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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattctagttggaataagacttgcatgtgtgtgatagacttaatttatgcatgaatattgccggttgtaaacttgacttcacattgatacttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGGTCAATATTATAGAAAAACCTTCAGCTGATAAAAGAGATGCATCAACTGC

Basic information

species Oryza sativa
transcript LOC_Os01g68380.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68380.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G401050_T03 (Zea mays), 3'ss of exon 8
-----------------------------------------------------------------------------------------tattctagttggaataagacttgcatgtgtgtga---tagacttaatttatgcatgaatattgccggttgtaaacttgacttcacattgatacttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGGTCAATATTATAGAAAAACCTTCAGCTGATAAAAGAGATGCATCAACTGC
                                                                                          |   |  || |  ||   ||||||||   ||     |   |||  ||||  |      | |        ||   ||    |  | ||  |   |||||||||||||||| |||||| | |||||||||||||| | | |||||| ||||| ||  | || | |||| |||||||||| |||||||| |||||||||||| | 
gtttatcttctcattccaatctaacacatatatttgttttgagttctcttctccagttaatctgagaaattttcctccagtcaatccttcagagttatttgtttacatcttgcatgcacgttgatgtgtgcttgttttagcctcatgcactaatatgcctattttttttgtttcttttctctgtttggacagAAAAGAAGCTCCTATATTCTAAATTGAGGAACATTCCTGTGAATGAGAGGGCAACTACTGTAGAGAAACCTTCAGTTGATAAAAAAGATGCATCAACCGT
















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|29670330|gb|CB666605.1|CB666605
EST:     AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG                         AAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
genomic: AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAGgtagttaccg ... ttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
EST: gi|29668085|gb|CB664360.1|CB664360
EST:     AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG                         AAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
genomic: AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAGgtagttaccg ... ttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
EST: gi|58681164|gb|CK069851.1|CK069851
EST:     AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG                         AAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
genomic: AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAGgtagttaccg ... ttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
EST: gi|66924680|gb|CX111528.1|CX111528
EST:     TCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG                         AAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
genomic: TCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAGgtagttaccg ... ttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
EST: gi|29668122|gb|CB664397.1|CB664397
EST:     AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAG                         AAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG
genomic: AGAGAAGGAGCGTCAACATCTTCAATCTACTGTTGAGGCTCTTCAAGAAGgtagttaccg ... ttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcatgaatattgccggttgtaaacttgacttcacattgatacttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGGTCAATATTATAGAAAAACCTTCAGCTGATAAAAGAGATGCATCAACTGC
                                    cattgat  putative branch site (score: 4)
                                          tactttt  CT-rich tract
     atgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattctagttggaataagacttgcatgtgtgtgatagacttaatttatgcatgaatattgccggttgtaaacttgacttcacattgatacttttggacagAAAAGAAACTCCTACACTCTAAATTGAGGAATACTTCTGTGACTGAGAAGGTCAATATTATAGAAAAACCTTCAGCTGATAAAAGAGATGCATCAACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG