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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 13
atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttcta-tgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
                          |    | | |        |   |  | | | || |||     ||     || || || |||     ||| ||||||| ||||| || || || ||| ||||  || |||| | ||||||||||||||||||||||||||| ||||||||||| || ||||||||  |  | ||||
-------------------------gtatggaggccttccaatctgtttcttgcttcttggttcttgctttacaattgtgtgacattatcggctactgcagCTGTGCAGTGGCGTCGACGAGGATGCACCTGGTGCGTGTGCACAGCTTGTCTTTGCTCCTATTGATGAATCTTTTGCCGACGATGCACCGTTGCTGCCCT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 12
atcccgattcttctccacataatccttgctcat--gacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctat-gcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
                  || |  ||| |   |  |    |||| |   |    |    ||| |  |    |  ||  | || || |||   | || | |||| | ||||||||  | |||||| ||||  |  |||| | ||||||||||||||| |||||||| || |||||||||||||| ||||||||  |  ||||||
----------------gtatgaggctttccagtttgtttcttgcttctgggatcatggttttctcaccacattgtgactgtgcgacattatctgctcttgcagTTGTGCAGCGGCATCGATGAGGATGCGCCGGGTGCTTGTGCACAGCTTGTCTTCGCTCCTATCGATGAATCTTTTGCTGACGATGCACCGTTGCTACCCT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 13
----atcccgattcttctccacataatc--cttgctcatgacaatt--gccttaagttgtacctgtt--tgt---tgcattttcctggttctgagagattgctttctatg-cagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
    |      ||  | | |   |  |     |||||||   | ||  ||  ||| | ||| |||||  |||   ||  ||||  |     |   |      ||  | || ||||| ||||| ||  ||||||| ||||| | | | || | |||||||||||| ||||| |||||||| ||||| ||||| |||||||| |   |  | || |
gtaaagttatttttgtgttcgggttgttggtctgctcatcttatttaagcagtaactagtaactgttactgtgaatgatttttatttaccttattatgcaatttgatgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATTGGAGCGTGTGCACAGCTTGTGTTTGCACCTATTGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 13
---------atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctatg-cagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
          |  |  ||   ||   |||| |   ||    |   ||  ||  ||  |  |  |||  |||  |||||       | ||  |     |||  | || ||||| ||||| || |||||||| ||||| | | | |||| ||| || ||||| ||||| |||||||| || || |||||||||||||| |   |  | || |
gtattgtgtgtgactttttggctttgcatattttatgtaactaggaa--gctatagctattttctg--tgtgacatttgatgacctttgctatgcgacttgatgtggcagCTGTGCAGTGGAGTTGATGAAAATGCAATTGGGGCATGTGCTCAACTTGTGTTTGCACCTATTGATGAGTCCTTTGCTGATGATGCTCTGTTGCTTCCAT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
--------atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcat----tttcctggttctgagagattgctttctatg-cagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
        ||     |  || |    |   |  ||| |  |   |  |   | |||  | | ||  ||  ||       |||  |     |   |      ||  | || ||||| ||||| ||  ||||||| ||||| |   | |||| |||||||||||| ||||| ||||| || ||||| ||||| |||||||| |   |  | || |
gtaaagtcatttttgtgtttgtgttta-ggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttttttaccttattatgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 13
atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
        | | ||  | |  |      |||| |   ||| | | ||| || |  | ||         ||| |||||        ||||||| | | |||||||| ||||| |||||||| ||||    | | |  | ||| |||||||||||||| || || || ||||| |||||||||||||||||  |  | || |
-------gtttgctttatactaaagacactcaggg--att-cttaaagatg-agttattgaaattgaattcttggtttcttt--tttgcttt-tgtccagCTTTGTAGCGGCGTTGATGAAAATGTGGTTGGAGGTTGTGCTCAGCTTGTCTTTGCCCCAATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 12
atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
             |  || | || |||   |   | | || |       | | |   ||||||   ||       || ||     ||| ||  | |  ||||||| ||||| |||||||| ||||    | | |  | |||||||||||| ||||| ||||| || ||||| |||||||||||||||||  |  | || |
-----------gtttgacttcatactttaactccaaagtttc-------tatgctcctttgttctcttcatgacattttggattcttgattcttgtctagCTTTGTAGCGGTGTTGATGAAAATGTGGTTGGAGGTTGTGCACAGCTTGTATTTGCCCCTATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 13
--------atcc-cgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagatt----gctttctatg-cagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
         ||    ||   | |  |    |    |  |  | |   ||  | || || | || |  |   |  || ||  ||      | |  |       ||||| || ||||| ||||| |||||||||||||||||  || |||| | ||| ||||| || ||||| |||||||| ||||| |||||||||||||| ||  |  | || |
gttggtttgtctataataaatatttatgggagtgattttgcttatctttttcataggtagaactttgtaagtttatcttattgacataaatatttcttaaattttctgtggcagCTATGCAGTGGGGTTGATGAGAATGCAGCTGGTGCCTGTGCTCAGCTGGTTTTTGCACCTATTGATGAATCATTTGCTGATGATGCTCCTTTGCTGCCAT

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|58686854|gb|CK075541.1|CK075541
EST:     GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAG                         CTTTGCAGCGGGGGGTTGATGAGA
genomic: GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAGgtattgtgga ... ttctatgcagCTTTGCAGCGGGG--TTGATGAGA
EST: gi|58682326|gb|CK071013.1|CK071013
EST:     GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAG                         CTTTGCAGCGGGGTTGATGAGAAT
genomic: GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAGgtattgtgga ... ttctatgcagCTTTGCAGCGGGGTTGATGAGAAT
EST: gi|58684992|gb|CK073679.1|CK073679
EST:     GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAG                         CTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTC
genomic: GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAGgtattgtgga ... ttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTC
EST: gi|58687044|gb|CK075731.1|CK075731
EST:     GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAG                         CTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTC
genomic: GTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAGgtattgtgga ... ttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTC
EST: gi|58683487|gb|CK072174.1|CK072174
EST:     TGTACCTTCTACAG                         CTTTGCAGGGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTC
genomic: TGTACCTTCTACAGgtattgtgga ... ttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 60 (upstream exon), 35 (downstream exon)
Score: 7

TTCTTGGAGGTTATTAGGCTCGAAGGACATGGTTTCAGCCATGATGAGGTGCTTCTATCACGGGATATGTACCTTCTACAGgtattgtgga ... ttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttgtacctgtttgttgcattttcctggttctgagagattgctttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT
                                        ttgctttct  CT-rich tract
                                            tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcccgattcttctccacataatccttgctcatgacaattgccttaagttgtacctgtttgttgcattttcctggttctgagagattgctttctatgcagCTTTGCAGCGGGGTTGATGAGAATGCTACTAGTGCATCTGCACAGCTTGTCTTTGCTCCTATTGACGAATCTTTTGCTGATGATGCACCACTTTTACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - ctccaca
- - - - - - - - - - - tccttgc
- - - - - - - - - - - - - - - catgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattgct