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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCAGATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATG

Basic information

species Oryza sativa
transcript LOC_Os07g22950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 2
----gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCAGATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATG
    ||||| || |  ||| |  ||    |    | |  | |      |||  || | | ||||| | ||      |  |   |  |||||||||| |||||| |||| ||| | ||||||||||| || ||||| |||||  ||||||| |||||||| ||||||||||||| |||||| || ||||||
gtaggtaatccaagttgaattcgacg--taagtgcattctagtcacctcatcctgca-tccttatatttgggactaaact---tgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG

upper sequence: LOC_Os07g22950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G032699_T01 (Zea mays), 3'ss of exon 2
--------gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCAGATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATG
        ||||| || |  ||| |  ||    |    | |  | |      |||  || | | ||||| | ||      |  |   |  |||||||||| |||||| |||| ||| | ||||||||||| || ||||| |||||  ||||||| |||||||| ||||||||||||| |||||| || ||||||
gtaggtaggtaatccaagttgaattcgacg--taagtgcattctagtcacctcatcctgca-tccttatatttgggactaaact---tgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG
















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|87005263|gb|CI283486.1|CI283486
EST:     ACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAG                         AGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
genomic: ACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAGgtaattcatg ... ctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
EST: gi|88995744|gb|CI037114.1|CI037114
EST:     GTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAG                         AGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
genomic: GTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAGgtaattcatg ... ctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
EST: gi|88402151|gb|CI614994.1|CI614994
EST:     TGTGCTCCAAACAGATAACGTCAATTCTGCCATGATCGCTTGACTAGCAG                         AGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTC-A
genomic: TGTGCTCCAAACAGATAAC-TCAATTCTGC-ATGATCGCTTGACTAGCAGgtaattcatg ... ctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
EST: gi|88244876|gb|CI242727.1|CI242727
EST:     GTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAG                         AGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
genomic: GTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAGgtaattcatg ... ctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
EST: gi|88369768|gb|CI680440.1|CI680440
EST:     GTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAG                         AGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA
genomic: GTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAGgtaattcatg ... ctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCAGATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATG
                              ttctgac  putative branch site (score: 2)
                                           ttctattc  putative PPT
              attatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCAGATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT