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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccgtattgggtctgcgggtgctgtgaggaggcaggctgtggatatctctcccttgaggagggtcaaccaggcaatctacctcctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG

Basic information

species Oryza sativa
transcript LOC_Os11g29190.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G156673_T02 (Zea mays), 3'ss of exon 1
cccgtattgggtctgcgggtgctgtgaggaggca-ggctgtggatatctctcccttgaggagggtcaaccaggcaatctacctc--ctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG----------------------
           | |||   || | || | |   |  |||    ||||  ||  | ||  | |     |   |  || ||           |  ||  || |  | || | | |  |  ||  ||    |||  |  ||  | |  || ||  | |   |   | ||||   |   |||| ||   ||                      
-------gtcatgtgcttttgatatgggaaactatagctcaatatatagcttacatgttgggtcgtgagatgtgaaactgttgtgatgtgctgctattgtcttgcagTG-GACCCCGTGAGGAT-GCCACCCGTATTGGTTCCGCTGGTGTTGTGAGGAGGCAGGCCGTGGATATCTCACCCCTGAGGAGGGTGAACCAGGCCATCTAC

upper sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 2
cccgtattgggtctgcgggtgctgtgaggaggcaggctgtggatatctc----tcccttgaggagggtcaaccaggcaatct--------acctcctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTG--AGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG-----
    |||  | | || |    |    |  |  ||  || | |||  | |    |  ||   |    ||||| | ||   |||        |    ||   || |||  |  | |||   |||  | | |         |   || ||  ||      |     |    | | |   | |  |||||   | |   |       
---ttatgtgctatgagatgtcaactataactcaaactattgattacacatgttggctcttgagatgtcaaactggtgttctgtgctgatattgtctttgcagTGGACCACGTGAGGATGCCACCCGTATTGGTTCAGCTGGTGTTGTGAGAAGGCAGGCTGTGGATATCTCACCCCTGAGAAGGGTGAACCAGGCCATCTAC

upper sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP01658 (Chlamydomonas reinhardtii), 3'ss of exon 5
---------------------cccgtattgggtctgcgggtgctgtgaggaggcaggctgtggata-------tctctcccttgaggagggtcaac-caggcaatctacctcctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG
                      | |  |     | |||  | |||      ||| | ||    | |       | | |||  || |     |   | ||||| |||||||| || |||||||| ||| | |||  ||||||| | ||||||||||||||||| |||||||| |||||||||||  | || || |||||||             
tgcacagctccgctatccatggctgcttgccagccgcgactactgcaccccggccgcctactcacaaatcgtctttgtcctctgtgcttcatgtgcacagGCCATCTACCTGCTGACCACTGGCGCCCGCGAGGCCGCCTTCCGCAACATCAAGACCATTGCGGAGTGCCTGGCTGACGAGCTGGTGAACGCTGCCAAGG-------------

upper sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S114_143V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------cccgtattgggtctgcgggtgctgtgaggaggcaggctgtggatatctctcccttgaggagggtca-accaggcaatctacctcctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTG-AGTG-CCTTGCTGACGA------GCTTATTAATGCCGCCAAGG-GCTCATCCAACAG---------------------------------------------
               | | | ||  | ||||   |   | |  ||||| ||   |||     |   |     |   |||   | |||| | |     |  |      || ||   ||    |   ||    |  |     |   || | |  ||||  | |  ||| ||      || |||     ||||    | | |||     |||                                             
gtaggttatctcgaacacttgtttag-ctgcatattggggggagaggcgggggatgggcgcatgggcgggaggagaggttgcaacaggaatttagggttatgcgggatgatgtggggctcgggagctgagaggtcgcggtgggaatgggtacagTGGTCCTCGTGAAGACGCAACGCGTATCGGATCCGCTGGAGTGATCAGGAGGCAGGCCGTGGATATTTCTCCATTGAGGAGGGTGAACCAGGCGATCTAC

upper sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------cccgtattgggtctgcgggtgctgtgaggaggcagg-------ctg--tggatatctctcccttgaggagggtcaaccaggcaatctacctcctcaccactggtgccagGGAGA----GCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG-----
             ||||| |    ||   |       ||||||  ||         |||  |  ||||       |||     |  | ||   |   ||     | |  |    |   ||  | |||     | | |   ||| |  |  ||   ||       | |  ||||  |    | |       |   |||| | | |   |       
gttcggacgcaatcccgtgtgatatc---gaacatcctgaggacacaattctttttctgattaaatattgtcaatttgtctctgagcgacagtgttttcccatacattgcagTGGACCCCGTGAAGATGCCACACGTATTGGATCTGCGGGA--GTTATCAGAAGGCAAGCTG-TGGATATTTCCCCATTGAGGAGGGTTAACCAGGCCATCTAC

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|86423685|gb|CI062446.1|CI062446
EST:     AGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAG                         GGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGA
genomic: AGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcg ... ctggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcccttgaggagggtcaaccaggcaatctacctcctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG
                                    tcctcac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccgtattgggtctgcgggtgctgtgaggaggcaggctgtggatatctctcccttgaggagggtcaaccaggcaatctacctcctcaccactggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - -ggtgctg
- - - - - - - - - - - - - - - ggcaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaggca