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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG

Basic information

species Oryza sativa
transcript LOC_Os02g39720.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G027105_T06 (Zea mays), 3'ss of exon 1
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatc-tgattcttccactttca-----actgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
    ||     | ||| || |   |||    | | | || | | || | |  |||||||  |  ||  |   ||||||     ||||| |||||  ||| ||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||| ||||||| |||||||| || ||||
----caagaaatgtattgaact-caataccatatcactttt-tttgtacaatagattattatagtttatatgctttcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATG

upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G027105_T02 (Zea mays), 3'ss of exon 2
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatc-tgattcttccactttca-----actgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG-----------
    ||     | ||| || |   |||    | | | || | | || | |  |||||||  |  ||  |   ||||||     ||||| |||||  ||| ||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||| ||||||| |||||||| || ||||           
----caagaaatgtattgaact-caataccatatcactttt-tttgtacaatagattattatagtttatatgctttcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATGGTACTTAATAA

upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G107896_T01 (Zea mays), 3'ss of exon 2
-aattcatagtctatatggagcagtaa-tgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
 |  |  |   ||  ||     |  || || ||| ||   ||     |   ||   ||| | | || | | |||||   ||||| |||||  ||| ||||||||||||||||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||| ||||||| ||||| ||||| ||||
aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgtattttat-atgcattcacttg-gactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG

upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatct--------gattcttccactttcaactga-gttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
        || |   ||  |   |  | |||| ||  ||   ||| | | |  | |||| |         ||  ||     || ||  |    | | |  | | |||||||| ||||||||  | | |||||| |||| ||| ||||||||||||||||||||||| || ||| | ||||| || ||||| || ||||
--------gttttgttgctgtgatt-ttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG

upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatct------gattcttccactttcaactgagt--tgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
        || | | | |  ||||  |  ||  ||  ||   | | | |||  |  ||| |       |       | |||    | | |  | | |  | | |||||||| ||||||||  | | |||||| |||| ||| ||||||||||||||||||||||| |||||| | ||||| || ||||| || ||||
------cggtttttgttg--cagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG

upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0026g00250.t01 (Vitis vinifera), 3'ss of exon 1
--------aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
        | || ||| | | |      ||   || | || ||| | ||  |||||  ||| |||      ||  |     || |     |||| |     |   |||||| ||||||||| | | |||||| |||| ||| ||| |||| |||| ||| || |||||||| | ||||||||||||||  || ||||
tttttaaaacttgatactattttcaacacatagattactttttagt-at-cctgcatttgaaatt------tttgttggtcttaacacatgttgctaaaatttatcagTGTTTGGGTTGCTCGGAGACCACCGGGTTATGCTTTTGTTGAGTTTGCTGATCGTAGGGATGCTGTAGATGCAATTCGTGGATTGGATG

upper sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
--aattcatagtcta---tatggagcagtaatgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
  || |  | || ||   | ||||| |  |    |   |  ||||||   |||| |   |||     |||  |  | ||||   |||  |||||  | | |||||||| ||||||||  | | ||||||||| | ||| ||||| |||||||||||||| || |||||| |||||||||||||||| |||||||
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttc---tgaaatgttt--tatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG

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|32948206|gb|BP184778.1|BP184778
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagatt ... ttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
EST: gi|29658266|gb|CB654541.1|CB654541
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagatt ... ttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
EST: gi|29660883|gb|CB657158.1|CB657158
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagatt ... ttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
EST: gi|325493520|gb|JG458044.1|JG458044
EST:     GAGTTCCGCGTGTTTGAGGTTCTGAGGAG                         TGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
genomic: GAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagatt ... ttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
EST: gi|84117541|gb|CD151308.1|CD151308
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagatt ... ttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG
            atctgat  putative branch site (score: 4)
                                      ttgtttcttct  putative PPT
       agattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG