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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT

Basic information

species Oryza sativa
transcript LOC_Os03g16980.5
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 7
--------------------------gtaatatttttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                            ||||||  ||| |||||  ||| |||||  ||||||   |   || || |  || |   | |  |||||||  || ||||| |||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||                             
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatca-tctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
--------------------------gtaatatttttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtat-tttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                            ||||||  ||| |||||  ||| |||||  ||||||   |   || || |  || |  ||  |||   | |||   |||||| |||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||                             
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 5
--------------------------gtaatatttttagttcatacctttttgtcttgtgatgta---ctgga-ttgtagttctcct-taataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                            ||||||  ||| ||||| |  | | | || |||  ||   ||||  || |  || |  | | |  |||||||  || ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||                             
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatca-tctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 8
--------------------------gtaatatttttagttcata--cctttttgtcttgtgatg-tactggattgtagttctccttaataa--gtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                            ||||||  ||| |||||  ||| |||||  ||||||    ||||  |   | | |  ||  |||  ||||||  || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||                             
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtatttatca-tctatgtctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 9
--------------------------gtaatatttttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaata-agtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTA-GGATGAACATTGATGATGGGCGTGTT-----------------------------
                            ||||||  ||| |||||  ||| |||||  ||||||   |   || || |  || |  |    | |||||||  || ||||| |||||||| ||||| |||||||||||||| ||||||||||| |||| ||||||||||||||||||| ||||||                             
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttgacagtatttatca-tctatgtctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 8
-----------------------gtaatatttttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                           || | |||| |||||  ||| ||| |  ||||||   |   || || |  ||   | | |  | |||||   ||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||                             
gtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttat-aatctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 4
---------gtaatatttttagttcatacctttttgtcttgtgatgta---ctgga-ttgtagttctcct-taataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
           ||||||  ||| ||||| |  | | | || |||  ||   ||||  || |  || |  | | |  |||||||  || ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||                             
acttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatca-tctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                                                           |     ||| ||    ||    |  ||| |  || |      ||  ||    | ||   |||||||  || | |||||  ||| || || ||||| || || |||||||| ||||||||  | ||||| ||||||||||||||||||                             
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctct-cagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctc--cttaataagtatt--ttccaatctat---ctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
|||| |||  |   || |      || |||||  |  |  ||  ||    || |   || | ||  ||||  ||| | | | |   |  ||||||||| || || || ||||| |||||||| ||||| ||| | ||||||||||||||||| || |||                             
gtaaaattaatcactcttttaccattttcttgaaaact-ttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatttttagttcat--acctttttgtcttgtgatgtactggatt--gtagttctcctta-ataagtattttccaatctatc-tctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
|| |  ||| || |||    | ||   ||  |     | | ||  ||   ||  |||   | | ||    |||  ||  | | || | |||||| ||||| ||||| || || |||||||| ||||| ||| | |||||||| |||||||||||||||                             
gtcagttttctacttccctaaactcactgcatcacttttttctttatccagtgattcctttaagattctcattggcctgtttgtcatttgtagAAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCG

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------------------------------------------------------gtaatatt-tttagttcatacctttttgtct-----tgtgatgtactggattgtagttctccttaataagtattttccaatc-tatctctgta---gAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
                                                                                          |||| ||| || | | | | ||  |   |||     | |||    ||   ||  | | | |  | |    ||||||  |||  |    || ||   ||||| || ||||||||||| ||||| || ||||||||  | ||||| |||||||| |||||||||                             
gtaaaattgggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactt-tattttgaaatggtgatcctataacagAGATACGGATTGCCAGGATATTCAATACTTATGGACCCCGAATGAATATTGATGACGGGCGTGTTGTCAGCAATTTCATTGCTCAAGCAATTCG

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|58590735|gb|CF989043.1|CF989043
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGATTTGC-AGGATTT-CAACAC-TATGGACCTAGGATGAACCTTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|33380802|gb|CF196145.1|CF196145
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACNNNNNATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATTGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT
                      ccttaat  putative branch site (score: 4)
                                          tctatctct  putative PPT
                        ttaataagtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG