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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgacttctccttgttacatttgatcagttcgttgtgcgagttcaattcttttaagattagcggctgttctgtttctcttatacactgctgagttg...

Basic information

species Oryza sativa
transcript LOC_Os03g63400.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63400.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G023242_T05 (Zea mays), 5'ss of exon 4
TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgacttc--tccttgtta-catttgatcagttcgttgtgcg--agttcaattcttttaagattagcggctgttctgtttctcttatacactgctgagttg
|||||||||||||||| ||||||||||||||||||||||| || |||||||| || |||| |     ||  |||| |||  ||||||||    | ||  || |  |    |   ||||     ||  ||     |   | |    |||| |  |        
TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGACGAAAAgtaagaatactcattcctcgttttcatttgatgtactggtgatgtggtaacctagagctttagctttttccgatcagtggatgttctatatatatggtca-----

upper sequence: LOC_Os03g63400.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S359_31V6.2 (Physcomitrella patens), 5'ss of exon 3
TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgacttctccttgttacatttgatcagttcgttg--tgcgagttcaattcttttaagattagcggctgttctgtttctcttata-cactgctgagttg
|||||||||||||||| || ||||||||||| || |||||  |  ||||||||||||||| |||  |  |   |      ||   |     | |||  | | | |  |||| |  | |  | |   | ||         || |||| |  |    ||   
TGCAAGCTTCCATCGCTGCCAACACATGGGTTGTAAGTGGACCATCACAGACCAAGAgtaagtgtttcttttcttccgtcttgctttgcacctttggcttcaattataattttccttatttaatatgttggctccgaaatcatatagcgttatgaag---

upper sequence: LOC_Os03g63400.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S359_31V6.1 (Physcomitrella patens), 5'ss of exon 3
TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgacttctccttgttacatttgatcagttcgttg--tgcgagttcaattcttttaagattagcggctgttctgtttctcttata-cactgctgagttg-----------------------
|||||||||||||||| || ||||||||||| || |||||  |  ||||||||||||||| |||  |  |   |      ||   |     | |||  | | | |  |||| |  | |  | |   | ||         || |||| |  |    |||||                       
TGCAAGCTTCCATCGCTGCCAACACATGGGTTGTAAGTGGACCATCACAGACCAAGAgtaagtgtttcttttcttccgtcttgctttgcacctttggcttcaattataattttccttatttaatatgttggctccgaaatcatatagcgttatgaagttgatctgtctgttttgttattgaag

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|88205126|gb|CI204975.1|CI204975
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88209060|gb|CI208909.1|CI208909
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88294933|gb|CI522887.1|CI522887
EST:     TCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|38477612|gb|CF961745.1|CF961745
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAACATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|55409416|gb|CV721792.1|CV721792
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|8528376|gb|AU093191.1|AU093191
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|86824271|gb|CI260854.1|CI260854
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88213427|gb|CI213276.1|CI213276
EST:     CGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: CGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|5005069|gb|AU069686.1|AU069686
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|86823386|gb|CI256364.1|CI256364
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|13807920|gb|AU182155.1|AU182155
EST:     GCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: GCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88839904|gb|CI017669.1|CI017669
EST:     GGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: GGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|87015910|gb|CI279662.1|CI279662
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88487959|gb|CI425230.1|CI425230
EST:     GTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: GTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88545640|gb|CI475212.1|CI475212
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|86594523|gb|CI253422.1|CI253422
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAAACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|426706|gb|D22776.1|D22776
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88977134|gb|CI024871.1|CI024871
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|3760604|gb|C97858.1|C97858
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|58597162|gb|CK007690.1|CK007690
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCCATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88970560|gb|CI384062.1|CI384062
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATTTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|86489014|gb|CI131647.1|CI131647
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|55440624|gb|CV733623.1|CV733623
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|86542346|gb|CI182552.1|CI182552
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|86821488|gb|CI266864.1|CI266864
EST:     TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: TTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
EST: gi|88831984|gb|CI014543.1|CI014543
EST:     GGGTGGTCAGTGGCTCCCCACAGACCAAGA                         AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG
genomic: GGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgact ... gacttgtcagAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGAgtatgtgacttctccttgttacatttgatcagttcgttgtgcgagttcaattcttttaagattagcggctgttctgtttctcttatacactgctgagttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctcc
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