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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttctgttttaacatcccaatcacatgccccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG

Basic information

species Oryza sativa
transcript LOC_Os08g29720.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G106703_T02 (Zea mays), 3'ss of exon 8
gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttct-gttttaacatcccaatcacatgcc-ccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG
|| ||   ||| |||   |||   |    ||     | || | | | ||||   |     |||| ||  |   | ||| |    || ||    ||||          |  ||  ||||| ||    || |   ||| |  |||   | |||    ||| |  | |    |  ||| ||     |||||||||||||  ||||||||||||| ||||| ||||||||||| ||| |||| || |||||
gtttgtgtattatttggtactctgtatacttcacgttcca-ttatttttcacctgttacctgttccttatgcgagcatactctacatatattgccatttcttgtccctctttctattttttttaatttattgccatttctttttcgtgtttctattttttgttccttcctgtttaaat-----ttcagaagGATACTGAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G059018_T01 (Zea mays), 3'ss of exon 8
gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttc-tgttttaacatcccaatcacatgccccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttc-gcattaattatatcatt--tttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG
                    ||| ||  | || ||  | | |   ||||   |    || |||| | || |||  || |     |   |     |||  |   ||||| | | | ||  ||||     || | |||    || | |  || |||||| || ||  | | | |||   |  |   ||||||||||||||  | ||||||||||| ||||| |||||||||||||||||||| || |||||
-------------------gttcgttattattatttggtactctttattattacacttaatgttccatgatttttcaccagctacctgtttttaatgcgggcatatttgtgtgacttcattgc-----tgcatatcgccatt-tcttgttcctgtttctatttttgtacttattcctttctaaatttcagAAGGATACTGAGAAGGCAATGAGGATGACTACAAGGCAAACATTAGCTGAGATATGGAG
















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|33683081|gb|CF311320.1|CF311320
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29661210|gb|CB657485.1|CB657485
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AACGATACGCAAAAGGCAATGAGAATG
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATG
EST: gi|218485410|gb|FG945021.1|FG945021
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG
                                 cattaat  putative branch site (score: 3)
                                            tcatttttc  putative PPT
                                  attaattatatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttctgttttaacatcccaatcacatgccccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG