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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttatatttatccttttaacttttgcttccttgaaaaatatccttctagagttctattatgttgacatcttgcctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG

Basic information

species Oryza sativa
transcript LOC_Os02g57510.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G101571_T02 (Zea mays), 3'ss of exon 4
gtattttatatttatccttttaacttttgcttccttgaaaaatatccttctagagttctattatgttgacatcttgcctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG
      || | ||  ||    | | |||||||  ||| || || |   ||||   | ||| |       ||  | | |  || ||||| || ||||||||| | |||||||||||||||||||| || |||||||| |||||||||
-----gtacacttgcccccc-atcctttgcttg-ttgtaagatctgaatctactatcctact-------cacgtggacaaattcagGGGAACGATATGGATACTTCAAGGGGTTTTCTGTCTGGGACCGTGGACAAATTCAAGATG

upper sequence: LOC_Os02g57510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G58170.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatttt-----atatttatccttttaacttttgcttccttgaaaaatatccttctagagttctattatgttgacatcttgcctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG
||||||      |||||| |  |  | |  |||  |   |||   |    |  | | |      |  || |||  |  || |   ||  ||||||||||||||||||| |||||||| ||||| || |||||  |||||   || || | |
gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttct--atgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG
















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|88844227|gb|CI005600.1|CI005600
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|87033084|gb|CI187708.1|CI187708
EST:     TCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: TCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88225322|gb|CI225238.1|CI225238
EST:     ATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: ATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|86252809|gb|CI010291.1|CI010291
EST:     TATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: TATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88240546|gb|CI239708.1|CI239708
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|86259248|gb|CI010549.1|CI010549
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|29677589|gb|CB673864.1|CB673864
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|86594404|gb|CI251276.1|CI251276
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88206344|gb|CI206193.1|CI206193
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88847279|gb|CI011222.1|CI011222
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|89163094|gb|CI099984.1|CI099984
EST:     GCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|86501990|gb|CI144623.1|CI144623
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|86870285|gb|CI319391.1|CI319391
EST:     AACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: AACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|86252311|gb|CI056048.1|CI056048
EST:     TCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: TCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88844063|gb|CI001120.1|CI001120
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|218494842|gb|FG955901.1|FG955901
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GCCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|58690451|gb|CK079138.1|CK079138
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88980662|gb|CI022375.1|CI022375
EST:     CATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: CATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88966184|gb|CI013060.1|CI013060
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88202410|gb|CI201272.1|CI201272
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88832609|gb|CI008205.1|CI008205
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|88902951|gb|CI088489.1|CI088489
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|89197729|gb|CI013719.1|CI013719
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
EST: gi|89180748|gb|CI009656.1|CI009656
EST:     GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATG                         GGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG
genomic: GTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGACCGAATGgtattttata ... cctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttgaaaaatatccttctagagttctattatgttgacatcttgcctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG
                                        tcttgcct  CT-rich tract
      aaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttatatttatccttttaacttttgcttccttgaaaaatatccttctagagttctattatgttgacatcttgcctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG