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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 8
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
||||| || | |  ||   ||       |||   |||||||||  ||   |  | ||| |||||||   | ||||| |    |||||| ||||  |  |||||                      || || |||||||||  |||    | ||||| ||||||| ||||||||| || ||||||||| |||| ||||||||||| || || ||||| ||||| |||||||| || |||||||||||||||
gttagcatttct--tttgaact------ccccactcccccaccttgagtgccagtaatttgattgattgcttcattctctttaaagatgttttcaatgtgaaa--------------------gcatcctaattatagtttcttttgggggtgcagGTTTGAGCAATATGTGGATTATGCATTAGATGTCCCCATGTATTTTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 8
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaa-acctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttga-tgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
         ||    || |      |  ||    |||||||||   |      | ||| ||||||||   |||||| ||         |  |||| | |||||  |                     | || || ||||||  | | |  |  ||||| ||||||| |||||||||||| ||||||||  |||| ||||||||||| || || ||||| ||||| |||||||| || |||||||| ||||||
-------gttagctctccttttgaactccctctctcccccacctttagtgtcagtaatttgattgaattgcctcatatt---------tcctttaaagatgaagcg--------------------gtcctaatcatagtttctgtttgggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 9
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatga-aggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
                                                   ||       ||| ||||    |  |||||  |    |||  |   | |||||    | |  |     ||| |  | | ||   | | ||||  || | || |  || |||||||  ||||| ||||||||| | ||| |||| ||||| |||| |||  | || || || ||||| ||||||||||||||| ||||||||
---------------------------------------------------tgtgttcaagatagaaagatgc--tttgg--atctttatccttctcttgaaacagcatggctaatcttaattttattgctctcttttgttc--ttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 9
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
                                                       || |  |          ||||||     | | |||| | |  |     |    | ||      ||  | | | ||  || |   |  ||||| || |||||||||||||  ||||| || || ||  | ||| | || ||||| ||||||||||| || |||||||| |||||||||||||||||||| || |||
-------------------------------------------------------aaaggaagctggttttccatttttttttatg-tattctgttgacagttttgttgattattgacaatggtattcctatttctttctattttctctggtgcagATTTGAGCAGTATGTAGATTATGCTCTTGATGTTCCAATGTACTTTGTCTATCGGAAGAAGAAGTATATTGACTGTACTGGAATGTCCTTCCGG

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|55411431|gb|CV723807.1|CV723807
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|11442624|gb|BF430527.1|BF430527
EST:     GCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58663354|gb|CK052040.1|CK052040
EST:     GACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58695197|gb|CK083884.1|CK083884
EST:     TGACTCA-TTGG                         A-TTGAGCGATATGTGGACTACGCATTA-ATGTCCCGATGTATTTTGTCTA
genomic: TGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     GACAACAAACGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         GTTTGAGCGATATGTGGACTATGCATT
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATT
EST: gi|218498945|gb|FG948066.1|FG948066
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|58663415|gb|CK052101.1|CK052101
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|218500233|gb|FG945122.1|FG945122
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTAAGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|33676123|gb|CF304362.1|CF304362
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         ATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGG                         GTTTGAGCGATATGTGGACTATGCATTAGATGTCCCGATGTATTTTGTCTA
genomic: GACAACAACCGCTCAGGGATGCTTCCTTTTGTGTTCGATGACTCATTTGGgttagtatct ... tttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
                                     ttcgtttcttt  CT-rich tract
                      aaattctgattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT