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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG

Basic information

species Oryza sativa
transcript LOC_Os02g03260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
gtacttccagtgaatgtgcta-atgcaggaatctggtggtttcata-------ggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
|||| |    ||| | | | |  | ||||   |  ||| ||  | |       ||  || | ||| || ||||||||| | ||||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||||||||||||||
gtacctt-gctgagttttccatgtacaggtcacctgtgattgtagaacatgttgggaagcactaatcttctccaattgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G133988_T01 (Zea mays), 3'ss of exon 1
gtactt---ccagtgaatgtgctaatgcaggaatctggt-ggtttcataggacag----gattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
|||| |   | |||   |  ||||  ||  |  | || | ||    || ||   |     |||||||||||||||||  ||| ||||||||| | || ||||||||||||||||||||||||||||||||||| || |||||||||||||| |||||||||||||||  |    ||     || | 
gtaccttgccgagtctttcagctacagctcgcctgtgattggacatattgggtggcgttaattaacctgctccaatttctgt-tagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCCTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCTTATAAGCTGTGCTACATTT

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
gtactt---ccagtgaatgtgctaatgcaggaatctggt-ggtttcataggacag----gattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
|||| |   | |||   |  ||||  ||  |  | || | ||    || ||   |     |||||||||||||||||  ||| ||||||||| | || ||||||||||||||||||||||||||||| ||||| || |||||||||||||| |||||||||||||| ||||||||| |||||||||
gtaccttgccgagtctttcagctacagctcgcctgtgattggacatattgggtggcgttaattaacctgctccaatttctgt-tagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 5
----------gtacttccagtgaatgtgctaatgcaggaatctggtggt--ttcataggacagga--ttaa--cctgct---ccaattgttgtct---------agGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
          ||    |||||   | |  || |  ||  |  |  || |  ||  |  ||||| |  ||    ||||||   | ||||  | |||         |||||||| | |||||||||||||| || || | ||||||||| |||||||||||||| || || ||||| || ||||||||||| |||||| |||| ||| 
ggttcgcttagtttaaccagtttttattttattatagtgaagtattgttcatttgtttgacagaagtttggttcctgctttgctaatttctctctgttacctgcaGGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGCCAATTTGCTACAGGGATTGGTAATACTGATGCTGGCTTTGTGCTGGGAACT-

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 5
----------------gtacttccagtgaatgtgctaatgcaggaatctggtggttt-cataggacaggattaacctgctccaatt-----gttgtct--agGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                    ||    | | | |  | | |||    ||   || ||  || | |   || |   |||   | ||||     |||  ||  |||||||| | |||||||||||||| || || | ||||||||| ||||| |||||||| || || ||||| || |||||||| || |||||| |||| ||||
gtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGTAATACTGATGCCGGCTTTGTGCTGGGAACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gtacttccagtgaatgtg---------ctaatgcaggaatctgg--tggtttcat-aggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
          ||| || || || ||         ||  ||   |||| |||  | |||| || | |   | | | |  || |     | || |  ||||| |  | || || || || || || || | ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||||||| | |||||||
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattat--agGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtacttccagtgaatgtgct-aatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                  |       | ||| || | |||     ||||   |   |||| |  ||  | | |||||  |   | | |     |||| || || |||||||| || || ||||| | |||||| || |||||||| ||||| |||||||| || ||||| ||||||||||||||  |||||||||
gtgcatttctcttgccaaatcattttttaatctgttcaattttttaatcctttatattcacaatacttgttgaacct--ttacactttctcacagGTCCTGCTGGGTACTGACTCCCACACATGTACTGCTGGGGCATTTGGCCAGTTTGCTACTGGAATAGGTAACACCGATGCTGGTTTTGTATTGGGCACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtacttccagtgaatgtgctaatgcaggaatctggtggtttcatagg-acaggattaacctgctccaat---tgttgtc-tagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                  || |||      ||| |    ||  |    | |  |   || ||| | |||  | |        || ||     || ||  |||| ||| | |||||||| || || ||||| | |||||| || |||||||| || || |||||||| || ||||||||||||| ||| ||  | |||||||
gtacatttctcttgccaagtcctttttcaaaatct----atttaaactttttatatctttatatgcacaacacttgttgaaccctatatacattctcacagGTCCTCTTAGGTACTGACTCCCACACATGTACTGCTGGGGCATTTGGCCAGTTCGCTACTGGAATAGGTAACACTGATGCTGCTTTCGTATTAGGCACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------gtacttccagtga-atgtgcta-atgca-ggaatctggtggtttcataggacaggattaacct--gctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                                                                |  | |||     | | | | ||  |  |  | |||   ||||  | |  |      | |   ||| |||| |  ||  |||||||| | || || ||||| || || |||||||||||||| ||||| || |||||||| || || || ||||||||||| || ||| | |||||||| |
gtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgt--agGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 4
gtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtct--agGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                   | |  | |   | || || | |  ||   |  ||   |  || | || |||||||||  |||||||  |||| ||||| || ||||| ||||  |||||||| ||||| ||||| || |||||||| |||||||| |||||||||||  | ||||| ||||
------------------gtgagtctgatctttgatg-tcttgtattgcgtga--gagatggttcagttgttgtctctagGTTCTTTTTGGAACTGACTCGCATACTTGCACCGCTGGAGCGTTTGGACAATTCGCTACTGGAATAGGAAACACCGATGCTGGTTTCATCATGGGAACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 4
gtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtct--agGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                   | |  | |  || || || | |  ||   |  ||   ||  | | || |||||||||  |||||||  |||| ||||| || ||||| |||| ||||||||| ||||| ||||| || |||||||| |||||||| |||||||||||  | ||||| ||||
------------------gtgagtctgatatttgatg-tcttgtattgcgtgagagac--ggttcagttgttgtctctagGTTCTTTTTGGAACTGACTCGCATACTTGCACTGCTGGAGCGTTTGGACAATTCGCTACTGGAATAGGAAACACCGATGCTGGTTTCATCATGGGAACTG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 2
gtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtct--agGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                   | |  | |   | || || | |  ||   |  ||   ||  | | || |||||||||  |||||||  |||| ||||| || ||||| |||| ||||||||| | ||| ||||| || |||||||| |||||||| |||||||||||  | ||||| ||||
------------------gtgagtctgatctttgatg-tcttgtattgcgtgagagac--ggttcagttgttgtctctagGTTCTTTTTGGAACTGACTCGCATACTTGCACTGCTGGAGCGTCTGGACAATTCGCTACTGGAATAGGAAACACCGATGCTGGTTTCATCATGGGAACTG

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|29628818|gb|CB633829.1|CB633829
EST:     GTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG                         GTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAA
genomic: GTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccag ... tgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG
                            gattaac  putative branch site (score: 2)
               tttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG