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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttctattttgtttcagaattgctctatttgatatattaagtatctcctagcaagttgtgtggggggcttgttatcattggctgattttgtcta...

Basic information

species Oryza sativa
transcript LOC_Os06g37440.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G059580_T03 (Zea mays), 5'ss of exon 5
AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttctattttgtttcagaattgctctatttgatatattaagtatctcctagcaa-gttgtgtggggggct--tgttatcattggctgattttgtcta
|||||||||||  | |||||||||||||||||| | |||||||| |||||||||||||||||||||||||| ||||||||||| ||  ||||||| ||||||||  || |  || | | | | ||||  | | |  ||  |     || |      |||    | |            | |||      ||| | ||||    
AATCCTCTTGACTTGCTGCCACCAAGCAAGATGGTCCTTGATGACTGGAAGAGGCTATACTCAAACACAAAGACCAACTTCCGGGAGGTTGCCATCAAAGgtatgtttgc--ttctttctaacaatttttatgtgcga-gtggctggtgttaaaaggcagtactttacaatctatcaatcttacaggaagctaaatttgggag

upper sequence: LOC_Os06g37440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G122871_T02 (Zea mays), 5'ss of exon 6
AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttctattttgtttcagaattgctctatttgatatattaagtatctcc-tagcaagttg----tgtggggggcttgttatcattggctgattttgtcta-
|||||||||||  | |||||||||||||||||| | |||||||| |||||||||||||||||||||||||| || |||||||| ||  ||||||| |||||||| || || |   |||||||    || | |  |  ||| |||   |   ||| || ||| ||     ||   | |||| ||| |      |||   ||  | | 
AATCCTCTTGACTTGCTGCCACCAAGCAAGATGGTCCTTGATGACTGGAAGAGGCTATACTCAAACACAAAGACTAACTTCCGGGAGGTTGCCATCAAAGgtatcatctcca---tgtttcaa---tgatatgatcaatacatttgcttcttccctaacaattttgaactgcaagtggctggtttttgaaatctgtactttgcaat

upper sequence: LOC_Os06g37440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G09640.1 (Arabidopsis thaliana), 5'ss of exon 7
AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtat-tatttctattttgtttcag--aattgctctatttgatatattaagtatctcctagcaagttgtgtggggggcttgttatcattggctgattttgtcta----------
|| ||||||||  | || |||||||||   ||| |||| ||||| ||||||||||| ||||||||||| ||| | |||||||| ||  |||| ||||||||| | |  |  ||| ||  |  |   | ||  ||   ||          | ||    |||| | | |  |     | || ||||||| | || || ||||             
AACCCTCTTGACTTGCTACCACCAAGCCCTATGGTTCTAGATGATTGGAAGAGGCTTTACTCAAACACCAAATCTAACTTCCGCGAGGTTGCTATTAAAGgtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcat-gtctaatattgtggctcaaatgcag

upper sequence: LOC_Os06g37440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G57720.1 (Arabidopsis thaliana), 5'ss of exon 7
AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttctattttgtttcag-aattgctctatttgatatatt-----aagtatctcctagcaagttgtgtggggggcttgttatcattggctgattttgtcta
|||||||||||  | || |||||||||   ||| |||| ||||| ||||||||||| ||||| ||||| ||| |||||||||||||  |||| || ||||||||  | | |  |   ||     ||||| ||| |   | | |||     | || | |   | ||| |||| |  |  |   | ||  |    | ||         
AATCCTCTTGACTTGCTACCACCAAGCCCAATGGTTCTCGATGACTGGAAGAGGCTTTACTCGAACACCAAATCCAACTTCCGTGAGGTTGCTATCAAAGgtatgttatatgatgacttctgttaattgttctttagaagaaattgttctaggtttatggaatcaacttgt-taagaagaaagctacaaaaatccgagaca-----

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|86487381|gb|CI130014.1|CI130014
EST:     CCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: CCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|218494696|gb|FG957584.1|FG957584
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|87028152|gb|CI269923.1|CI269923
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|89176656|gb|CI111372.1|CI111372
EST:     GAGGCTATACTCAAACACTTTAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88995578|gb|CI022901.1|CI022901
EST:     GAGGCTATACTCACACACACAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|218478774|gb|FG963471.1|FG963471
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88841208|gb|CI080662.1|CI080662
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86418792|gb|CI053593.1|CI053593
EST:     CTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: CTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|89174149|gb|CI042042.1|CI042042
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86420898|gb|CI056887.1|CI056887
EST:     GAGGCTATACTCAAACACTAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|89193822|gb|CI018140.1|CI018140
EST:     ATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: ATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88245407|gb|CI245256.1|CI245256
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86420108|gb|CI054909.1|CI054909
EST:     GAGGCTATACTCTAACACGGAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|89185372|gb|CI051700.1|CI051700
EST:     AATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: AATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86594360|gb|CI251232.1|CI251232
EST:     GAGGCTATACTCAAACACTTATACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|218482086|gb|FG956200.1|FG956200
EST:     AGGCTATACTCAAACACAAAAACCAACTTCCAGTGAAATTGCCATTAAAG                         GTTTCTGGAGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGAC
genomic: AGGCTATACTCAAACACAAAAACCAACTTCC-GTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGG-GACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGAC
EST: gi|86251430|gb|CI055563.1|CI055563
EST:     CCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: CCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|89193266|gb|CI050564.1|CI050564
EST:     TCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: TCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88215021|gb|CI214870.1|CI214870
EST:     GAGGCTATACTCAAACACTAAAACCTACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88904119|gb|CI006352.1|CI006352
EST:     GAGGCTATACTCAAACACGAAAACCGACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86520927|gb|CI161133.1|CI161133
EST:     AGGCTATACTCAAACACTAAAACCAACTTCCGGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: AGGCTATACTCAAACACAAAAACCAACTTCC-GTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86420897|gb|CI056886.1|CI056886
EST:     GAGGCTATACTCAAACACGAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|89189167|gb|CI048706.1|CI048706
EST:     GAGGCTATACTCAAACACGGAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88993692|gb|CI112596.1|CI112596
EST:     TTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: TTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86420577|gb|CI056566.1|CI056566
EST:     TCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: TCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|25803934|gb|CA759895.1|CA759895
EST:     CTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: CTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86528253|gb|CI168459.1|CI168459
EST:     GAGGCTATACTCAAACACGAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88965858|gb|CI006686.1|CI006686
EST:     TCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: TCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|29642158|gb|CB647165.1|CB647165
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|58679648|gb|CK068335.1|CK068335
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|86256027|gb|CI068476.1|CI068476
EST:     GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
EST: gi|88844707|gb|CI021282.1|CI021282
EST:     GAGGCTATACTCATACACAAAAACCNACTTCCGTGAAATTGCCATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT
genomic: GAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 53 (upstream exon), 40 (downstream exon)
Score: 6

AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttc ... tatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACTACAAGTACAACGATGAGAACACCGTATCGTTTGTGACGATGAACAAGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCCTCTTGATCTACTGCCACCAAGCAAGATGATTCTTGATGAGTGGAAGAGGCTATACTCAAACACAAAAACCAACTTCCGTGAAATTGCCATTAAAGgtattatttctattttgtttcagaattgctctatttgatatattaagtatctcctagcaagttgtgtggggggcttgttatcattggctgattttgtcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggggg