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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g56000.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
gtacatttagcattgtc-tttatcaatgcatgcaactagacatattattgttcacagtataataaactg-taattttttcct------------gctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG
  | |    |  || || ||||  |||  |         |||  |  || ||   |||  || |  ||  |||| |||| ||             ||||||||||||||||||||| |||||||||||  | ||||||||||| |||||||| ||||| |||||||| || || || ||||||||||||
-catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgc---tacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG
|||||  |    || |  ||  |||| |||| |  |   ||  || |     |     |   |||    | | |||   ||    ||||||||||| || || ||||| ||||||||| | || |||||||||||||| ||||| || || ||||||||||| || ||  | || |||
gtacaaatctttttctgatt-ccaattcatgtatttctgcactttctcagctatttgct--caaatcacattctttggttgagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtacatttagcat--tgtctttatcaa--tgcatgcaactagacat-atta--------ttgttcacagtataataaactgtaattttttcc------tgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG
                       ||||| |  |||  | | ||||||||  || ||     | || || || |        |  |   |||  |  |  ||| ||   |||||       |  | ||||||||| ||||| || || || |||||||| ||||||||||||||  |||||||||| ||||| || || ||||| ||  | ||||||
gtaaaccattattggtttagcactacatctttcatgatatttttatcaaaatggatttggattgaaattatcaaggtgaactcatgagcagcctccttgactatagacttttctgccttttattgcagTGAAGTGAGTGGAGATAGGGAGGTGCAGCGGACAATGTTGGAGTTATTGAATCAGCTTGATGGCTTTAGCAGTGATGATCGCATAAAG

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------gtacatttagcattg-tctttatcaatgcatgcaactagacatattattgttcaca----gtataataa--actgtaatt---ttttcctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG
                                       | ||||  |   | |   |  |  | ||  |||   |   |  | ||  | | |    ||  | | |    ||| |||   || |  | ||||||||| || ||||| || |||||||||||||| ||||||||||| ||||| |||||||| ||||| || |||||||| ||  | ||||||
gtatctcgtgttctatcttgcaaattagttgctctttacaaatttgacggagatgcattacggtacaaccaatggggagtgctgtttattaaaaagtgttcagtgattgttgttattgtgttattttactacagTGAGGTGAGTGGAGATAGAGAAGTGCAGCGAACAATGTTGGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGTATAAAG

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------gtacatttagcattgtctttatcaatgca---tgcaactagacatatta--ttgttcacagtataataaact-----gtaattt--tttcctgct-------acagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG
                                | |||| | | |  |  ||| |  | | |   | ||  ||      | |  ||| | | | ||| | || ||     || | ||  | | | | |        ||||||||| ||||| ||  | ||||||||| | || ||| |||||||||| |||||||| ||||||||||| ||||| ||| | || || 
gtttgtaatgttctcttcaaagtgtctatacagaacatcttgtagagcgtttttagaggaagggtacacttatcttggtcaaattgattatattatgacaatcttatttgtgacttgatcttcggtttatgttggcagTGAAGTAAGTGGAGATCGTGAAGTGCAGAGAACTATGCTGGAGTTGCTTAATCAGCTGGATGGATTCAGCAGTGATGAGCGCATTAAA

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|3759941|gb|C97199.1|C97199
EST:     TCATTTTTATTGATGAAATTNACGCAATTGGGACAAAGCGTTTTTGATAG                         TTAAGNTAGTGGTTACAGAGAAGT
genomic: TCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTT-GATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGT
EST: gi|29660288|gb|CB656563.1|CB656563
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|88844827|gb|CI022181.1|CI022181
EST:     AAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: AAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29682547|gb|CB678822.1|CB678822
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGTTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|86415268|gb|CI069671.1|CI069671
EST:     ACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|87031011|gb|CI270159.1|CI270159
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|88828977|gb|CI073847.1|CI073847
EST:     GCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: GCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|8859408|gb|AU096726.1|AU096726
EST:     TCATTTTTATTGATGAAATTGNCCGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: TCATTTTTATTGATGAAATTG-ACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|89198421|gb|CI007481.1|CI007481
EST:     ATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29626138|gb|CB631149.1|CB631149
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|8527269|gb|AU092084.1|AU092084
EST:     ATCATTTTTATTGATGAAATTGACGC-ATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29661398|gb|CB657673.1|CB657673
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|94362567|gb|CI052686.1|CI052686
EST:     AATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: AATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|22304809|gb|BQ906031.1|BQ906031
EST:     TCATTTTTATTGATGAAATTGACGCNATTGGAACACAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: TCATTTTTATTGATGAAATTGACGCAATTGGAACA-AAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|88849565|gb|CI089473.1|CI089473
EST:     AAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: AAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29659490|gb|CB655765.1|CB655765
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|86858935|gb|CI275141.1|CI275141
EST:     ACGCCATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29615761|gb|CB620773.1|CB620773
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|11173135|gb|AU164630.1|AU164630
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29615719|gb|CB620731.1|CB620731
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|86593962|gb|CI260191.1|CI260191
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|218495770|gb|FG962501.1|FG962501
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29683382|gb|CB679657.1|CB679657
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29682519|gb|CB678794.1|CB678794
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGTTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|86823621|gb|CI258693.1|CI258693
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29615715|gb|CB620727.1|CB620727
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|89197922|gb|CI117400.1|CI117400
EST:     AAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: AAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29684874|gb|CB681149.1|CB681149
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
EST: gi|29615721|gb|CB620733.1|CB620733
EST:     ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAG                         TGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA
genomic: ATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactagacatattattgttcacagtataataaactgtaattttttcctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG
                                       ttttttcctgctac  CT-rich tract
                      agtataataaactgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT