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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgttggggggcttgctggatattgttctgtgctagctgcaatttaatttcttcattgtgcctttggtatagcatattgatgtgagtgatctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGC

Basic information

species Oryza sativa
transcript LOC_Os05g41900.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G073535_T01 (Zea mays), 3'ss of exon 1
ttatgttggggggcttgctggat-attgttctgtgctagctgcaatttaatttcttcattgtgcct-ttggtatagcatattgatgtgagt--gatctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAA---TCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGC
       |      |  ||| || ||   |||||||||| | |    |  ||     ||  | ||     || |||||| |   ||  | |  ||| |  |||| |||  |||||  || |   |  |||||||||||| |  ||||||| || ||   ||||||| ||||||||||||||||||||||||| |||||||||||   
----accgtccttatctctgcatcatctatctgtgctagtttctgcgtgcttctcaaatatttccggcctgtgtagcatgtgactgataatatgattttggcagCTTCTGCATAAGAACAACAAATCAAAAGCTTGATCAGCTCGGTGCCTACAAAACCTCAACAACCAAGTTTCATGTCTGATCTCGACGTCCAGCTTCCATC---

upper sequence: LOC_Os05g41900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G073535_T03 (Zea mays), 3'ss of exon 2
ttatgttggggggcttgctggatattgttctgtgctagctgcaatttaatttcttcattgtgcctttggtatagcatattgatgtgagtgatctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAA---TCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGC-----
                                                                                                                               |||||||| |  ||||||| || ||   ||||||| ||||||||||||||||||||||||| ||||||||||||||     
-------------------------------------------------------------------------------------------------------------------------------gcTTGATCAGCTCGGTGCCTACAAAACCTCAACAACCAAGTTTCATGTCTGATCTCGACGTCCAGCTTCCATCTGCCTTTG
















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|88578112|gb|CI674745.1|CI674745
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88321737|gb|CI672879.1|CI672879
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88345430|gb|CI656088.1|CI656088
EST:     CCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: CCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCG-AAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88335109|gb|CI658116.1|CI658116
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88570561|gb|CI661934.1|CI661934
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88742013|gb|CI765521.1|CI765521
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88851628|gb|CI674830.1|CI674830
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88336029|gb|CI645630.1|CI645630
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|5004472|gb|AU069621.1|AU069621
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88762082|gb|CI771638.1|CI771638
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|95100761|gb|CI692473.1|CI692473
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|58586098|gb|CF984406.1|CF984406
EST:     TCTCGCCTTCCG-CTCGCGTGCGCTCCACCACCGAAAAGAAGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|58592380|gb|CF990688.1|CF990688
EST:     AAAAAGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: AAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88317352|gb|CI628001.1|CI628001
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88340721|gb|CI657213.1|CI657213
EST:     CCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: CCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCG-AAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88308075|gb|CI647902.1|CI647902
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|58587137|gb|CF985445.1|CF985445
EST:     CCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCA-CGAGGAGAAAGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: CCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGA-AAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88342123|gb|CI636481.1|CI636481
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88571462|gb|CI662835.1|CI662835
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|87017183|gb|CI301219.1|CI301219
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88419668|gb|CI686886.1|CI686886
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|33686145|gb|CF314384.1|CF314384
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88576901|gb|CI673440.1|CI673440
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGAACAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|55431355|gb|CV728690.1|CV728690
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|87017263|gb|CI301299.1|CI301299
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCG-AAAAAAGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|95101042|gb|CI692770.1|CI692770
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
EST: gi|88580466|gb|CI697397.1|CI697397
EST:     TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGNNNNNNNGGACAG                         GTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA
genomic: TCCTCTCGCCTTCCGCCTCGCGTGCGCTCCACCACCGAAAAAAAGGACAGgtattcccct ... atctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttcttcattgtgcctttggtatagcatattgatgtgagtgatctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGC
                               tattgat  putative branch site (score: 3)
                              atattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgttggggggcttgctggatattgttctgtgctagctgcaatttaatttcttcattgtgcctttggtatagcatattgatgtgagtgatctgtgcagGTTCCACATAAAGACCAACGAGTAAAAGCTTGATCTGTCCGGTGCCAACCAATCAACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT