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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttaatatttcctagctgaaatgctcaacagatagcaaatttctatacatgtttgtcaactcgcattgcttatttacgtatctttgataacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA

Basic information

species Oryza sativa
transcript LOC_Os08g44280.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
-gtttaatattt--cctagctgaaatgctcaacagatagcaaatttctatacatgtttgtcaactcgcattgcttatttacgtatctttgataacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA
| | || || || | | ||| | ||| ||| |||| | ||||| |||| | ||| || ||| || || ||||||| || |||||||| |||||||| || | |||||||||||||||||||||||||||||||| ||||||||||||||||||||| || | |||| |||
tgccaggcagttatcccagtccacgaagcaagcaggccctatattag-atatttgttgtttaactcattttgcctgttt--gtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA

upper sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttaatatttcctagctgaaatgctcaacagatagcaaatttctatacatgtttgtcaactcgcattgcttatttacgtatctttgat-aacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA
| | | || | | |||| | | | ||| || | || | ||| || || | ||| || |||||| |||| |||||||| ||| ||||||||||| | |||||||| || ||||||| |||||||| || || ||||| |||| ||| || |
-----------------------gtttgttttactttctcttcttgaattagttttgtacattcttcttcttgcttttgaatat--gatgaattttgatagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA
















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|58593894|gb|CF992202.1|CF992202
EST:     CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAG                         GCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
genomic: CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAGgtctcccgta ... acttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
EST: gi|33817247|gb|CF334460.1|CF334460
EST:     CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAG                         GCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTG
genomic: CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAGgtctcccgta ... acttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTG
EST: gi|33814508|gb|CF333118.1|CF333118
EST:     CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAG                         GCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
genomic: CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAGgtctcccgta ... acttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
EST: gi|33817249|gb|CF334461.1|CF334461
EST:     ATGTTGGATCAG                         GCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
genomic: ATGTTGGATCAGgtctcccgta ... acttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
EST: gi|9866234|gb|AU101984.1|AU101984
EST:     CTGGAGAAGCACCTTCAAGCCTGGNATGCGTGCTCTGGATGTTGGATCAG                         GCACAGGGTACCTAACAGCCTT-NTTCGCGATTATGGTTGGCCCAGAAGGG
genomic: CTGGAGAAGCACCTTC-AGCCTGGCATGCGTGCTCTGGATGTTGGATCAGgtctcccgta ... acttcaacagGCACAGGGTACCTAACAG-CTTGCTTCGCGATTATGGTTGGACCAGAAGGG
EST: gi|29689479|gb|CB685754.1|CB685754
EST:     CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAG                         GCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC
genomic: CCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAGgtctcccgta ... acttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatgtttgtcaactcgcattgcttatttacgtatctttgataacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA
                                        tgataac  putative branch site (score: 2)
 ttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatatttcctagctgaaatgctcaacagatagcaaatttctatacatgtttgtcaactcgcattgcttatttacgtatctttgataacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - ctagctg
- - - - - - - - - -aaatgct
- - - - - - - - - - - - - caacaga
- - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttat