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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT

Basic information

species Oryza sativa
transcript LOC_Os01g19450.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G033226_T01 (Zea mays), 3'ss of exon 5
ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgt--tgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
|| | ||| ||| ||||| |||| | | |||||| || | || |||| || | || | | | |||| ||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||| ||||||||||
ttcatccaatcatcctagac-attgctactggcacactc-catgtcttgtcatctgcatattgtcccttatttttggtaaacagctttaatatggtttgtagGTCATCATTGGACCTGCAACAGTTGGAGGAATTCAAGCTGGTGCTTTCAAGATTGGTGATACCGCTGGAACCATTGATAACATAATTCAGTGCAAGCTTT

upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G03700.1 (Glycine max), 3'ss of exon 4
-ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
| | | | ||| | || | | | | ||| | || || | ||| | | || ||| ||||| | ||||| ||||| || ||||||||||| |||||||||||||| ||||| ||||| || ||||| || ||||| ||||| ||||| |||||||| |
gtgagaggagaaatggaaattca---aattaaataaatcaacttcataactaaagagaataggctggaaatactaattttagtggc-gatgatgtgg-tagGTTGTTATTGGGCCAGCCACTGTTGGAGGAATTCAAGCTGGTGCTTTTAAGATAGGTGACACAGCTGGGACAATTGATAACATAATTCATTGCAAGCTCT

upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G36840.1 (Glycine max), 3'ss of exon 6
-ttggtgttggcatgctatttta---ttgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
| | | | ||| | || | | | | | ||| | | || || | || |||||| || || ||| |||||| | ||||| ||||| || ||||||||||| |||||||||||||| ||||| ||||| || |||||||| ||||||||||| ||||| |||||||| |
gtgagaggagaaatggaaattcaaattaaatagatgaacttcatagctaaagagaataggc-tggaaatagta-attttagtgg-----tgatgatgtg-ctagGTTGTTATTGGCCCAGCCACTGTTGGAGGAATTCAAGCTGGTGCTTTTAAGATAGGTGACACAGCTGGAACAATTGACAACATAATTCATTGCAAGCTCT

upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G04000.1 (Glycine max), 3'ss of exon 5
-ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
| || |||| || || | | || | || | | | | | || | | |||||| || ||| | || ||||| | ||||| ||||| ||||||||||| || ||||| |||||||| || |||||||| || |||||||| |||||||| || ||||| |||||||| |
gtgggagttgaaatagatattggtcgact------taatagctat-atagtaacatggaaaa-----actgattttaatg-----ctcttgat-ttgatagGTTGTTATTGGCCCAGCCACAGTTGGAGGCATTCAAGCAGGTGCTTTTAAAATTGGTGACACAGCTGGAACAATTGACAATATAATTCAGTGCAAGCTCT

upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 5
ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
| | || || | | | || | | | | | ||| | ||| ||| | | ||| ||| |||| | |||||||| || || |||||||| || |||||||| || || ||||||||||||||||| ||||| ||||| |||||||| || |||||||| |
-----------------gtgtgttttgtgtgatg-attagctt---cagttaaccgtatggtg--aacttaatttgtgagactgattgaattggttc-agGTTGTTATTGGACCGGCTACTGTTGGAGGTATTCAAGCTGGAGCCTTTAAGATTGGTGATACTGCAGGAACAATTGATAACATTATCCAGTGCAAGCTAT

upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 5
-ttggtgttggcat---gctattttattgcctgccaggcactaacgctg-------acggcggcctgcatgtttctcgtttat-----tttaccaagtaactgttgttgt------------ttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
||||| | || || | ||| | | ||| || || || | | ||||| || || || || ||| | | || || | || |||| || ||||||||||| || |||||||| | |||||||| || || || |||||||| || |||||||| |||||||| || || ||||||||| | |
gttggttataacactaaactgactcattcctcatgatgcagtattcctaggaacttactattgatcgatcttttcttattgatgtgagctttccgagttaatcttcttttactgattggtcattacagGTTATTATTGGACCAGCTACTGTTGGAGGCGTTCAAGCTGGAGCCTTTAAAATTGGTGACACAGCTGGAACTATTGACAATATCATCCAATGCAAGTTGT

upper sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 5
----ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttc-tagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
| | || | | ||| || | || | || | || | |||| | | ||| | || | | | | | | | | || |||| |||| ||||||| ||||| || || ||||| || || |||||||| ||||| |||||||||||||| || || | ||||| || ||||| ||||||||||
gccgtagttgattacctgcagttctgttagcatacaaata--aatg-tgacatcaaac--gatgactttcatcaagtgttcttcattaagaatattctttcacagGTCGTCATTGGCCCAGCCACTGTAGGAGGTATACAGGCTGGTGCATTCAAAATTGGTGATACTGCAGGCACGTTGGACAATATCATTCACTGCAAGCTTT

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|58609317|gb|CK037350.1|CK037350
EST:     CTGAATCAGATACAAAACAACTTATTAGTTATGCACGTGCCAACAACAAG                         GTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAG
genomic: CTGAATCAGATACAAAACAACTTATTAGTTATGCACGTGCCAACAACAAGgtagggatta ... ttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAG
EST: gi|58671643|gb|CK060329.1|CK060329
EST:     CTGAATCAGATACAAAACAACTTATTAGTTATGCACGTGCCAACAACAAG                         GTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTC
genomic: CTGAATCAGATACAAAACAACTTATTAGTTATGCACGTGCCAACAACAAGgtagggatta ... ttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTC
EST: gi|29624997|gb|CB630008.1|CB630008
EST:     CTGAATCAGATACAAAACAACTTATTAGTTATGCACGTGCCAACAACAAG                         GTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAG
genomic: CTGAATCAGATACAAAACAACTTATTAGTTATGCACGTGCCAACAACAAGgtagggatta ... ttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT
                                 aagtaac  putative branch site (score: 2)
 ttgtttct  putative PPT
 tttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtgttggcatgctattttattgcctgccaggcactaacgctgacggcggcctgcatgtttctcgtttattttaccaagtaactgttgttgtttctagGTAATCATTGGACCAGCAACAGTTGGAGGAATCCAAGCTGGTGCTTTCAAGATTGGTGATACTGCTGGAACCATTGACAACATTATTCAATGCAAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT