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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgaacaacgccgtttccttactgagtttattgcctttttattttactgaatgtttgtctctgtatgtttactaatgctcctgtttcccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA

Basic information

species Oryza sativa
transcript LOC_Os04g59624.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G138125_T02 (Zea mays), 3'ss of exon 13
gtacctgaacaacgccgtttccttac-tgagtttattgcctttttattttactgaatgtttgtctctgtatgtttactaatgctcctgtttccc-atcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
||| |||| | | |     |   |   ||  | ||| |  ||    ||||  ||||||    | ||  |       || |  | | |||||  | || | |||||| |||||||||||||||||||||||||| |||||||| ||||  ||| |||| || ||||||||| | ||||||||||  ||||| ||||||||||||
gtatctgagctatgatacgtatctgtatgtctgtatcga-ttgaagttttcttgaatgaagttttcaat-------cttacacccttgtttttctatttacagTACAGACAATCAAAGTGTTGATCGTGCTTACCGAATTGGACAGACTAAAAATGTGATTGTATACCGCTTGATGACATCTGCGACCATTGAAGAAAAGATA

upper sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G00400.1 (Glycine max), 3'ss of exon 15
gtacctgaacaacgccgtttccttactgagtttattgcctttttattttactgaa-tgtttgtctctgtatgtttactaa-tgctcctgtttcccatctt---cagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
     ||    |   | ||    || |  |    |||  |  ||  || |  ||  | |||   | ||| |  ||  |||   ||    | |    | |    ||||||||| |||||||||||||| || || ||||||||||| || | |||||||||  | |||||  | || |||||||  |||||  | ||||||||||| 
-----tgctgtatttctttcttataatttgcaatttgagtccttcattgagggaggtattttcttatgt-tacttgttaagcactataatattttgtttctaccagTACGGATAATCAAAGTGTTGACCGGGCATATCGAATTGGTCAAAAGAAAGATGTTCTGGTATATAGACTGATGACATGCGGAACTGTTGAAGAAAAGATC

upper sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G32740.1 (Glycine max), 3'ss of exon 13
gtacctgaacaacgccgtttccttactgagtttattgcctttttattttactgaa-----tgtttgtctctgtatgtttactaa-tgctcctgtttcccatctt--cagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
        |    |    || ||||   | |||      |   |  || | |||      | | ||  | ||| |  ||  |||   || |  |||    |  |  ||||||||| |||||||||||||| || || ||||||||||| || | |||||||||  | |||||  | || |||||||  |||||  | ||||||||||| 
-------tattgtgtttctttcttat--aatttgcaatttgagtcattcattgagggaggtatctgcttatgtttacttgttaagcactacaattttttgttctaccagTACGGATAATCAAAGTGTTGACCGGGCATATCGAATTGGTCAAAAGAAAGATGTTCTGGTATATAGACTGATGACATGCGGAACTGTTGAAGAAAAGATC

upper sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G63950.1 (Arabidopsis thaliana), 3'ss of exon 15
gtacctgaacaacgccgtttcctta---ctgagtttattgcctttttattttactgaatgtttgtctctgtatgtttactaatgctcctgtttcccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
     ||||    |  ||   || |     | ||||     || |  || || |||     |||    |   | | |   | || |  | |      | | ||| |||||||| || ||||||||||| || ||| ||||||||||||  || ||||||||||||||  |  | ||||| || | |||  | ||||||||||||
---tgtgaaacttgatgtagtctaaaactagtgtttggaagctgtccatatttctggtctcttgaaaatacttttgtgaca-tgattttctgatatctatgcagCACGGACAACCAGAGTGTTGATCGAGCATATAGAATTGGGCAGACAAAGGATGTCATCGTATATAGGTTAATGACCTCAGCAACTGTTGAAGAAAAGATA

upper sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 14
gtacctgaacaacgccgtttccttactgagtttattgcctttttatt-ttactgaatgtttgtctct--gtatgtttactaatgctcctgtttcccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
     |   |  |    |||  ||  | | |   ||   || | |   | ||| | ||  |  ||    | |||  |  || |      ||||      | ||||||||| || ||||||||||| |||||||| |||||||| || |  || || ||||| || ||| |  | ||||||| ||| ||||| ||||||||||||
----tttttcctcttttttttttttttaaataagttttgttgtaagaatcactcagtgcataacttgtgggatgagtgttacttacatcgttttattgttgcagTACGGATAACCAAAGTGTTGACCGTGCTTACCGAATTGGCCAAACAAAGGACGTCATTGTGTACAGGTTAATGACATGTGGCACCATTGAAGAAAAGATA

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|58685729|gb|CK074416.1|CK074416
EST:     CTCACCAAGGCAGCTCGTGTCATAGTAGTTGATCCTGCTTGGAATCCAAG                         TACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGA
genomic: CTCACCAAGGCAGCTCGTGTCATAGTAGTTGATCCTGCTTGGAATCCAAGgtacctgaac ... ccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactgaatgtttgtctctgtatgtttactaatgctcctgtttcccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA
                           tactaat  putative branch site (score: 1)
                                   ctcctgtttcccatct  CT-rich tract
                         tttactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgaacaacgccgtttccttactgagtttattgcctttttattttactgaatgtttgtctctgtatgtttactaatgctcctgtttcccatcttcagTACGGACAATCAAAGTGTTGATCGTGCTTATCGAATTGGGCAGATGAAAGATGTCATCGTATACCGCCTTATGACATCTGGAACCATCGAAGAAAAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA