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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttgtagtgctcaattgttactcagtttaatgcattcttttttttttctagttttgttatattggtctcactgttgccttacgtttttgtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAG

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 4
--tacttgtagt-gctcaattgttactcagtttaatgcattcttttttttttctagttttgttatattggtctcactgttgccttacgtttttgtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAG
  || |||||||  ||  | ||| ||  | | |     |||   | |  | |  | ||    | ||| | |||||| ||| ||||   || ||||||| |||| ||||||||||||||||||||| ||| ||| ||||||||||||| |||||| |||||||||||||| |||||||| || || ||||||||||||||||||
tttagttgtagttacttcactgtgaccaaatatgtcctattgcctgtgctatg-aattcatctgtatggatctcaccgttccctt--tttgttgtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG
















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|29673001|gb|CB669276.1|CB669276
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|218492553|gb|FG956401.1|FG956401
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58661241|gb|CK049921.1|CK049921
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29665502|gb|CB661777.1|CB661777
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|396941261|gb|HO188470.1|HO188470
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGGTG
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCAT-GGTG
EST: gi|58667485|gb|CK056171.1|CK056171
EST:     CCNNNNNNNCTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: CC-AAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|27577056|gb|CA999750.1|CA999750
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58603501|gb|CK014029.1|CK014029
EST:     GTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: GTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58601372|gb|CK011900.1|CK011900
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|218485257|gb|FG950272.1|FG950272
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAAGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|33797209|gb|CF324468.1|CF324468
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58597866|gb|CK008394.1|CK008394
EST:     AAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAACGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
genomic: AAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAA-GGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
EST: gi|58672684|gb|CK061370.1|CK061370
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29627563|gb|CB632574.1|CB632574
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGCGCAAAGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAAGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|13420811|gb|AU174901.1|AU174901
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGNGTTGTCATGGTG
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATG-GTTGTCATGGTG
EST: gi|27576325|gb|CA999019.1|CA999019
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGT-GGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
EST: gi|116875639|gb|EC366147.1|EC366147
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
genomic: ACCAAAAAACTGTCTTTGTCACGGAATGCTCTGTGCACAAAGTGCAAGGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGC
EST: gi|3763799|gb|AU030551.1|AU030551
EST:     CGGAATGCTCTGTGCACAAAGT-NAAGGGG                         TAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG
genomic: CGGAATGCTCTGTGCACAAAGTGCAA-GGGgtaagtatct ... gtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctagttttgttatattggtctcactgttgccttacgtttttgtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAG
                                gccttac  putative branch site (score: 3)
                                        tttttgt  CT-rich tract
     tagttttgttatatt  TA-rich tract