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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccttttagcatatttggatgcttcatgtttatgtgaaggacacggttgttttgaaatcggttccattccctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCAAACCCTCCAGCAGTAACACATCCTGCTGTGTCTGGTGGAGCTATTGGAT

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 7
gtaagtccttttagcatatttggat------gcttcat----------gtttatg---tgaaggacacggttgttttgaaatcggttccattccctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCAAACCCTCCAGCAGTAACACATCCTGCTGTGTCTGGTGGAGCTATTGGAT
||||||   |  | |||||||||||      |||||||          ||||||    ||   |  || ||||||| |||   |  |    |  | ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||| || |||||||
gtaagtttgtcaatcatatttggatttggctgcttcatatgtacaattgtttataacttgtttggtacagttgtttagaatatgactt--atgtcctttacagCCTTTTCAACCTGCACCAACACCTGTCCCACCTCTGGCTGGGTGGATGTCAAACCCTCCAGCAATAACACATCCTGCTGTGTCTGGTGGTGCCATTGGAT
















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|58653134|gb|CK041814.1|CK041814
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCATGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
EST: gi|29656775|gb|CB653050.1|CB653050
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
EST: gi|58661312|gb|CK049992.1|CK049992
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCATGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
EST: gi|29629469|gb|CB634478.1|CB634478
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCATGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCT
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCT
EST: gi|27334445|gb|CA882896.1|CA882896
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
EST: gi|163918634|gb|EG710316.1|EG710316
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
EST: gi|29656774|gb|CB653049.1|CB653049
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
EST: gi|87023591|gb|CI286342.1|CI286342
EST:     TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCG                         CCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA
genomic: TTGGATCTATACCAAAACCTGGAGGTTTCCCCCCATTGGGTGCTCACGCGgtaagtcctt ... cctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtttatgtgaaggacacggttgttttgaaatcggttccattccctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCAAACCCTCCAGCAGTAACACATCCTGCTGTGTCTGGTGGAGCTATTGGAT
                                     ttccattccctttttc  CT-rich tract
                         ttttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccttttagcatatttggatgcttcatgtttatgtgaaggacacggttgttttgaaatcggttccattccctttttcagCCATTTCAACCTGCACCTACACCTGTCCCACCTCTGGCTGGCTGGATGTCAAACCCTCCAGCAGTAACACATCCTGCTGTGTCTGGTGGAGCTATTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT