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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatataactactcactgaaatatttgcattctttatattggttccttacctccaggccagtgctgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT

Basic information

species Oryza sativa
transcript LOC_Os07g19060.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G123807_T02 (Zea mays), 3'ss of exon 2
acaaatataact-actcactgaaatatttgcattctttatattggttccttacctccaggccagtgct---gcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT
 ||||| |  || | |        |  ||  ||| |||   |  || |  | |  | | ||  || ||   ||| | | |||||   ||| |||||| | |||||||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| | |||||||| || |||||||||
-caaatctgtctcagttttctgtgtgatta-atttttttagtcagtgcaatgctccaatgcatgtacttctgcagactcaaccat--tttttgttcatattcagATATACCATGGAGCGTCCACGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTCTGGTCAGAGCTGTTCAAGAAACAGATTGACAAT

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
acaaatataactactcactgaaatatttgcattctttatattggttccttacctccaggccagtgc---tgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT
 || || |  |   |  |||   |  ||   || |||   |  || |   ||  | | ||  || |   |||| | | ||||||| ||  |||||| | |||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| | ||||||||||| |||||||||
-cagatctgtcagttttctgtg-tgattattttttttg-gtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
acaaatataactactcactgaaatatttgcattctttatattggttccttac------ctccaggccagtgctgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT
       |||||    | |||  || |    ||||  ||  ||  ||  ||        |       | |       | |||   ||| ||   |||     | || ||||| |||||||| ||||| || |  |||||||| || || ||||| || |||||||| || |||||||| ||| | ||||||||||| |||||||| 
-----gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaattagt-aaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
acaaatataactactcactgaaatatttgcattctt-tatattggttccttacctccaggccagtgctgcaaagttaaccaaagtttctgtt-caaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT
     | |  ||||  |   |    ||| || | || |||  |||    |      ||    | |          ||||   ||  | | ||      | || || ||||||||  | ||  | || ||||| ||||| || |||||||| ||||||||||||||||| ||||| ||| | ||||||||||| ||||| |||
--gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
acaaatataactactcactgaaatatttgcat--tctttata-ttggttccttacctccaggccagtgctgcaaagttaaccaaa--gtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT
         | |  |||   | |||    |||  || ||| | ||  ||  ||   |        |||  |  |   |||  |||  || | | ||     | ||||||||||||||| | || || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||| | |||||||||||||| ||||| 
-----agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC

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|88422163|gb|CI688963.1|CI688963
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|86887581|gb|CI294215.1|CI294215
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttacctccaggccagtgctgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT
                                      tttctgttc  CT-rich tract
                        aaagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatataactactcactgaaatatttgcattctttatattggttccttacctccaggccagtgctgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
acaaata
- - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg