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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtaggatttgtttcatttaactatttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG

Basic information

species Oryza sativa
transcript LOC_Os06g04510.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G446253_T01 (Zea mays), 3'ss of exon 13
gtaagagttgcaagttgtaact---ctttcagctgttttcattgtttgtaggatttgtttcatttaactatttttgtc--------atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
|||    ||| |  |  |   |   ||||       ||    |   |||  ||| |||||   | || |  || | ||        |||| |||||||| ||||||||||| ||||||||| |||||||||||||||| ||| |||||
gtagccattgtagttcttttgttcgcttttgaaaacttgacgttcctgtttgatctgttttgct-aattggttctatcttctctctatctgttcagTGGCGAGACAGAGGACACCTTCATTTCTGACCTCTCAGTTGGCCTGGCTACG

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G064302_T03 (Zea mays), 3'ss of exon 14
gtaaga--gttgcaagttgtaactcttt--cagctgttttcattgtttgtagg----------atttgtttcatttaactatt----------tttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG------------------------------------------------
||||        |   |||||  |||||  | ||| |||| |    ||  | |          || |||||   | || | |           ||| | || | |||||||| ||||||||||| |||||||||||||||||||||||||| |||||||||                                                
gtaaacccaccacccattgtagttctttgtccgcttttttgaagacttaaacgttcctatttgatctgttttgctcaattgtccaatcttctctttattatttgttcagTGGCGAGACAGAGGACACCTTCATTGCTGACCTCTCAGTTGGCCTGTCTACGGTACGCTGTCAACTGGTCAAGATACTGTCGAATCGAACGTCTTGCGTA

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G064302_T02 (Zea mays), 3'ss of exon 14
gtaaga--gttgcaagttgtaactcttt--cagctgttttcattgtttgtagg----------atttgtttcatttaactatt----------tttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
||||        |   |||||  |||||  | ||| |||| |    ||  | |          || |||||   | || | |           ||| | || | |||||||| ||||||||||| |||||||||||||||||||||||||| |||||||||
gtaaacccaccacccattgtagttctttgtccgcttttttgaagacttaaacgttcctatttgatctgttttgctcaattgtccaatcttctctttattatttgttcagTGGCGAGACAGAGGACACCTTCATTGCTGACCTCTCAGTTGGCCTGTCTACG

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 14
--------------------------gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtaggatttgtttcatttaactatttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
                           |   |       ||| ||  | | | |  |  | | ||| |||||| |       | || |   |  | |||   |  ||  |||||||| || ||||||||||||||||||||||| ||||||||  |  | || 
gtactgaatgtttcattattcttccctttgtatccatttgttcta-ttttgtgacatactattattctttgtatgtgcacactaatgtgtttcatcttgc--ttattgtagTGGTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 14
gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtaggatttgtttcatttaactatttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
        |    ||| |   |  |     ||| || ||| |||||      |  |   ||| |   | ||| |  |      |||||||| || ||||||||||||||||||||||||||||||||  |  | || 
-------gtatttgttctgttttgtgacattgtatt-attctttgtgcacactaatgtgtttcatcttgtttattgt------agTGGTGAAACTGAGGATACCTTCATTGCTGACCTCTCAGTTGGATTAGCAACT

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ32861 (Selaginella moellendorffii), 3'ss of exon 11
gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtagg--atttgtttcatttaact-atttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
                                 ||| |   ||   |    | ||| ||  | | ||| |    | | | | || ||||||||||||||||||||| |||||||| || ||  | || || ||| | || 
---------------------------gtaaagtttgacgattcacaaaccacttgcttgctgttactgaaacctcttaaccttgcagTGGTGAGACAGAGGATACATTCATTGCAGATCTTGCTGTCGGGCTGGCAACT

upper sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 11
gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtagg--atttgtttcatttaact-atttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
                                 ||| |   ||   |    ||||| ||  | | ||| |    | | | | || ||||||||||||||||||||| |||||||| || ||  | || || ||| | || 
---------------------------gtaaagtttgacgattcacaaaccatttgcttgctgttactgaaacctcttaaccttgcagTGGTGAGACAGAGGATACATTCATTGCAGATCTTGCTGTCGGGCTGGCAACT

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|86873503|gb|CI329881.1|CI329881
EST:     GAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|58692066|gb|CK080753.1|CK080753
EST:     GTTAGAATGTCCCAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|29665937|gb|CB662212.1|CB662212
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|29672229|gb|CB668504.1|CB668504
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|313083969|gb|HO213752.1|HO213752
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|29665934|gb|CB662209.1|CB662209
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|86908642|gb|CI318967.1|CI318967
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|38481164|gb|CF965253.1|CF965253
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|88204137|gb|CI203986.1|CI203986
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|88252254|gb|CI350682.1|CI350682
EST:     GTCCAAGCGTGCTGGATGGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTCCAAGCGTGCTGGAT-GGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|88980790|gb|CI022484.1|CI022484
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|29686058|gb|CB682333.1|CB682333
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|89168755|gb|CI020836.1|CI020836
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|33798085|gb|CF324902.1|CF324902
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|29665935|gb|CB662210.1|CB662210
EST:     GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|89185847|gb|CI047716.1|CI047716
EST:     GTTAGAATGTCCCAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: GTTAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|86843174|gb|CI341340.1|CI341340
EST:     CTGGATGGGGAGTGATGGCAAGCCATAGGGG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: CTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|66928758|gb|CX115606.1|CX115606
EST:     TAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
genomic: TAGAATGTCCAAGCGTGCTGGATGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTAC
EST: gi|88258312|gb|CI360898.1|CI360898
EST:     TGGGGAGTGATGGCAAGCCATAGGAG                         TGGTGAGACAGGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTA
genomic: TGGGGAGTGATGGCAAGCCATAGGAGgtaagagttg ... atcttttcagTGGTGAGACA-GAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcattgtttgtaggatttgtttcatttaactatttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG
                            atttaac  putative branch site (score: 3)
                                     tttttgtcatcttttc  putative PPT
                   atttgtttcatttaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagttgcaagttgtaactctttcagctgttttcattgtttgtaggatttgtttcatttaactatttttgtcatcttttcagTGGTGAGACAGAGGATACCTTCATTGCTGACCTCTCAGTTGGTCTGTCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT