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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctttcaaagttctcatctactaatatgttggcttgttgctatctccatgtttaggtgtagccttgctctttgtgtatctactctacttgcagcatgcactaactgaggctcgccaacatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG

Basic information

species Oryza sativa
transcript LOC_Os10g36780.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36780.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G082502_T01 (Zea mays), 3'ss of exon 11
gtgagctttcaaagttctcatctactaatatgttggcttgttgctatctccatgtttaggtgtagccttgctctttgtgtatctactctacttgcagcatgcactaactgaggctcgccaacatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG
|||||    | |      ||| ||| |       | ||| | ||  | | | |||  | |||   | | ||| |   |  || | || |  ||   |  || ||| |  || |     |||||  || |||||| || |||||||| ||||| ||||| ||||||||||| ||||||||||| || || || ||    ||||||||||| ||||
gtgagtccgccagagctccatatacgagc-----gacttatcgcgctgtgcctgtgcaagtg---cttcgctttagatagat-tgctttgttttttg--tgtactgatagatgtctcacaacacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGAGGGGCTGTCCGCAGTGGCCTTTCAGGATCGAAG
















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|33793324|gb|CF322543.1|CF322543
EST:     CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATA                         TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTG
genomic: CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttc ... acatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTG
EST: gi|88198073|gb|CI197923.1|CI197923
EST:     CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATA                         TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
genomic: CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttc ... acatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
EST: gi|157649959|gb|EX449593.1|EX449593
EST:     CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATA                         TGCCATCATACATAATCAAATGTAGAAATTGCTGACATGGCACTGATCTGA
genomic: CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttc ... acatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
EST: gi|88263249|gb|CI367023.1|CI367023
EST:     CGCCATGCCTCGAAACAGAAATCGTCGAAATATA                         TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
genomic: CGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttc ... acatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
EST: gi|86904683|gb|CI321591.1|CI321591
EST:     CTCTCAAGATCCATGGCGCCATCCCTCGAAACAGAAATCGTCTAAATATA                         TGCCATCATACATAATCAAATGTAGAAATTGCGGACAT-GCACTGATCTGA
genomic: CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttc ... acatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
EST: gi|88968629|gb|CI098843.1|CI098843
EST:     CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATA                         TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA
genomic: CTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttc ... acatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtatctactctacttgcagcatgcactaactgaggctcgccaacatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG
                          cactaac  putative branch site (score: 1)
                                            aacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctttcaaagttctcatctactaatatgttggcttgttgctatctccatgtttaggtgtagccttgctctttgtgtatctactctacttgcagcatgcactaactgaggctcgccaacatttgtagTGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG