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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA

Basic information

species Oryza sativa
transcript LOC_Os01g56670.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 13
---------tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
         |     | |   |       |  ||   |||  | |||  |||||| || |  ||| |||||||| ||   |||||||| ||  |    || ||| ||||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||
atctagaagtgcactcttttttgggacagagggcgtaaataca-tgc-cattttcctttatttatcctctattgctg---aaatctaactacct----gcacataccagGTCAAGTATCTCTGGCTTCTTTTTGATTTAGCTGCTGGCCCTGACAATATTGTTGAAAATGGACCATATAA

upper sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 13
tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctatt-gttggttaaatctaattaattattagcgcatt--ccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
   |  | | || |     |    |    || |  ||  | ||| |      ||||| | ||||     |  ||||     || | |     ||       ||||||| ||||| |||||||| |||||||| ||||  || ||||| ||| |||| ||||||||||| || ||
--ctaccattaacatttgtcttgcctttcatattttgtct-tttccccccctctattatttatttaaaagaaaaatgctgctactaacctatgctacaattagGTCAAGTATCTGTGGCTTCTGTTTGATTTGGCTGTGGGTCCTGACAATCTTGTGGAAAATGGGCCTTACAA

upper sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 15
tctttgcctaaataaccagcaatgcaacaattta--ctgcatat-tttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
| | |  |||   |        |  |     ||   || | | | |||| ||  | |||  | |    ||   |  || || | || |||   |   |   ||||||| ||| | ||||||||||||||||| ||||| ||  | || ||  ||||||||||||||||||| ||
tgtctttctag-catttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttttcattgat-tattgaactatccacat-tattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA

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|33796226|gb|CF323979.1|CF323979
EST:     AACCCACCAGCAGGATGACCACATGNGAGAGTTTTTTCCTTGCAGAAACA                         GTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
genomic: AACCCACCAGCAGGATGACCACATG-GAGAGTTTTTTCCTTGCAGAAACAgtgagtttat ... cgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
EST: gi|58601755|gb|CK012283.1|CK012283
EST:     AAACCCACCAGCAGGATGACCACATGGAGAGTTTTTTCCTTGCAGAAACA                         GTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
genomic: AAACCCACCAGCAGGATGACCACATGGAGAGTTTTTTCCTTGCAGAAACAgtgagtttat ... cgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
EST: gi|33799597|gb|CF325659.1|CF325659
EST:     AAACCCACCAGCAGGATGACCACATGGAGAGTTTTTTCCTTGCAGAAACA                         GTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
genomic: AAACCCACCAGCAGGATGACCACATGGAGAGTTTTTTCCTTGCAGAAACAgtgagtttat ... cgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
EST: gi|29667977|gb|CB664252.1|CB664252
EST:     ACCACATGGAGAGTTTTTTCCTTGCAGAAACA                         GTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
genomic: ACCACATGGAGAGTTTTTTCCTTGCAGAAACAgtgagtttat ... cgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
                                aattaat  putative branch site (score: 3)
               tattgttggttaaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
-ctttgcc
- - - - -aaataac
- - - - - - - - - -caatgca
- - - - - - - - - - - - - - - - tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgttg