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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT

Basic information

species Oryza sativa
transcript LOC_Os07g22720.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 5
-tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
 | | ||  ||    | | ||| |     | || |         | | ||   ||  | |||| | | |  |  |     || |   |  |||   ||||||| |||||||| | |||||| |||||||||||||| |||||||| |||||||| ||||| || || ||||| |||
gtatattcattgcccaaaaattgttagtatgaactg--aatgatagc-cgaatggaaactcatattgctgcttgtctttattctgtata-atttcttgtagGGAAACATTGCCAAGTGGCTTAAGAAGGAAGGAGACAAGGTCTCCCCTGGTGAGGTTCTCTGCGAAGTGGAAACT

upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 1
---tgttt-tagttttgtacatatta-tgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
   | ||| |        ||  |||| | |||| | | |    || | |  |   |  | ||||   ||  ||  | |||  |  || |     ||| | ||||||| |||||||| | |||||| ||||||||||||||||||||||| ||||| || ||||| ||||||||||| |||
gtatatttgttacccaaaactcattagtacaacctgaataatagctgaactgaaaccag-tatt--gctgcttgtttttattctgtaaa-----attctttgtagGGAAACATTGCCAAGTGGCTTAAGAAGGAAGGAGATAAGGTCTCCCCTGGCGAGGTTCTCTGTGAGGTGGAAACT

upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
            || | || |||     ||||| ||  |      |      | |  |     |  ||  |  || |  |||| |    ||  | |  |||| ||||||||||| ||| ||||||| ||||| |||||  |||| ||||||||||| || ||||| || || |||
------------gttcctactat----tttaatcttatgagattgctgtatagtgggtc---atgatttctcctaaa--ttattccca-atgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT

upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
               ||| |    |    ||  | |    |  |       ||  ||||  | ||  |  |  |||     |||  |||     ||  |||| |||||||| |||||||||||||| ||||| ||||| ||  | ||||||||||| |||||||| || || |||
--------------gcatgtacctctgaatacctcttacgaaaattaacatggtttattgtttta--tcattctactaaagatatctgttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT

upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 7
tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
               ||| |          |  | |  | |   |  |   |    ||| |     |||  |||  |  || |  ||  ||    || |||| |||||||| |||||| ||||||| || || |||||  |||| ||||||||||| || ||||| || ||||||
--------------gcatgtgcctttctgaagctatgagaatacaaaccatgctcaatttactgttttatgattgaatgttttgttt--atcaaatgcagGGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACT

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|58607751|gb|CK035784.1|CK035784
EST:     CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAG                         GGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGT
genomic: CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAGgtatatctca ... ttgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGT
EST: gi|117233831|gb|CT842341.1|CT842341
EST:     CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAG                         GGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGT
genomic: CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAGgtatatctca ... ttgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGT
EST: gi|58665439|gb|CK054125.1|CK054125
EST:     CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAG                         GGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGT
genomic: CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAGgtatatctca ... ttgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGT
EST: gi|29636053|gb|CB641062.1|CB641062
EST:     CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAG                         GGGAACATTGCA
genomic: CACCACATCAGGAAATAGGGATGCCATCACTCTCTCCTACAATGACCGAGgtatatctca ... ttgtctgtagGGGAACATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
                     ttagtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA