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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatgctatttttgtgcctatattgcatatatcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC

Basic information

species Oryza sativa
transcript LOC_Os04g57540.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081387_T01 (Zea mays), 3'ss of exon 2
-----agatgctatttttgtgcctatattgcatatatcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
       |   |   || ||  | ||   ||||  |   || |   |||||    |  |  | ||||     || ||    | |   |||  ||||| |||  ||||||||||||||||||||||  ||||||| ||||| ||||| ||||| ||||||||||| | | || |||||| ||| ||||| ||||||||||||||||
gcattgaacagtggattggtatccatg--gcattcaatcttaacatcaacatgtgttgaagaattgtagggcctaat---attgttttatcatgtgccttgtcagGAGATACTTGAAGGAGTCACAAATATTGACTTGGTGATCAATCTCAAGCTCCGAGAAGAAGTTGTGGTTGCAAGATGTCTTGGCAGAAGGATGTGCAGCC

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G150014_T03 (Zea mays), 3'ss of exon 2
agatgct---atttttgtgcctatattgcatatatcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
  || |    |||| | |  | |  ||  |  |   ||  |  |  | |  |          || |   || ||   |||||   |||  |||||  ||  |||||||||||||||||||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||||||||| || |||||||||||||
--atccctggatttctatctcaacgttataacttgtgtcaaaccttagacactggggtagactgcttggtcctaat-actggttttatcatgtgccctgtcagGAGATACTTGAAGGAGTCACAGACATTGATTTGGTGATCAATCTCAAACTCCGAGAAGAAGCTCTGCTTGCGAAATGCCTTGGCAGGAGGATGTGCAGCC

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G347841_T01 (Zea mays), 3'ss of exon 2
---agatgctatttttgtgcctatattg-catatatcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
     |||| |||         | ||   ||| | | |  ||     | |  |       | ||||     || ||    | |   |||  || || |||  ||||||||||||||||||||||  ||||||| ||||| ||||| ||||| || |||||||| |||||| |||||| ||| ||||| ||||||||||||||||
tatccatgccattca-accttaacatcaacatgtgttgaagaactttagagactgggtagaattgtagggcctaat---attgttttatcatgcgccttgtcagGAGATACTTGAAGGAGTCACAAATATTGACTTGGTGATCAATCTCAAGCTTCGAGAAGAAGCTCTGGTTGCAAGATGTCTTGGCAGAAGGATGTGCAGCC

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G05530.1 (Glycine max), 3'ss of exon 2
agatgctatttttgtgcctatattgcatat-atcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
       | || |||  || | || | | | || |  |  |   | ||   | ||  ||    ||       || ||      | | || | |  | | |||| ||| | ||||| || || || ||||| ||||| ||||| || || ||||||||||| | ||||||||  |||||||||||||| || || ||||  |
-tgcaacagttctgttgctttcttacttttcatagaagcagtttaaaactttaaaaaacggaatactcaaattctacaatgtttttgtttttcgctcgcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTAATCAATCTGAAGCTCCGAGAAGATGTTCTGCTTGAGAAATGCCTTGGTAGGAGAATTTGCAATC

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G36120.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------agatgctatttttgtgcctatattgcatatatcgttga-ggccaacaatcatcaactacttgttaaatcttatccactggaactat-tttgtgctttgg-----tagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
                                                                                |    | |     ||| |||||||   | | || | || |     |   |||  |||  |  | || |   ||| |||  || | |  |||     ||       |||| ||| | ||||| || || || ||||| |||||  |||| || || |||| |||||| || |||||||||||||||||||||||||| || || |  |
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctatattt--tctgtcctcgacgatttcctgacattcacttttcat-aactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC

upper sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G33390.1 (Glycine max), 3'ss of exon 2
agatgctatttttgtgcctatattgcatatatcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttg------tgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
      ||||||    |||        ||  | |          |   |||  |||  |  | | | |  ||  |||  || | |  |       ||  ||   |||| ||| | ||||| || || || |||||  ||||  |||| || || |||| |||||| || |||||||||||||||||||||||||| || ||||  |
-----atattttctgtcctcccccctttaagttgcgacaatttcctgacattcacttttcataacagcg-atttactaaaattgtgcttaaaatctgtgttctcagGAAATATTGGAAGGGGTAACTGACATTGACCTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGCAATC

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|29673765|gb|CB670040.1|CB670040
EST:     ATAAGACAAGCG                         GAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTC
genomic: ATAAGACAAGCGgtgagctagt ... gctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTC
EST: gi|29679123|gb|CB675398.1|CB675398
EST:     GTGAGCTGGGCTTCATCCTTGATGGTTTTCCAAGAACCATAAGACAAGCG                         GAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTC
genomic: GTGAGCTGGGCTTCATCCTTGATGGTTTTCCAAGAACCATAAGACAAGCGgtgagctagt ... gctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTC
EST: gi|29658755|gb|CB655030.1|CB655030
EST:     CCAAGAACCATAAGACAAGCG                         GAGATAC-TGAAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACT
genomic: CCAAGAACCATAAGACAAGCGgtgagctagt ... gctttggtagGAGATACTTG-AAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACT
EST: gi|218504868|gb|FG963478.1|FG963478
EST:     GTGAGCTGGGCTTCATCCTTGATGGTTTTCCAAGAACCATAAGACAAGCG                         GAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTC
genomic: GTGAGCTGGGCTTCATCCTTGATGGTTTTCCAAGAACCATAAGACAAGCGgtgagctagt ... gctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTC
EST: gi|2431503|gb|C73923.1|C73923
EST:     GTGAGCTGGGCTTCATCCTTGATGGTTTTCCAAGAACCATAAGACAAGCG                         GAGATACTTTGAAGGAGTCACGGATATTGGATTTTGGTCAATCAACCTNAA
genomic: GTGAGCTGGGCTTCATCCTTGATGGTTTTCCAAGAACCATAAGACAAGCGgtgagctagt ... gctttggtagGAGATACTT-GAAGGAGTCACGGATATTG-ATTT-GGTCA-TCAACCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
             ttgttaaatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatgctatttttgtgcctatattgcatatatcgttgaggccaacaatcatcaactacttgttaaatcttatccactggaactattttgtgctttggtagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG