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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctgcacactctttgctgcttgttattgttgtgggtctagttttagaaaatccatgaccttgaatattgcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 14
gttcctgcaca-ctctttgctgcttgttattgtt--gtg------ggtctagttttagaa--aatccatgaccttga-----atattgcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG
||||   || | || ||||     | || || ||  |||       | || |||||   |   | ||   ||| |||      | ||| ||||||||||||| |||||||||||||||||   ||| |||||||| || || || ||||||||| | || |||||||||||||||||||||||||||||  ||
gttctaacagaactttttgactgctatttttatttagtgcttcatagcctcgtttttagattgaccctgaaccctgacactagttttgaatttacagGTCTCAGGTGCTCCTGTTGTTGCTACCATATCTCCTAACATAGGCCGAATGGATCACTTGGATAGGAATTCTCCTGCAAAGCCATCTCCTATGCTG

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 16
gttcctgcacactcttt--gctgct--tgttattgt------tgtgggtctagttttagaaaatccatgaccttgaata------ttgcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG
|||||| || |   |||   |||||  | ||||| |        | |   |  |||||||     | |||||    | |      ||| ||||||||||||| |||||||||||||||||  |||| |||||||| || || || ||||||||| | || |||||||||||||||||||||||||||||| ||
gttcctacagaactttttaactgctatttttattttgtgattcatagacttgtttttagattgatcctgacccctgacactaattttggatttacagGTCTCAGGTGCTCCTGTTGTTGCTAGCATCTCTCCTAACATAGGCCGAATGGATCACTTGGATAGGAATTCTCCTGCAAAGCCATCTCCTATACTG
















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|58595855|gb|CK006383.1|CK006383
EST:     CCGACCTTTCGAAGCATTTAGATCGCAATATGAAGGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: CCGACCTTTCGAAGCATTTAGATCGCAATATGAAG-CTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|58679784|gb|CK068471.1|CK068471
EST:     ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|58661141|gb|CK049821.1|CK049821
EST:     TTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCGATTTCTCCTAATATTGGTCGGAT
genomic: TTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGC-ATTTCTCCTAATATTGGTCGGAT
EST: gi|29630452|gb|CB635461.1|CB635461
EST:     ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGGTGTTGCGGGCATGTCTCCTAATATTGGTCGGATG
genomic: ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|29626131|gb|CB631142.1|CB631142
EST:     ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     GCATTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: GCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|29630393|gb|CB635402.1|CB635402
EST:     ACCGACCTTTCGAAGCATTTAGATCGCAATATGATTCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|29625310|gb|CB630321.1|CB630321
EST:     ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
EST: gi|33675602|gb|CF303841.1|CF303841
EST:     ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAG                         GTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG
genomic: ACCGACCTTTCGAAGCATTTAGATCGCAATATGAAGCTTCTTCTATGAAGgttcctgcac ... gcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttgtgggtctagttttagaaaatccatgaccttgaatattgcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG
              tagttttagaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctgcacactctttgctgcttgttattgttgtgggtctagttttagaaaatccatgaccttgaatattgcatttacagGTCTCTGGTGCTCCTGTTGTTGCGGGCATTTCTCCTAATATTGGTCGGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG