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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttggttcaaacttattgttgttttgctctattccttgatttttgccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA

Basic information

species Oryza sativa
transcript LOC_Os02g33180.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G156105_T01 (Zea mays), 3'ss of exon 2
gtatgtttttggttcaaacttat-tgttg--ttttgctctattccttgattttt---gccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA
|||||| | |   ||||| |||| ||||   || ||||    |   | | | ||   ||||||||| | ||  |  |||         || |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||| |||||||| ||||||||||| |  ||||||  | 
gtatgtatcta--tcaaagttatatgttagtttctgcttctgtaaataactattcccgccatcactaaatcctaggtct--------gttcttgcagTGGAAATGCTGTGATATTCATGTCAAGGAATTTGATGAGTTTATGGAGATACCTCCATGCACAAAAGGTTGGCATAATGCTGATGCGGTGTGAATTCACG

upper sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G868908_T01 (Zea mays), 3'ss of exon 4
------gtatgttt------ttggttcaaacttat-tgttgttttg-----ctctattccttgatttttgccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA
       ||| |||      ||  ||  ||  ||| ||||| |||      || ||  |    ||| | |||||| || |  |  | |||| ||      || |||||||||||||| |||||| ||||||||||||| ||||| || ||||||||||| ||| | ||||||||||||||||| ||||||||||| |  ||||||  | 
gtatgtatatatttgaaggatttatttgaagctatatgttgatttctgcctctgtaaacagctattctcgccatccctaaaccccatatctgttc---tgttcttgcagTGGAAATGCTGTGATGTTCATGTCAAGGAGTTTGACGAGTTTATGGAGATACCTACATGCACAAAGGGTTGGCATAATGCTGATGCGGTGTGAATTCACG

upper sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G38720.1 (Glycine max), 3'ss of exon 4
-------------------------gtatgtttttggttc------aaacttat---tgttgttttgctctattccttgatttttgcca-tcactgactctgacatctttttaaaaat-ttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA-
                         | ||||| | | |||      ||| | ||   ||| ||| ||   | |    ||||||  |  | | ||    | |     |||| | | | | ||||||||||||| || |||||||||||||| || ||||||||||| ||||||   || ||||||||| ||||||| ||||| ||||| ||| ||  |    |  ||| 
gtcagtattgagtattcattcctttgaatgttctcgtttctttaataaaataatgcttgtggttgtgacttgtgatatgatttcagagaattacattttatttttcctttatcacattattttgcagTGGAAGTGCTGTGATATTCATGTAAAAGAATTTGATGAGTTTATGAGCATTCCTCCGTGCGCAAAGGGATGGCATAATGCGGAT-CCAGAGTCCTGATCAC

upper sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv16s0022g02040.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtatgtttttggttcaa----acttattgttgttttgctctattccttgatttttgccatcactgactctgacatctttttaaa-aatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA-
                       |   | ||   ||||     | ||||||||  ||| || | ||  ||| ||  || | ||  ||| |   |     |  |    || ||||| |||||||||| || || |||||||| ||||| || |||||||| |||   || || || ||||| ||||| |||||||||||| |  | || | | |   || 
gtgggatatgtgttttatgacattgcatcttaaattcagttgcatttattgttacttt-ctattttgattggttcctgacttc--tgaatacaatgctatgatgtgtaacttttgtagTGGAAATGCTGCGACATTCATGTGAAGGAGTTCGATGAATTCATGAGTATACCACCTTGCACCAAGGGATGGCACAATGCTAACCCAGCGTCA-TAAGCAG

upper sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S505_16V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------gtatgtttttggttcaaacttattgttgttttgctctattccttgatttttgccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA-
                    | |   ||   |||||   | ||  | || | ||  |     ||| | |||  || ||  | ||  |  ||||||      ||| |||||||||||||||||||| | ||||| || ||||||||||| ||  |||| || || || ||| | |||||||||||  | ||  || || || ||     |  
gtatgatattgcatctaatttgtaagttgccttcaattgtgttcatattcttcttcacaatctgagtcttgagatgac-aattcatatttctttt---gtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAAT-CCACAGGATGCGGCGT

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|86595463|gb|CI264560.1|CI264560
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|25798558|gb|CA754519.1|CA754519
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|86600681|gb|CI356438.1|CI356438
EST:     ATGCGATTACCATCCAGGACCTCCACGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: ATGCGATTACCATCCAGGACCTGCA-GTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|87034434|gb|CI189058.1|CI189058
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATATTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|86542960|gb|CI183166.1|CI183166
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATATTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|11025769|gb|AU162370.1|AU162370
EST:     CAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|88904218|gb|CI001951.1|CI001951
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|6934838|gb|AU082375.1|AU082375
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|218479917|gb|FG953240.1|FG953240
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|86843204|gb|CI341358.1|CI341358
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|88473078|gb|CI410349.1|CI410349
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
EST: gi|88273372|gb|CI393778.1|CI393778
EST:     CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGG                         TGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC
genomic: CATGCGATTACCATCCAGGACCTGCAGTTTTTCGCGACAGGATTAGAGGGgtatgttttt ... atttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattccttgatttttgccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA
                                              tttttgc  CT-rich tract
                             tgacatctttttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttttggttcaaacttattgttgttttgctctattccttgatttttgccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT