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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttggaccaaacttcctgtactcattacacatatagattgccttgacaagaatattttgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCG

Basic information

species Oryza sativa
transcript LOC_Os03g25940.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25940.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G075153_T01 (Zea mays), 3'ss of exon 4
------------------gtaagtgtttggaccaaacttcctgtactcattacacatatagatt-gccttgacaagaatattttgt--------tttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCG
                  || |||   |  ||  || | | | | ||||||| |  | |  ||| ||  | |||||| ||||   |        ||   ||||||||||||| ||| ||||||||||||||||| ||||||||||||| || || || |||||||||||||||||||||||||| |||
attgctggacacaatgatgtgagttggtatactgaaatccat-ttctcattaaagctgtgtatttgcactaacaagagtattcgatacttcaatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG

upper sequence: LOC_Os03g25940.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G075153_T02 (Zea mays), 3'ss of exon 6
gtaagtgtttggaccaaacttcctgtactcattacacatatagatt-gccttgacaagaatattttgt--------tttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCG
|| |||   |  ||  || | | | | ||||||| |  | |  ||| ||  | |||||| ||||   |        ||   ||||||||||||| ||| ||||||||||||||||| ||||||||||||| || || || |||||||||||||||||||||||||| |||
gtgagttggtatactgaaatccat-ttctcattaaagctgtgtatttgcactaacaagagtattcgatacttcaatttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG

upper sequence: LOC_Os03g25940.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 6
gtaagtgtttggaccaaacttc--ctgtactcattacacatat--------agattgccttgacaagaatattttgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCG
|| |||   |  ||  |||  |  ||   ||||||| |  |||        | |||||  | || || |  ||    ||   ||||||||||||| ||| ||||||||||||||||| | |||||||||||||| || ||||||||||| ||||||||||||||||| |||
gtgagttgatatactgaaccccatctcccctcattaaagttatgtgtttgcacattgcactaactagtac-ttcaacttcccagGTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTGGTTTCCAAAGTCCGTATTTATCACCATGTGGTTGGTGGTGTTCTAAACCCG

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|58695584|gb|CK084271.1|CK084271
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|12622757|gb|AU172970.1|AU172970
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|38478380|gb|CF962513.1|CF962513
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATCGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|29673041|gb|CB669316.1|CB669316
EST:     GTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: GTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|58596991|gb|CK007519.1|CK007519
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCGGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|29660677|gb|CB656952.1|CB656952
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|29625315|gb|CB630326.1|CB630326
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|29671055|gb|CB667330.1|CB667330
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|428295|gb|D24443.1|D24443
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|88397733|gb|CI684672.1|CI684672
EST:     CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: CTGACTTAGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|29639161|gb|CB644170.1|CB644170
EST:     AGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: AGTTATCCATTCAGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
EST: gi|29614166|gb|CB619179.1|CB619179
EST:     AGCAACAAAGTACATTGCTGGGCACAATGAT                         GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC
genomic: AGCAACAAAGTACATTGCTGGGCACAATGATgtaagtgttt ... tgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgtactcattacacatatagattgccttgacaagaatattttgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCG
                            ccttgac  putative branch site (score: 4)
                                          ttttgtttttt  putative PPT
                                 acaagaatattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttggaccaaacttcctgtactcattacacatatagattgccttgacaagaatattttgttttttagGTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG