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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgctaatttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG

Basic information

species Oryza sativa
transcript LOC_Os03g14260.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 6
---gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgctaatttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
    ||||  |||||   ||  |||| ||||||| || || || |||||   | | |||    |||| ||| |   || || |||    | ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || |
gtgctgctagttgcagtcttccatattttagtttgagaatcatgataaa---atcttttatcattcttatgttctcttcttatggtggtggattgcctcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACATGTGTTTCTCGTTTTGAAAATCTACATCTTGTTG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 6
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgctaattt---gttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
     || |  ||     |    |  | || ||  |||     ||        |   || || |     | | ||    || ||  || |||||| || | |||  ||| |    ||||| ||||| ||||| |||||||| |||||||| ||||||||||| |||||||||||||| || |||||| ||||||||||  |||
--ttatacttaattccacttaggacgaattataaaatatctgaaagcaattgttaaactcttgtggatttgacttcagattttgcatatgaattg-ttgatagGTGATTGTTACTATTGCTGATGAGGATGGGAATTACTTACAAGAAGCTTGGGAGCATATCTTGACCTGTGTTTCCCGATTTGAACATCTACATCTTCTAG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 6
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgcta--atttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
 |  |||  |  | |  |  | ||||  |  || |  ||   |   |||||  |||  || |  |||  ||  | |     || |  |   ||  ||   |||||||  |  | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||| || |||||  ||||||||||  | |
-tttttaa-gttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacatgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 6
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgcta--atttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
 |  ||   | || |  | || | ||  |  || |  ||    | ||||||  |||  || |   ||  ||  | |    ||| |  |   ||  | |  |||||||  |  | ||||| ||||| |||||||||||||| |||||||| ||||| | ||| ||||| |||||||| || |||||  ||||||||||  | |
-tattttaagtattgggtaatgtgttcctggtacctgaactcaatattcagtttttgttgattatattatatgactgaacgtgtcatctgtttattac-tagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgcta--atttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
 |  |||  |  | |  |  | ||||  |  || |  ||   |   |||||  |||  || |  |||  ||  | |    ||| |  |   ||  ||   |||||||  |  | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||| || |||||  ||||||||||  | |
-tttttaa-gttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatgactgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G45360.1 (Glycine max), 3'ss of exon 7
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgctaatttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGA---CCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG---------------------------------------------------
                                                   |  ||   | | | |    |     || ||  || |||||| || | |||  ||| |    || || ||||| ||||| |||||||| |||||||| ||||||||||| ||||    ||   | |         |    |  || ||  |                                                     
--------------------------------------------------actcttgtggatttgacttcag---attttgcatatgaattg-ttgataggtgattgttactatcgctgatgaggatgggaattacttacaagaagcttgggagCATATCTTGAACATCTACATCTTCTAGGAGAAGGGGCCCCACCTGATGCCACATTCTTTACATTTCCTCAAAATGATTCTGAAAAAACAAAACAAGCGAA

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgcttattgcatggt-tttatatattagttttagcataatcataaattcagccttttctgttctcatgctaatttgtt-----gtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
     | |  | |  | | |  || ||| ||    | | ||| ||| |   ||||||||   ||| |   |   | | |      |   ||    ||| |   ||||| |||||   | |||| |||||||| || || || |||||||| || |||||||||||| | || |||||||| ||||||||  | ||||||||| | |
-----tgtcactttttatctcgatgttatttccttcctgatc-taactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgttctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 6
gtgcttattgcatg---gttttatatattagttttagcataatcataaattcagccttt---tctgttctcatgctaatttgttgtggctacgaattgctt-cacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
     ||| |  ||   | |  ||   | | |||||    ||| |  | ||  || |||   ||||   |  || |  |   |||    |     ||| ||  |||||||||  |    ||||||||||||||||| || ||||| || || || ||||| ||||| ||||| ||||| ||||| |||||  || | |||||| | |
-----tatggtgtgagcgataaattcttgaattttaagcaaatgaccattt--gcttttaaatctgaagttgtgattgtgatttggcattctactttgtttgtacagGCAATAGTTACTATTGCAGATGAAGATGGGAACTACTTACAGGAGGCCTGGGAACATATTTTGACATGTGTGTCTCGGTTTGAGCATTTGCATCTCTTGG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S264_74V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------gtgctt-attgcatggtttt-atatat-tagttttagcataatcataaattcagccttttctgttct-catgctaatttgttgtggctacgaat---------tgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
                                             |  || | | |  |   |  | || |  ||||  || ||     |   || |      | | | || || |  ||||| |   |    | |||         | | |||||||||||| | | ||| ||||||||||| || || ||||| || || || ||||||||||| |||||||||||||| || || ||  |||| |||||  | |
gtattgacgcttttatggtcctggctatgttatttacaaacgttttatttgaatacgcgacctccaaatgtacagttgaaggatctcagttgctttatgtacatttttgctacacgagaatttatgaggttctctaatatccactgttacatcacagGCAATTATTTCAATCGCAGATGAAGACGGGAACTACTTACAGGATGCTTGGGAGCATATTTTGACCTGTGTTTCGCGCTTCGAGCATCTTCATCTTATTG

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|572171|gb|D41682.1|D41682
EST:     AAGCCATTAAG                         GCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGG
genomic: AAGCCATTAAGgtttgttcta ... tgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagccttttctgttctcatgctaatttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
                     tgctaat  putative branch site (score: 2)
                                            ttgcttc  putative PPT
                        taatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgctaatttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA