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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacag

Basic information

species Oryza sativa
transcript LOC_Os05g32110.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G071970_T01 (Zea mays), 5'ss of exon 4
------GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttc---tgcaaaattgctaacaagttccatgcatttccacag
      |||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||       |||||     || |||||| ||||||||| || |        |||||| |||   || | ||| ||  | | ||||    |||||  || ||||  | ||   |||||||   |||
CCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCGACATGCTCATGTGGCTGCCAGAAC------CCAAGTGGGTCAAACTGTGTGAAgtgagtttatca-------gctcttaattcatgtcatattggggttctattttttatttgcaatttttctaatgaatttattgcattttt-cag

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 4
------------------------------------------------------------GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacag
                                                            |||||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||| |||       |||||     || |||||| ||||||||| ||    |                                                                            
TGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTatcatcgttttataatgacacaattgtgaactgcccaacatgctcatgtggctgccagaac------ccaagtgggtcaaactgtgtgaagtgagttgatctgcct---------------------------------------------------------------------------

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G826714_T01 (Zea mays), 5'ss of exon 4
------GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttc-tgcaaaattgctaa-caagttccatgcatttccacag
      |||||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||| |||       |||||     || |||||| ||||||||| ||    |     |||||| |||   || | ||  ||  | | ||||  |  ||| ||  |||   | ||| ||    ||   |||
CCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAACTGCCCAACATGCTCATGTGGCTGCCAGAAC------CCAAGTGGGTCAAACTGTGTGAAgtgagttgatctgccttttgctcttaattcatgtcctattagggttctattttttatctaaagtttttaaatgaattctattgcattttgcag

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G32130.1 (Glycine max), 5'ss of exon 4
---GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaa----------accaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaat-tgct----aacaagttccatg--catttccacag--------------------------------
   |||| || |||||||| || |||||||||||  |||| ||||||||||| ||| | ||||| |||| ||||||    |||   ||||| ||||||||| ||| |||    ||           |   | | |   |  |  ||| || ||   | | |    ||   |||| | ||||    |  || ||   |   ||||||| ||                                 
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACCGTTGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAA---AACAGAACCTGGCAGCTGTGTAGAgtaagtctccaatttatcttttcatagatatttgaaactgtctttttttttgtgtctagtagtttgccaaagtatgctccaaagtaacttttgtcatcatttccccattcttatgatttgtttttctgaatgtcttgcag

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G22410.1 (Glycine max), 5'ss of exon 4
---GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaactttt-----ctgcaaa-attgct----aacaagttccatg--catttccacag--------------------------------
   |||| || |||||||| || |||||||||||| | || ||||||||||| ||| | ||||| |||| ||||||    |||   ||||| ||||||||| ||| |||    ||       |   || | | | |  |||     | | |  ||||     || |||| | || |    |  || ||   |   ||||||| ||                                 
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAA---AACAGAACCTGGCAGCTGTGTAGAgtaagtctccaattt----atctttccatagatatttgaaactgtctattttttagtgtctccaaagaatgttccaaagtaacttttgtcatcatttccccattctgatgatttgtttttctgaatgtcctgcag

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 4
GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacag------------------------------------
|||| || |||||||| || || ||||||||||||||   ||||||||||||| | ||||| ||||| |||||    ||    || || ||||||||| ||| |||| ||  | ||||  |    |  |  ||| |||||   |||   | |          | ||| |  | ||  ||  ||  ||                                        
GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttcattcagccaagtca---atattactttttgtttgagcct--cctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag

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|29629256|gb|CB634267.1|CB634267
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58662260|gb|CK050940.1|CK050940
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|66918925|gb|CX105773.1|CX105773
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGCAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|66947309|gb|AU312153.1|AU312153
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58686271|gb|CK074958.1|CK074958
EST:     TGCTCTTGTGGCTGCCAAAAGAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58654342|gb|CK043022.1|CK043022
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATCTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|24208701|gb|AU225728.1|AU225728
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|33676440|gb|CF304679.1|CF304679
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|3061251|gb|C91883.1|C91883
EST:     GGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: GGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|24208702|gb|AU225729.1|AU225729
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58663357|gb|CK052043.1|CK052043
EST:     CAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: CAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|29684532|gb|CB680807.1|CB680807
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG