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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
----------------------------------------------gttctaaaagcttgccaagg----aaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
                                               |||   |  ||| | | ||    || ||  | | ||  |      ||     |  | | |    || || | | ||| |||||        |||| |||||||||||||||||  ||||||||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||
gtaaatttcctcatgcaacaaagacataagactggcatgccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaattt------cttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtact-atgtaatttgatcattatgt-gcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
      || | |        ||          | | |  | | ||||| ||    |    | | |  || | ||||  | || |  |  | | |  ||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||
--atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 6
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgc-cataatggt--actatgtaatttg-atcatta--tgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
    |  ||  |  |  ||  || || |     | |   ||  ||||| ||   | |||  ||    ||  | | | | | ||| || |||   | |  |||||||||||||||||| || || ||||| || || || ||||||||||||||| ||||||| ||||| ||||| |||||||||||||||||
----tgcaacatcccttagataatgagctttgataacagttattgtaagatc--aatgcatatggcagtttaatttatgacttgtattatttcctttctctcttagTTTGACCCAGTAAAGCTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATTGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 7
-gttctaa----aagcttgccaaggaaaagatcacatttgaacatttctgtaatatttta-gtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
  |||||     ||  | |  |    |   || |  ||||   ||   || | |    ||     ||  ||  |  ||| |  |||  |  |  | ||||    |||||||  | |  ||  |    || || || || ||||||||||||| ||| ||| ||||||||||||| |||||||| || |||||
acttctagctgcaaattagttactatagtcattagttttgtgtatacttgcagttgaatacaaatcaatatattgttatat--tttccttttcctatgcc----agTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 5
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatatttt-agtgccataatggtac-tatgtaatttgatcattatgtgcctct--tagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
   ||   |||| || |        |  | | |  |  |||| |||  || ||| |||   |||    ||  ||| |  ||  ||  |  | | ||| |   |||||||  | |  ||  |    || || || || ||||||||||||| ||| ||| ||||||| ||||| |||||||| || |||||
--acttctagct-gctattattgttactatagtc-attatttttgtcttactttcagttgaatacaaataaatatattgttatattttccttttcctatgccagTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcc----tcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
    || | |   || || ||||   |     || |  ||  ||  || |  | ||  | |   | |||  || |  |      || ||||  |    ||| |||||||  | |  ||| ||| ||| ||||||||||||||||| |||||||| || |||||||| ||||| ||||| ||||| |||||
-cattacacgtcagcaaatgaaa--cttgtggttaag-ataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 8
---gttctaaaagcttgccaaggaaaagat-cacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
   |||||   ||      ||   | |||| || | |  | || |  |    |  |||  |   |||    || | | ||  ||| || |    |   |  ||||||||||| |||||| | ||||||||||| || ||||| ||||||||||| ||| |||| ||||| || ||||||||||| |||||
ttagttctttgagaaaataaatatatagatacagaatcaatcaatattacc-ttctttgttaatata-cattaatgtcta--ttgctcttgtgctttttgctagTTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG

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|29640958|gb|CB645965.1|CB645965
EST:     GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAG                         TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
genomic: GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAGgtacaatcta ... tgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
EST: gi|33678061|gb|CF306300.1|CF306300
EST:     GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAG                         TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
genomic: GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAGgtacaatcta ... tgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
EST: gi|33683367|gb|CF311606.1|CF311606
EST:     GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAG                         TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT
genomic: GGAGAGGGAAACCACCGGTACTTGTTGACAAAGATGAGGGCCTGGACAAGgtacaatcta ... tgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
                               atttgat  putative branch site (score: 5)
                                             tgcctctt  putative PPT
                             taatttgatcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG