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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG

Basic information

species Oryza sativa
transcript LOC_Os02g10310.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029566_T02 (Zea mays), 3'ss of exon 5
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
                                                                                           |   || |     | |||||       |  || | |  | ||| | |  | | || |||  | ||| ||    ||||||||||   || | ||||||||||||||||||| ||||||||||| |||||||||||||| || |||||||| ||||||||||| || ||||||||||| ||||||||||   | ||||||||||||||||
-------------------------------------------------------------------------------------------tcaattatgggactagtataggtaactgtggtttatt-tcagtgacaattttctttatt--cactgtat----tatatcataataatt-gctggcttgttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttccc-ctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
                                                                                                  |     | |||||  |    |   | |||  ||||| |||| | | || |||  |  |   ||   |||   | |   |  |||||  ||||||| |||||||| ||||||||||| ||||| |||||||| || ||||| || ||||| |||||||||||||||||||| ||||||||||   | |||||||||||||| |
--------------------------------------------------------------------------------------------------taggactagtataggaaactgtgctttgtt-ttagtgatagttttctttattcactaccttatgtcataatgcttgttggcttgttc-cttgttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAATGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G12100.1 (Glycine max), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
                                                                                                | || |  | ||||| | | ||  |  |   | |||  |    |     |  |||  | |  ||   || ||   | |   |   || | || |||    |||||  | ||||||||||| || |||||||||||||||||| | ||||||||  |||||||||| || |||||||| ||  |  ||||||| ||||||||||
----------------------------------------------------------------------------------------------aatttcttctttgtatatagtttgttctaaatgagttatcttggtactgcattgtttttcatttattttatttaagcttaaaatc--ttagtttattg---gcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTTGATATTAACAATGCTGAAGATCACATCTTTGGACTTGTTGTAATGAACGATTGGAGTG

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G20850.1 (Glycine max), 3'ss of exon 2
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
                                                                                                          ||||| | |     | |   || |   ||||   | ||||  ||     | ||| |||| ||| | ||     |  | | || ||   | |||||  | | ||||||||| || |||||||||||||||||| | ||||||||  ||||| |||| || |||||||| ||  |  |  ||||||| |||||||
----------------------------------------------------------------------------------------------------------gtatatagtt--atcatg-atactgcattatttttcttttgtttcaatttagattaaat-tattaaaa-----tcatagtttatt---tgcagGCTACTAATGTTGGACCGGGAAATGAATTGGGAAAACCTGTGGATATTAACTATGCTCAAGATCACATCTTTGGACTTGTTCTGCTGAATGACTGGAGTG

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G15210.1 (Glycine max), 3'ss of exon 2
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaatta--gttatagatattttcatttcccctggatcaaat-atatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
                                                                                                                         |||| || |||   | |||     || | ||||   ||  |||| | | || | |    |    |      ||  || |||||  | | ||||| ||| || |||||||||||||||||| | ||||||||  |||||||||| || |||||||| ||  |  |  | ||||| |||||||
-------------------------------------------------------------------------------------------------------------------------gtatatatttatcatgatactgcattacttttcttttgtttcaatttagattaaattattaaaatcatagtttatttgcagGCTACTAATGTTGAACCGGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTGAAGATCACATCTTTGGACTTGTTCTGCTCAATGACTGGAGTG

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattc-ttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaat-atatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
||||| || ||    |    |    || | |    |  || ||  | || ||    ||  |    |  |  |    | | ||| |||||  |||     |  ||    | |    | ||    ||  ||    | ||  |  ||| |  ||||   ||  |||  | | || | |    |    |      ||  || |||||  | ||||||||||| || |||||||||||||||||| | ||||||||  ||||| |||| || |||||||| ||  |  | |||||||| |||||||
gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgag--gttaaacattgtttcattttcttctttgtatatagttatcatggtactg-cattatt-tttcatttgtttcattttagattaaattattaaaatcatagtttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG

upper sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0187g00340.t01 (Vitis vinifera), 3'ss of exon 6
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaact-gttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
||||||   | | |  | | || |  |    |||||   | | || ||||  | ||| |  |   | |   || |||||   ||  ||    ||  | || | ||    |     ||| | |||  |  ||  ||| |   |  ||  ||||        | || |||||           | |   || ||||   ||||| || || ||||| || || |||||||| ||||| ||| | ||| ||||||| |||| ||| ||||||||||| ||  |||| |||||||| |||||||
gttagt---tgatatgcatttttatcc----tatttaagaattttaaactcatgattaattttagtatcaaat-tttgtcttat--gatgaatttatcgttactgcacca-gttgtcttgtcgt--gatatgtgttgtctctgattctattt-------gttaattatatg----------gcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCATATCTTTGGACTTGTGATCATGAATGACTGGAGTG

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|29643533|gb|CB648540.1|CB648540
EST:     CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATG                         GCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
EST: gi|88324389|gb|CI566202.1|CI566202
EST:     CTCGACCTTATTTTGGTCCTTCTTCTAAGCTTGATTTTGAACTTGACATG                         GCAGCCATTGTTGGACCACGGAATGAATTGGAAAAAC-TATCGATATTAAT
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
EST: gi|4969133|gb|AU066037.1|AU066037
EST:     CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTNAGATG                         GCAGCCATTGTTGGACCAGGGGATGAATTTGGGAAA
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATT-GGGAAA
EST: gi|27548667|gb|CA766758.2|CA766758
EST:     CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATG                         GCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT
genomic: CTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttct ... ttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG
                        tcataac  putative branch site (score: 2)
                                             ttgctttc  putative PPT
              atcaaatatatcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttcttacaaacctcttgactcacagtatttggtattcttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG