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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcattttcaattagtcatcttcagaagtccaggaaactatcctccgcattaatcatattagttaatactgttgttatgttgatcactttgtctactagGTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g25189.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25189.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G473533_T06 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------tctcattttcaa---ttagtcatcttcagaagtccagg-----aaactatcct-----ccgcat---taatcata--------ttagttaatactg----ttgttatgttgatcactttgtctactagGTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA
                                                                       |||  | | |||    | || ||  |   |||  || |     | | |||        |||  |   | ||   |        |||||||| |  |    || || || |||| ||||||| || ||||||||| |||||||| || ||||||||||| |||| ||||||||||||
gtacttctagaaaactctatattgtgtttgtatataaaactatgactcgcttatttttgacacataagttttcttgtctacaaattcttgttattattgaaagatcaagcaaacagaatatttcactggccgtgtattttattgcaattctcttttagttaacaacgacactttttgtgctgatgactttgtttaatagGTGGTTTGGAGTGCAACTTAATCCTCATTTTATGGAAGTTGACCTCAA
















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|88381595|gb|CI682259.1|CI682259
EST:     AAAAGTTCTTCCTTGAAACCGCATGTCAGTGGGAATTTCATACAAGATTG                         GTGGTTGGGAGTGC
genomic: AAAAGTTCTTCCTTGAAACCGCATGTCAGTGGGAATTTCATACAAGATTGgtacttctaa ... tgtctactagGTGGTTGGGAGTGC
EST: gi|88578322|gb|CI687245.1|CI687245
EST:     AAAAGTTCTTCCTTGAAACCGCATGTCAGTGGGAATTTCATACAAGATTG                         GTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA
genomic: AAAAGTTCTTCCTTGAAACCGCATGTCAGTGGGAATTTCATACAAGATTGgtacttctaa ... tgtctactagGTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA
EST: gi|58679610|gb|CK068297.1|CK068297
EST:     AGTGGGAATTTCATACAAGA-TG                         GTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA
genomic: AGTGGGAATTTCATACAAGATTGgtacttctaa ... tgtctactagGTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA
EST: gi|88392073|gb|CI683901.1|CI683901
EST:     AAAAGTTCTTCCTTGAAACCGCATGTCAGTGGGAATTTCATACAAGATTG                         GTGGTTGGGAG
genomic: AAAAGTTCTTCCTTGAAACCGCATGTCAGTGGGAATTTCATACAAGATTGgtacttctaa ... tgtctactagGTGGTTGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcattaatcatattagttaatactgttgttatgttgatcactttgtctactagGTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA
                                          ctttgtct  CT-rich tract
     ttaatcatattagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcattttcaattagtcatcttcagaagtccaggaaactatcctccgcattaatcatattagttaatactgttgttatgttgatcactttgtctactagGTGGTTGGGAGTGCAGCTGAATCCTCATTTCATGGGAGTTGACCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA