgctcgttatcaataatacaaaattaagacattttttctttttttcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG
 |    ||   | |  |||| |   ||| |  |||    |||  ||    ||   | || | | |     | ||| ||||     ||   | |||  |||| ||| || |||||||| | ||| |||||||| ||||| ||||||||||| || |||||||| |||||| | |||||||||||||||
tagcgccgtttggaaccttgattcctatgttatatatttttcagattgtgatttcccttctgagtgcccaagaataaaga-----ttatctctttatgtgtgtagGGCTGACAAATGTGTACTGGCATCTTCTGGCTTTCAAGGTGATATTAAGGCTCTGCAGAAGAACCTAGCTGCCAGAGAATTG

upper sequence: LOC_Os09g32800.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074386_T01 (Zea mays), 3'ss of exon 2
aaaaaacggaggaagtctt---gttctttattgctatgacattc-caatatgctcgttatcaataatacaaaattaagacattttttctttttttcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG
||   | | |      |||   | | ||| |  |  |||         |||     || |   |  | |  ||  || | |  || ||| |||    ||| ||| || |||||||| | |||||||||||| ||||| || |||||||| |||||||||||||||||| | |||||||||||||||
aatctatgcataggtgcttagtgctgtttgtaaccttgattcctgtgttatatatattttaggttgtgcccaag-aataaagattctctcttt---atgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG

upper sequence: LOC_Os09g32800.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074386_T02 (Zea mays), 3'ss of exon 2
aaaaaacggaggaagtcttgttctttattgctatgacattccaatatgctcgttatcaataatacaaaattaagacattttttctttttttcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG
              ||  ||||  | |     ||  |  |   ||||     |||         ||| | |||   ||| | |||||      ||| ||| || |||||||| | |||||||||||| ||||| || |||||||| |||||||||||||||||| | |||||||||||||||
--------------gtgctgtttgtaaccttgattcctgtgttatatatattttaggttgtgcccaagaataaag-attctctcttt-----atgtgtagggctgacaaatgtgtactagCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG

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|33804936|gb|CF328345.1|CF328345
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|58599894|gb|CK010422.1|CK010422
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|218499612|gb|FG949767.1|FG949767
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33818104|gb|CF334878.1|CF334878
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|38472549|gb|CF956681.1|CF956681
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33678412|gb|CF306651.1|CF306651
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33660627|gb|CF291594.1|CF291594
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33683337|gb|CF311576.1|CF311576
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|38477362|gb|CF961495.1|CF961495
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|58694905|gb|CK083592.1|CK083592
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|55439808|gb|CV733214.1|CV733214
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33681495|gb|CF309734.1|CF309734
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33683521|gb|CF311760.1|CF311760
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|66915431|gb|CX102279.1|CX102279
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|58593878|gb|CF992186.1|CF992186
EST:     TCCGTCGGATACAACATCCTCAGGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|58678279|gb|CK066966.1|CK066966
EST:     TCCGTCGGATACAACACCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTT
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTT
EST: gi|55413999|gb|CV726375.1|CV726375
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|218497460|gb|FG955186.1|FG955186
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|87023706|gb|CI286457.1|CI286457
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33823301|gb|CF337451.1|CF337451
EST:     TCCGTCGGATACGACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33803800|gb|CF327774.1|CF327774
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|56158103|gb|C73010.2|C73010
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|58667664|gb|CK056350.1|CK056350
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|55412184|gb|CV724560.1|CV724560
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|58674446|gb|CK063132.1|CK063132
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
EST: gi|33818151|gb|CF334904.1|CF334904
EST:     TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCT                         AGTGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC
genomic: TCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGC

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: 66 (upstream exon), 75 (downstream exon)
Score: 64

TGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATACCCGCCTTTCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccg ... tcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctcgttatcaataatacaaaattaagacattttttctttttttcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG
                              cattttttcttttttt  CT-rich tract
       ttatcaataatacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaacggaggaagtcttgttctttattgctatgacattccaatatgctcgttatcaataatacaaaattaagacattttttctttttttcgtgtttagAGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
aaaaaac
- - - - - - - - -ttgttct
- - - - - - - - - - - - - - tgctatg
- - - - - - - - - - - - - - - - - -acattcc
- - - - - - - - - - - - - - - - - - - - - - tatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacaaaa