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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacctagctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
gtatcacctag-ctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
|||||||||   || ||| | |  || |||||| |     | |  |||| ||  || | || | | ||  |  | ||  ||| | ||| |||   |   ||||||  |||||||||||||||||||| | || | ||||||||| || || ||||||||||| ||||| |||||||||||||| || || ||||||||||| |
gtatcaccttttctgtttcacacattttttcctctt--tctgcttgttgata--gtgtgttctggcctttttggggtgtaaattttat-tttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
gtatcacctagctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
                 ||    | || | || |  |||| || ||   | | |||| || || |   || |   |     || | |      ||||   || |  | ||||| |||      || |||||    || ||||||||  | ||||| ||||| |||||||| |||||||||||||| || ||||||||||| |
----------------gtaacaatgctgtgctgt-aagttacatgtaacttg-gtttgttttttagaaat-tatcttgctcatttgttgcaattttc---agATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------------------gtatcacctagctattttagagtttctttcctttcgagtttcacgttggtagagttt--attgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
                                                                               ||  ||  ||| |   ||| |  || | | |||    || || | | ||| | |  |  | | |    |  | | ||  || | | | |       ||  ||||||  | || || ||| |    ||||||||  | || || |||||  | || || |||||||||||||| |||||||||||||| || ||||| || ||||
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatcttt-caagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
------------------gtatcacctagctatttta-gagtttctttcctttcg-------agtttcacgttggtagagttta---ttgttgactgatgtga-gtaaaaaatctatgtt---tcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
                   |  | | |   | ||||| ||| |||  ||||||         | ||| |  ||  |  |||| |   |||||| ||  ||||    ||   |  | |  |   |  ||   | ||||  | ||||| ||||| | |||||| ||  | || || ||||| ||||| || ||||||||||||||||||||||||||||| || |||||||| ||||
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------------------------gtatcacctagctatt----ttagagtttctttcctttcgagtttcacgttggtagagtttatt---gttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
                                           ||    |  ||       ||| |||| |    ||||    ||  |  ||   | | | |  |   | | || |   | | |    | ||  ||||    | |   || |  |||| || ||  |   ||| || ||    |  | |   || ||||| || ||||||||||| ||||||||||||||||| || ||| |||| ||||
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaat-ttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC

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|88334745|gb|CI676538.1|CI676538
EST:     CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG                         GTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
genomic: CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAGgtatcaccta ... ctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
EST: gi|88405106|gb|CI685555.1|CI685555
EST:     CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG                         GTCATTGCAATAGCATCAAATGCACTAGACAGGTTCAAAAATGATGCAAAA
genomic: CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAGgtatcaccta ... ctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
EST: gi|88585403|gb|CI703033.1|CI703033
EST:     CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG                         GTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
genomic: CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAGgtatcaccta ... ctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
EST: gi|29622847|gb|CB627858.1|CB627858
EST:     CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG                         GTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
genomic: CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAGgtatcaccta ... ctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
EST: gi|58668422|gb|CK057108.1|CK057108
EST:     CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG                         GTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA
genomic: CAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAGgtatcaccta ... ctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
                gactgat  putative branch site (score: 3)
                                   tctatgtttcctttc  putative PPT
                            taaaaaatctatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcacctagctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC