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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 12
gtatgactcttg-tgcatcttt-ggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
|||  ||| | | ||  ||||| ||||  ||||  |||     |||  | ||| ||  || | |   ||   | ||||||||||||||||||||||| ||||| || |||||| ||||||| || ||||||||||| ||||||||||  ||||| |||||||| ||||| ||||| |
gtacaactttagctgtctcttttggttcttccatttccccattttcagtttctgaaggatgcaagtggaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 11
gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattc-tacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
|||  ||| | |       ||||||  ||||  |||     |||  | ||| ||  || | | ||| | | | |||||||||||||||||||||||||| || || || ||| ||||||| || ||||||||||| ||||||||||  ||||| |||||||| ||||| || ||||
gtacaactttagctgtctcttggttcttccatttccccattttcagtttctgaaggatgcaa-gtggtacatgcagATAGAGGTTGAAGCAGTTGATAGGACAGGAACGTTCATAGGTTCTTTGTGGGAGTCCAAGACCAACATGGGCTCTGTGCTTCTGGAAGCTGGACTTGCCA

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 12
-----gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
       |   |  || || |  || ||||  |  |      |   ||   ||| |||||| |    | |  || | ||||||||||||||| | |||||||||||||| || ||||| || |||||||||||||| |  |||||  ||||   |   || || || |||||||| || |
gtaaatcaattcctttctgaactttaggttcctgtatgctgcttattttattgt-taaata-ttttgtattgtt-tgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 12
-----gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
       |   |  || || |  || | ||  |  |   ||     ||  ||   |||||| |      |  || | ||||||||||||||| | |||||| ||||||| |||||||| || |||||||||||||| |  |||||| ||||   |   || || || ||||||||||| |
gtaaatcaattcctttctgaactttagattcctgtatgcccgcttattttattgttaaatattttttatt--ttttgcagATAGAGGTTGAAACCGTTGATCGAACTGGAACATTCTTGGGATCCTTATGGGAGTCGAGGACCAACGTGGCAATTACACTGCTCGAAGCTGGTCTGGCAA

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 12
----gtatgactcttgtgcat-ctttggttaatccacctccatggcttcgatgtc--taaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
     || |  || | || |  |||   ||  ||||  |       ||   | |   ||||  |||   | | ||| | ||||| ||||| ||  | ||||| |||||||| || ||||| ||||||||||||||||| |  ||||| |||||   |   || || || |||||||| || |
gtaattaggtttcctctgtaaacttaaattcctccatgttgtcaatttttttcttaataaaatatattttttaatttt-cagATTGAGGTAGAGACTGTTGACAGAACTGGAACTTTCTTGGGTTCCTTATGGGAGTCAAGGACCAATATGGCAATTACACTGCTCGAAGCTGGTCTTGCAA

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattct-------acagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
                           ||    ||  |  |||         ||   |  |   |  |||  |  |  || |  |   |    |||||       |||||| || |||||| |||| |||||||| ||||||||||| || || |||||||| || || || || ||||||   || |||||||| ||||| ||||| |
gtcctgcccttctctattaaccttttggttgctctacttagcaaaaaaaaaaaaaaaaggttgctcactttaagctacaagttgtttaagtctattctttcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGGGAATCAAAGACAAATATGGCTGTGGTACTTCTGGAAGCTGGACTGGCGA

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|218501667|gb|FG956183.1|FG956183
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|29622581|gb|CB627592.1|CB627592
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|29674464|gb|CB670739.1|CB670739
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|33795444|gb|CF323592.1|CF323592
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|33793429|gb|CF322594.1|CF322594
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|29623578|gb|CB628589.1|CB628589
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|66916134|gb|CX102982.1|CX102982
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|33795788|gb|CF323763.1|CF323763
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGNAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTG-AAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATG
EST: gi|29627293|gb|CB632304.1|CB632304
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|29631512|gb|CB636521.1|CB636521
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|25800307|gb|CA756268.1|CA756268
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|38565897|gb|CK085350.1|CK085350
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|218500523|gb|FG958817.1|FG958817
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|58679279|gb|CK067966.1|CK067966
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|29644259|gb|CB649266.1|CB649266
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
EST: gi|58692787|gb|CK081474.1|CK081474
EST:     ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAG                         ATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG
genomic: ACGAAGCTATTGCTTTGATGAGGAGGAGAATTCTACAGCGAGATGTGGAGgtatgactct ... gattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
                           gtctaaa  putative branch site (score: 3)
                         atgtctaaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG