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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG

Basic information

species Oryza sativa
transcript LOC_Os02g35870.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 9
gtatgtttcctatgc---catgccatgcaaaa---------tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG
||||||||  |  |    || | ||| |||||         ||| | | |  | |||   ||| ||| | | |  ||| |||| ||||||||||||| |||||||  || |||||||| || || ||||| || ||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| || 
gtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttt-tcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 9
gtatgttt--cctatgc-catgccatgcaaaa---tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG
||||||||     |||  |||| ||| || ||   ||  |    |  ||     ||||||| | ||| |||| |||  ||||||||||||| ||||||| ||| || ||||| || || ||||| |||||||| |||||||| ||||| ||||| || |||||||| ||||||||||| || 
gtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatattt-atcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGA

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 9
--------------------gtatgtttcctatgccatgccatgcaaaatccttat---gaccgaaaaaatactaatgtttc-caatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG
                      | ||||  | |   ||     |  ||   |||||   |||     ||      |  |||  | ||  || ||   |||||| ||  | ||||||| ||| ||||||||||| ||||||||| | |||||||||||| | |||||  | || || |||||  | ||| | || || |||
aaatgctttgaatgatcagaaaaggtttgatgtttgattgatcgttaatatcttattcagacttgttaaccttggagatttggctattttgattatccagGCCAATTCTGCACAAATATGCCAACGAAGATGTGTCACTTGGTGCCTGGTTTATTGGTCTCGAAGTTGAGCACATAGATGATCGCAACTTATGTTGTGGG

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|58666495|gb|CK055181.1|CK055181
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST: gi|163922994|gb|EG712767.1|EG712767
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST: gi|29682555|gb|CB678830.1|CB678830
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST: gi|58666808|gb|CK055494.1|CK055494
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcaaaatccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG
                          tactaat  putative branch site (score: 1)
                                              ttttgtc  putative PPT
                    aaaaaatactaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC