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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcctttctatgtccatgggatacacttacctaccctgtaaaacaactagcagtgcaattctttggtctttctacttaagatttgatttgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAAGGGGATTTTCGCCCATGGAGGGAGCAGTTAAACTTCCTGCCAGTGTTCT

Basic information

species Oryza sativa
transcript LOC_Os08g33850.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G152457_T03 (Zea mays), 3'ss of exon 4
-ggttcctttctatgtccatgggatacacttacctaccctgtaaaacaactagcagtgcaattctttggtctttctacttaagatttgatt-tg-ttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAAGGGGATTTTCGCCCATGGAGGGAGCAGTTAAACTTCCTGCCAGTGTTCT
 |  |||    | |||  ||       | ||   |      ||| | ||||  |||     ||| |   ||||  |   |  ||| ||| | || |||||||||||| |||||||| ||||||||||||||||||| ||||||||||||||||||||||||| | | ||| |  ||| ||| |||||||||||   |||||||
cgtatccaacttctgtggatatctatgatttgttttaaagctaacataactc-cagcatgtttcatgaatcttcatgtct--gatctgactatgcttatgcagTGGCCACACATTTGATTTCTCAAGCTAAGTACAAAGATCCTTGCACTCCAAGGGGATTTACACGCATAGCAGGATCAGCTAAACTTCCTGTTGGTGTTCT
















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|58662334|gb|CK051014.1|CK051014
EST:     TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAA                         TGGCAACACATTTAATTTCTCAAGCTAAGTACAG
genomic: TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAAgtaagttgat ... tgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAG
EST: gi|568839|gb|D39688.1|D39688
EST:     TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAA                         TGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAA
genomic: TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAAgtaagttgat ... tgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAA
EST: gi|66923290|gb|CX110138.1|CX110138
EST:     TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAA                         TGGCAACACATTTAATTTTCTCAAG
genomic: TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAAgtaagttgat ... tgttatgcagTGGCAACACATTTAATTT-CTCAAG
EST: gi|58691243|gb|CK079930.1|CK079930
EST:     TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAA                         TGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAA
genomic: TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAAgtaagttgat ... tgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAA
EST: gi|58691215|gb|CK079902.1|CK079902
EST:     TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAA                         TGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAA
genomic: TGCGTACGAATCACTCCATGACATGCTGAGCACACCTGGGCATAAATCAAgtaagttgat ... tgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactagcagtgcaattctttggtctttctacttaagatttgatttgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAAGGGGATTTTCGCCCATGGAGGGAGCAGTTAAACTTCCTGCCAGTGTTCT
                                     atttgat  putative branch site (score: 5)
                                ttaagatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttcctttctatgtccatgggatacacttacctaccctgtaaaacaactagcagtgcaattctttggtctttctacttaagatttgatttgttatgcagTGGCAACACATTTAATTTCTCAAGCTAAGTACAGAGATCCTTGCACTCCAAGGGGATTTTCGCCCATGGAGGGAGCAGTTAAACTTCCTGCCAGTGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG