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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g02350.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143602_T01 (Zea mays), 3'ss of exon 5
----------gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
            ||||| ||  ||  |||    | |  | ||    |       ||| |||   |    |  || || ||     ||| |||||||| |||||| |||  |          ||| ||||||| || || ||||| ||||||||||| || ||||||||||||||||||||||||||||| || |||
gtatttacccacattactattccacctatttgctgccatatcctgatatcctcctttggtatctctgacggtttcttata-----gaaataactggtactgatttgctgtt---------ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 4
gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
||||||||   ||   |||  ||  || |||    |   |||  |||| | | | |  |    |  |   | | |||  | ||   |  | ||    | || || || |||||  ||||||| || || |||||||||||||| || |||||||||||||||||||||||||||||||| || |||
gtattacccacacgactat-tatacctatttgctgtcatatcccttttttta-gtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
----gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattc--gctaataatgtg--ttgt--tgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
     | | |     |  |  |||  |   |  | ||   ||     | |||||        ||  ||  | | |     | ||   ||    ||||||  | |||  | |||  |||   ||| ||||||| || || ||||||||||| || ||||| ||||||||  ||||||||||||| ||||| || |||
gtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagttt-ttgagcttgattctcgttaaacaggtgaattgaagtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtattaccatgac--atttatacattactttttctcatttcatcaattttgta----atgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
     ||||   |       ||||  ||| || | ||||    || |    |||   |     || | ||||  |||| |      ||| ||  |   | |     |   | | || || |||    ||||||||| || ||||||||||| || ||||| ||||||||  ||||||| ||||| ||||| || |||
gtaacgtatcctcgcagtttattttaacactaatctttcgttatttacagttttcccatgatgtgtatctgcgattttttcattctgaagtacttctcgttatgctgaagagattgcgtggtt----gcagATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAG

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 5
gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggt-gctgattcgctaa--taatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
          |  |   ||  |||   | || | | ||   ||  |   |     ||   | || | | ||||  |||  | | ||| ||  |   |  |   ||   | |  || | || |||| |||||||||||||| ||||||||||||||||||||  ||||||| ||||| |||||||| |||
----------gtaaggaatgtattctatattttgaattttgcatgtacattcctgaagcccattatcccataat-gaaccagcaggttgcaaacctgacaggctaccatttgtttaattgtagATTTTCCGCAAGGAGCCGTTTTTCTATGGTCATGACAATTATGATCAGCTTGTCAAGATCGCTAAG

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgca--actgcctttttctataaaag-aattaactggtgctgattcgctaataatgtgttgttgagtgc-agATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
                |    |  ||  |||||   || |  | ||||   |||||    |||| || | | || ||  ||  | ||  | ||      || ||| |   |  ||| |||  |||| |||||||||||||| ||||||||||| || |||||  ||||||||||||| ||||| ||||||
---------------gtgaggaagacggtttctg--ttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagct--tcctatagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG

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|29661177|gb|CB657452.1|CB657452
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCCGCAAG-AGCCATTTTTCTATGGTCAT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCC-GCAAGGAGCCATTTTTCTATGGTCAT
EST: gi|58686212|gb|CK074899.1|CK074899
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29616864|gb|CB621876.1|CB621876
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|58691077|gb|CK079764.1|CK079764
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29663346|gb|CB659621.1|CB659621
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|58598121|gb|CK008649.1|CK008649
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29657466|gb|CB653741.1|CB653741
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29662230|gb|CB658505.1|CB658505
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTTCGCAAGGAGCCATTTTTCTATGGTCATG
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATG
EST: gi|29662231|gb|CB658506.1|CB658506
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|27577759|gb|CB000454.1|CB000454
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29663347|gb|CB659622.1|CB659622
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29661178|gb|CB657453.1|CB657453
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT
EST: gi|29619982|gb|CB624994.1|CB624994
EST:     ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATCTTCCGCAAGGAGCCANNNNNNNATGGTCATGACAACCATGATCAACTT
genomic: ATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTT

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: 66 (upstream exon), 69 (downstream exon)
Score: 29

GTACTTCAAGGGACCTGAGCTTCTTGTTGACTTGCAAGATTATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccat ... ttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG
     taaaagaattaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG