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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgatgtctttaaaactttaccttcagcttgtttgaattttctggtggtttgttgacttatgcattctatctttctaacacattattatgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGT

Basic information

species Oryza sativa
transcript LOC_Os01g59440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G121820_T01 (Zea mays), 3'ss of exon 3
-tattgatgtctttaaaactttaccttcagc-ttgtttgaattttctggtggtttgttgacttatgcattctatctttctaacacattattatgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGT
 | |   |||  ||  | ||||    |   | |||||    |  | |   | | || |  |  || |||| |||||| |||||||||  ||   ||||| ||||| |||||||||||||  ||||||||||| |||||||||||||| || |||||||||||||| ||||||||
ctttaactgtggtttgaccttttttatggccattgttcttgtaatttta-gctatgctttcacat-cattatatcttgctaacacatggttgcactttgtagGCGTCTCAATGGCAATCATTTGACTGGGCCCATCCCAAGGGAACTCGCTGGAATATCTAGTCTCAAAGTTGT

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 3
-tattgatgtctttaaaact--ttaccttcagcttgtttgaattttctggtggtttgttgacttatgcattctatctttctaacacattattatgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGT
 ||    ||  ||   |  |  |||   |||   |  ||| |  || |     |   || || |   |||| || ||| |||||||||  ||  |||||| |||||||||||||||||||  ||||||||||| ||||||||||||||  | |||||||||||||| ||||||||
ttaactgtggtttggcatttaattatggtcattattcttgtaacttttaactatgctttcacat---cattataccttgctaacacatggttgcgctttgtagGCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGGAATATCTAGTCTCAAAGTTGT
















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|2317317|gb|C22371.1|C22371
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|88241413|gb|CI241262.1|CI241262
EST:     CTGGGACTATACCTCCAACACTTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: CTGGGACTATACCTCCAACAC-TTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|66916421|gb|CX103269.1|CX103269
EST:     CTCCAACACTTGGG-AATT-ACTG-CCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGTGCCAATCCCAATGGAACTGGCCGG
genomic: CTCCAACACTTGGGAAATTAAC-GTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|29642936|gb|CB647943.1|CB647943
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|87018477|gb|CI252231.1|CI252231
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|55440912|gb|CV733769.1|CV733769
EST:     CCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: CCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|87034659|gb|CI189283.1|CI189283
EST:     CCTT-TATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: CCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|86424519|gb|CI063280.1|CI063280
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|87036087|gb|CI189534.1|CI189534
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAAACGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|27577115|gb|CA999809.1|CA999809
EST:     GAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: GAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|88515042|gb|CI442696.1|CI442696
EST:     CAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: CAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|88239634|gb|CI238796.1|CI238796
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATGAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|86492888|gb|CI135521.1|CI135521
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|86424517|gb|CI063278.1|CI063278
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATGAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|89163681|gb|CI100571.1|CI100571
EST:     TGGGACTATACCTCCAACACTTGGGAAATNAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|157652581|gb|EX452215.1|EX452215
EST:     GTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: GTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|8856670|gb|AU093988.1|AU093988
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|11173068|gb|AU164597.1|AU164597
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|11442641|gb|BF430544.1|BF430544
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|24468891|gb|CA305840.1|CA305840
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|86253994|gb|CI058721.1|CI058721
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|3548933|gb|AF074734.1|AF074734
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|86434587|gb|CI105820.1|CI105820
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATNAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|86252357|gb|CI056094.1|CI056094
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|88199587|gb|CI199437.1|CI199437
EST:     TCTGGGACTACACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|218479908|gb|FG956823.1|FG956823
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
EST: gi|88245833|gb|CI245682.1|CI245682
EST:     TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTT                         GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG
genomic: TCTGGGACTATACCTCCAACACTTGGGAAATTAACGTCCCTTGTATTCTTgtaagtttgt ... tgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggtttgttgacttatgcattctatctttctaacacattattatgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGT
                             ttctaac  putative branch site (score: 1)
                                taacacattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgatgtctttaaaactttaccttcagcttgtttgaattttctggtggtttgttgacttatgcattctatctttctaacacattattatgctttgaagGCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGT

- ttgatgt
- - - - - - - - - - - -cttcagc
- - - - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - - -ctggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgttga