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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatatatatcgctcctgcaagagatgccgtttaattttttttatcacagcgcttattacaaaacaagatatcagcgaaactgactattgattcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCAGCTGCACCTGGTGATCTTCTTGCTGTAGAGATCTGCAACCTTGGTCCAC

Basic information

species Oryza sativa
transcript LOC_Os01g55950.1
intron # 1
splice site 3'
intron type U2

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|58689497|gb|CK078184.1|CK078184
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|88399708|gb|CI583442.1|CI583442
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58690055|gb|CK078742.1|CK078742
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCGCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58605516|gb|CK033549.1|CK033549
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58690210|gb|CK078897.1|CK078897
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|88416075|gb|CI594187.1|CI594187
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|700563|gb|D46854.1|D46854
EST:     TCAGTNATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|32947801|gb|BP184373.1|BP184373
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58690901|gb|CK079588.1|CK079588
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58688911|gb|CK077598.1|CK077598
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|88425822|gb|CI571722.1|CI571722
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|88433405|gb|CI594219.1|CI594219
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|88414810|gb|CI604168.1|CI604168
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|88760777|gb|CI770333.1|CI770333
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58695533|gb|CK084220.1|CK084220
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAAGTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
EST: gi|58596156|gb|CK006684.1|CK006684
EST:     TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATT                         ACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA
genomic: TCAGTGATGATAACTCCGCAGATGACATCAAATTCCTGGATCTCACAATTgtaagtatat ... attcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacagcgcttattacaaaacaagatatcagcgaaactgactattgattcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCAGCTGCACCTGGTGATCTTCTTGCTGTAGAGATCTGCAACCTTGGTCCAC
                                              ttcccac  CT-rich tract
        ttattacaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatatatatcgctcctgcaagagatgccgtttaattttttttatcacagcgcttattacaaaacaagatatcagcgaaactgactattgattcccacagACTCATTATCTTAGTGGGCCCTTAAGAATAGTTGATGCTGAAGGGGTTCCAGCTGCACCTGGTGATCTTCTTGCTGTAGAGATCTGCAACCTTGGTCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC